Schema "cmlreact.xsd"
Target Namespace:
http://www.xml-cml.org/schema/cml2/react
Defined Components:
112 global elements, 59 simpleTypes, 170 attribute groups
Default Namespace-Qualified Form:
Local Elements: qualified; Local Attributes: unqualified
Schema Location:
/Users/rafa/projects/intenz/intenz-xml/src/main/resources/cmlreact.xsd; see XML source
Imported by Schema:
enzyme.xsd [src]
All Element Summary
abundance The abundance of an isotope.
Type:
anonymous complexType (extension of xsd:float)
Content:
simple, 7 attributes
Defined:
globally; see XML source
Used:
at 1 location
action An action which might occur in scientific data or narrative.
Type:
anonymous complexType
Content:
mixed (allows character data), 14 attributes, elem. wildcard
Defined:
globally; see XML source
Includes:
definition of elem. wildcard
Used:
never
actionList A container for a group of actions.
Type:
anonymous complexType
Content:
mixed (allows character data), 13 attributes, elem. wildcard
Defined:
globally; see XML source
Includes:
definition of elem. wildcard
Used:
never
alternative An alternative name for an entry.
Type:
anonymous complexType (extension of xsd:string)
Content:
simple, 3 attributes
Defined:
globally; see XML source
Used:
at 2 locations
amount The amount of a substance.
Type:
anonymous complexType (extension of xsd:float)
Content:
simple, 5 attributes
Defined:
globally; see XML source
Used:
at 4 locations
angle An angle between three atoms.
Type:
anonymous complexType (extension of nonNegativeAngleType)
Content:
simple, 11 attributes
Defined:
globally; see XML source
Used:
at 2 locations
annotation A documentation container similar to annotation in XML Schema.
Type:
anonymous complexType
Content:
mixed (allows character data), 2 elements
Defined:
globally; see XML source
Includes:
definitions of 2 elements
Used:
at 4 locations
appinfo A container similar to appinfo in XML Schema.
Type:
anonymous complexType
Content:
mixed (allows character data), 1 attribute, elem. wildcard
Defined:
globally; see XML source
Includes:
definition of elem. wildcard
Used:
at 1 location
arg An argument for a function.
Type:
anonymous complexType
Content:
complex, 7 attributes, 5 elements
Defined:
globally; see XML source
Includes:
definitions of 5 elements
Used:
at 2 locations
array A homogenous 1 dimensional array of similar object.
Type:
anonymous complexType (extension of xsd:string)
Content:
simple, 13 attributes
Defined:
globally; see XML source
Used:
at 14 locations
atom An atom.
Type:
anonymous complexType
Content:
complex, 24 attributes, 8 elements
Defined:
globally; see XML source
Includes:
definitions of 8 elements
Used:
at 5 locations
atomArray A container for a list of atoms.
Type:
anonymous complexType
Content:
complex, 19 attributes, 1 element
Defined:
globally; see XML source
Includes:
definition of 1 element
Used:
at 2 locations
atomicBasisFunction An atomicBasisFunction.
Type:
anonymous complexType
Content:
complex, 10 attributes, 1 element
Defined:
globally; see XML source
Includes:
definition of 1 element
Used:
at 1 location
atomParity The stereochemistry round an atom centre.
Type:
anonymous complexType (extension of xsd:float)
Content:
simple, 5 attributes
Defined:
globally; see XML source
Used:
at 1 location
atomSet A set of references to atoms.
Type:
anonymous complexType (extension of atomRefArrayType)
Content:
simple, 5 attributes
Defined:
globally; see XML source
Used:
at 1 location
atomType An atomType.
Type:
anonymous complexType
Content:
complex, 7 attributes, 7 elements
Defined:
globally; see XML source
Includes:
definitions of 7 elements
Used:
at 2 locations
atomTypeList A container for one or more atomTypes.
Type:
anonymous complexType
Content:
complex, 5 attributes, 3 elements
Defined:
globally; see XML source
Includes:
definitions of 3 elements
Used:
at 1 location
band A band or Brillouin zone.
Type:
anonymous complexType
Content:
complex, 7 attributes, 1 element
Defined:
globally; see XML source
Includes:
definition of 1 element
Used:
at 1 location
bandList A container for bands.
Type:
anonymous complexType
Content:
complex, 4 attributes, 1 element
Defined:
globally; see XML source
Includes:
definition of 1 element
Used:
never
basisSet A container for one or more atomicBasisFunctions.
Type:
anonymous complexType
Content:
complex, 6 attributes, 3 elements
Defined:
globally; see XML source
Includes:
definitions of 3 elements
Used:
never
bond A bond between atoms, or between atoms and bonds.
Type:
anonymous complexType
Content:
complex, 9 attributes, 3 elements
Defined:
globally; see XML source
Includes:
definitions of 3 elements
Used:
at 4 locations
bondArray A container for a number of bonds.
Type:
anonymous complexType
Content:
complex, 8 attributes, 2 elements
Defined:
globally; see XML source
Includes:
definitions of 2 elements
Used:
at 1 location
bondSet A set of references to bonds.
Type:
anonymous complexType (extension of bondRefArrayType)
Content:
simple, 5 attributes
Defined:
globally; see XML source
Used:
at 1 location
bondStereo A container supporting cis trans wedge hatch and other stereochemistry.
Type:
anonymous complexType (extension of stereoType)
Content:
simple, 7 attributes
Defined:
globally; see XML source
Used:
at 1 location
bondType The type of a bond.
Type:
anonymous complexType
Content:
complex, 6 attributes, 7 elements
Defined:
globally; see XML source
Includes:
definitions of 7 elements
Used:
at 2 locations
bondTypeList A container for one or more bondTypes.
Type:
anonymous complexType
Content:
complex, 5 attributes, 3 elements
Defined:
globally; see XML source
Includes:
definitions of 3 elements
Used:
at 1 location
cml A general container for CML elements.
Type:
anonymous complexType
Content:
complex, 4 attributes, elem. wildcard
Defined:
globally; see XML source
Includes:
definition of elem. wildcard
Used:
never
conditionList A container for one or more experimental condition.
Type:
anonymous complexType
Content:
complex, 6 attributes, 4 elements
Defined:
globally; see XML source
Includes:
definitions of 4 elements
Used:
at 2 locations
crystal A crystallographic cell.
Type:
anonymous complexType
Content:
complex, 5 attributes, 2 elements
Defined:
globally; see XML source
Includes:
definitions of 2 elements
Used:
at 1 location
definition The definition for an entry.
Type:
anonymous complexType
Content:
mixed (allows character data), elem. wildcard
Defined:
globally; see XML source
Includes:
definition of elem. wildcard
Used:
at 1 location
description Descriptive information.
Type:
anonymous complexType
Content:
mixed (allows character data), 5 attributes, elem. wildcard
Defined:
globally; see XML source
Includes:
definition of elem. wildcard
Used:
at 5 locations
dictionary A dictionary.
Type:
anonymous complexType
Content:
complex, 5 attributes, 4 elements
Defined:
globally; see XML source
Includes:
definitions of 4 elements
Used:
never
dimension A dimension supporting scientific unit.
Type:
anonymous complexType
Content:
empty, 5 attributes
Defined:
globally; see XML source
Used:
at 1 location
documentation Documentation in the annotation of an entry.
Type:
anonymous complexType
Content:
mixed (allows character data), 2 attributes, elem. wildcard
Defined:
globally; see XML source
Includes:
definition of elem. wildcard
Used:
at 1 location
eigen An element to hold eigenstuff.
Type:
anonymous complexType
Content:
complex, 6 attributes, 2 elements
Defined:
globally; see XML source
Includes:
definitions of 2 elements
Used:
never
electron An electron.
Type:
anonymous complexType
Content:
empty, 10 attributes
Defined:
globally; see XML source
Used:
at 5 locations
entry A dictionary entry.
Type:
anonymous complexType
Content:
complex, 20 attributes, 7 elements
Defined:
globally; see XML source
Includes:
definitions of 7 elements
Used:
at 1 location
enumeration An enumeration of value.
Type:
anonymous complexType
Content:
complex, 3 attributes, 1 element
Defined:
globally; see XML source
Includes:
definition of 1 element
Used:
at 1 location
expression An expression that can be evaluated.
Type:
anonymous complexType
Content:
complex, 5 attributes, 2 elements
Defined:
globally; see XML source
Includes:
definitions of 2 elements
Used:
at 3 locations
formula A molecular formula.
Type:
anonymous complexType
Content:
complex, 7 attributes, 2 elements
Defined:
globally; see XML source
Includes:
definitions of 2 elements
Used:
at 4 locations
gradient A gradient.
Type:
anonymous complexType
Content:
complex, 4 attributes, 4 elements
Defined:
globally; see XML source
Includes:
definitions of 4 elements
Used:
at 2 locations
identifier A structured identifier.
Type:
anonymous complexType
Content:
complex, 7 attributes, elem. wildcard
Defined:
globally; see XML source
Includes:
definition of elem. wildcard
Used:
at 5 locations
isotope A specific isotope.
Type:
anonymous complexType
Content:
complex, 8 attributes, 1 element
Defined:
globally; see XML source
Includes:
definition of 1 element
Used:
at 1 location
isotopeList A container for one or more isotopes.
Type:
anonymous complexType
Content:
complex, 5 attributes, 1 element
Defined:
globally; see XML source
Includes:
definition of 1 element
Used:
never
label A text string qualifying an object.
Type:
anonymous complexType
Content:
complex, 4 attributes, elem. wildcard
Defined:
globally; see XML source
Includes:
definition of elem. wildcard
Used:
at 12 locations
lattice A lattice of dimension 3 or less.
Type:
anonymous complexType
Content:
complex, 6 attributes, 4 elements
Defined:
globally; see XML source
Includes:
definitions of 4 elements
Used:
never
latticeVector A vector3 representing a lattice axis. a lattice can be represented by 1-3 non-linearly dependent latticeVectors.
Type:
anonymous complexType (extension of vector3Type)
Content:
simple, 6 attributes
Defined:
globally; see XML source
Used:
at 1 location
length A length between two atoms.
Type:
anonymous complexType (extension of xsd:float)
Content:
simple, 11 attributes
Defined:
globally; see XML source
Used:
at 2 locations
line3 A line in 3-space.
Type:
anonymous complexType (extension of line3Type)
Content:
simple, 5 attributes
Defined:
globally; see XML source
Used:
never
link An internal or external link to other objects.
Type:
anonymous complexType
Content:
complex, 10 attributes, elem. wildcard
Defined:
globally; see XML source
Includes:
definition of elem. wildcard
Used:
at 1 location
list A generic container with no implied semantics.
Type:
anonymous complexType
Content:
complex, 5 attributes, elem. wildcard
Defined:
globally; see XML source
Includes:
definition of elem. wildcard
Used:
at 3 locations
map A container for links There has been some confusion between map and link.
Type:
anonymous complexType
Content:
complex, 4 attributes, 1 element
Defined:
globally; see XML source
Includes:
definition of 1 element
Used:
at 1 location
matrix A rectangular matrix of any quantities.
Type:
anonymous complexType (extension of xsd:string)
Content:
simple, 14 attributes
Defined:
globally; see XML source
Used:
at 11 locations
mechanism The mechanism of a reaction.
Type:
anonymous complexType
Content:
complex, 4 attributes, 4 elements
Defined:
globally; see XML source
Includes:
definitions of 4 elements
Used:
at 1 location
mechanismComponent An information component within a reaction mechanism.
Type:
anonymous complexType
Content:
complex, 4 attributes, elem. wildcard
Defined:
globally; see XML source
Includes:
definition of elem. wildcard
Used:
at 1 location
metadata A general container for metadata.
Type:
anonymous complexType (extension of xsd:string)
Content:
simple, 6 attributes
Defined:
globally; see XML source
Used:
at 1 location
metadataList A general container for metadata elements.
Type:
anonymous complexType
Content:
complex, 6 attributes, 2 elements
Defined:
globally; see XML source
Includes:
definitions of 2 elements
Used:
at 28 locations
module A module in a calculation.
Type:
anonymous complexType
Content:
complex, 6 attributes, elem. wildcard
Defined:
globally; see XML source
Includes:
definition of elem. wildcard
Used:
never
molecule A container for atoms, bonds and submolecules.
Type:
anonymous complexType
Content:
complex, 12 attributes, 20 elements
Defined:
globally; see XML source
Includes:
definitions of 20 elements
Used:
at 11 locations
name A string identifying a object.
Type:
anonymous complexType (extension of xsd:string)
Content:
simple, 3 attributes
Defined:
globally; see XML source
Used:
at 19 locations
object An object which might occur in scientific data or narrative.
Type:
anonymous complexType
Content:
mixed (allows character data), 7 attributes, elem. wildcard
Defined:
globally; see XML source
Includes:
definition of elem. wildcard
Used:
at 2 locations
observation An observation or occurrence.
Type:
anonymous complexType
Content:
mixed (allows character data), 6 attributes, elem. wildcard
Defined:
globally; see XML source
Includes:
definition of elem. wildcard
Used:
at 1 location
operator An operator within an expression.
Type:
anonymous complexType
Content:
empty, 5 attributes
Defined:
globally; see XML source
Used:
at 1 location
parameter A parameter describing the computation.
Type:
anonymous complexType
Content:
complex, 9 attributes, 6 elements
Defined:
globally; see XML source
Includes:
definitions of 6 elements
Used:
at 3 locations
parameterList A container for one or more parameters. parameterList can contain several parameters.
Type:
anonymous complexType
Content:
complex, 6 attributes, 3 elements
Defined:
globally; see XML source
Includes:
definitions of 3 elements
Used:
never
particle An object in space carrying a set of properties.
Type:
anonymous complexType
Content:
complex, 8 attributes, elem. wildcard
Defined:
globally; see XML source
Includes:
definition of elem. wildcard
Used:
never
peak A peak; annotated by human or machine.
Type:
anonymous complexType
Content:
complex, 20 attributes, 4 elements
Defined:
globally; see XML source
Includes:
definitions of 4 elements
Used:
at 2 locations
peakGroup A list of closely related peaks or peakGroups.
Type:
anonymous complexType
Content:
complex, 20 attributes, 6 elements
Defined:
globally; see XML source
Includes:
definitions of 6 elements
Used:
at 2 locations
peakList A list of peaks or peakGroups.
Type:
anonymous complexType
Content:
complex, 5 attributes, 3 elements
Defined:
globally; see XML source
Includes:
definitions of 3 elements
Used:
at 1 location
plane3 A plane in 3-space.
Type:
anonymous complexType (extension of plane3Type)
Content:
simple, 5 attributes
Defined:
globally; see XML source
Used:
never
point3 A point in 3-space.
Type:
anonymous complexType (extension of point3Type)
Content:
simple, 5 attributes
Defined:
globally; see XML source
Used:
never
potential An explicit potential.
Type:
anonymous complexType
Content:
complex, 5 attributes, 1 element
Defined:
globally; see XML source
Includes:
definition of 1 element
Used:
at 1 location
potentialForm The functional form of a potential.
Type:
anonymous complexType
Content:
complex, 5 attributes, 3 elements
Defined:
globally; see XML source
Includes:
definitions of 3 elements
Used:
never
potentialList A container for explicit potentials.
Type:
anonymous complexType
Content:
complex, 4 attributes, 1 element
Defined:
globally; see XML source
Includes:
definition of 1 element
Used:
never
product A product within a productList.
Type:
anonymous complexType
Content:
complex, 8 attributes, 10 elements
Defined:
globally; see XML source
Includes:
definitions of 10 elements
Used:
at 1 location
productList A container for one or more products.
Type:
anonymous complexType
Content:
complex, 7 attributes, 4 elements
Defined:
globally; see XML source
Includes:
definitions of 4 elements
Used:
at 2 locations
property A container for a property.
Type:
anonymous complexType
Content:
complex, 7 attributes, 5 elements
Defined:
globally; see XML source
Includes:
definitions of 5 elements
Used:
at 6 locations
propertyList A container for one or more properties.
Type:
anonymous complexType
Content:
complex, 6 attributes, 4 elements
Defined:
globally; see XML source
Includes:
definitions of 4 elements
Used:
at 4 locations
reactant A reactant within a reactantList.
Type:
anonymous complexType
Content:
complex, 8 attributes, 10 elements
Defined:
globally; see XML source
Includes:
definitions of 10 elements
Used:
at 1 location
reactantList A container for one or more reactants.
Type:
anonymous complexType
Content:
complex, 7 attributes, 4 elements
Defined:
globally; see XML source
Includes:
definitions of 4 elements
Used:
at 2 locations
reaction A chemical reaction or reaction step.
Type:
anonymous complexType
Content:
complex, 13 attributes, 15 elements
Defined:
globally; see XML source
Includes:
definitions of 15 elements
Used:
at 4 locations
reactionList A container for one or more reactions or reactionSchemes with no interrelations.
Type:
anonymous complexType
Content:
complex, 6 attributes, 3 elements
Defined:
globally; see XML source
Includes:
definitions of 3 elements
Used:
never
reactionScheme A container for two or more related reactions and their relationships.
Type:
anonymous complexType
Content:
complex, 9 attributes, 7 elements
Defined:
globally; see XML source
Includes:
definitions of 7 elements
Used:
at 3 locations
reactionStep A child of reactionStepList and a container for reaction or reactionScheme.
Type:
anonymous complexType
Content:
complex, 7 attributes, 5 elements
Defined:
globally; see XML source
Includes:
definitions of 5 elements
Used:
at 1 location
reactionStepList A container for one or more related reactionSteps.
Type:
anonymous complexType
Content:
complex, 7 attributes, 4 elements
Defined:
globally; see XML source
Includes:
definitions of 4 elements
Used:
at 1 location
reactiveCentre The reactiveCentre in a reaction.
Type:
anonymous complexType
Content:
complex, 4 attributes, 5 elements
Defined:
globally; see XML source
Includes:
definitions of 5 elements
Used:
at 1 location
region A region of the system.
Type:
anonymous complexType
Content:
empty, 8 attributes
Defined:
globally; see XML source
Used:
never
relatedEntry An entry related in some way to a dictionary entry.
Type:
anonymous complexType
Content:
mixed (allows character data), 2 attributes
Defined:
globally; see XML source
Used:
at 1 location
sample An analytical or spectral sample.
Type:
anonymous complexType
Content:
complex, 6 attributes, 4 elements
Defined:
globally; see XML source
Includes:
definitions of 4 elements
Used:
at 1 location
scalar An element to hold scalar data.
Type:
anonymous complexType (extension of xsd:string)
Content:
simple, 11 attributes
Defined:
globally; see XML source
Used:
at 11 locations
spectator A spectator object in a reaction.
Type:
anonymous complexType
Content:
complex, 5 attributes, 4 elements
Defined:
globally; see XML source
Includes:
definitions of 4 elements
Used:
at 1 location
spectatorList A container for spectators in a reaction.
Type:
anonymous complexType
Content:
complex, 4 attributes, 1 element
Defined:
globally; see XML source
Includes:
definition of 1 element
Used:
at 1 location
spectrum A spectrum and relevant data or metadata.
Type:
anonymous complexType
Content:
complex, 11 attributes, 5 elements
Defined:
globally; see XML source
Includes:
definitions of 5 elements
Used:
at 1 location
spectrumData Data for the spectrum.
Type:
anonymous complexType
Content:
complex, 5 attributes, 2 elements
Defined:
globally; see XML source
Includes:
definitions of 2 elements
Used:
at 1 location
spectrumList A container for one or more spectra.
Type:
anonymous complexType
Content:
complex, 6 attributes, 4 elements
Defined:
globally; see XML source
Includes:
definitions of 4 elements
Used:
at 1 location
sphere3 A sphere in 3-space.
Type:
anonymous complexType (extension of sphere3Type)
Content:
simple, 5 attributes
Defined:
globally; see XML source
Used:
never
stmml An element to hold stmml data.
Type:
anonymous complexType
Content:
complex, 4 attributes, elem. wildcard
Defined:
globally; see XML source
Includes:
definition of elem. wildcard
Used:
never
substance A chemical substance.
Type:
anonymous complexType
Content:
complex, 9 attributes, 5 elements
Defined:
globally; see XML source
Includes:
definitions of 5 elements
Used:
at 4 locations
substanceList A list of chemical substances.
Type:
anonymous complexType
Content:
complex, 7 attributes, 4 elements
Defined:
globally; see XML source
Includes:
definitions of 4 elements
Used:
at 4 locations
symmetry Molecular, crystallographic or other symmetry.
Type:
anonymous complexType
Content:
complex, 8 attributes, 1 element
Defined:
globally; see XML source
Includes:
definition of 1 element
Used:
at 3 locations
system The complete system of components in a calculation.
Type:
anonymous complexType
Content:
complex, 6 attributes, elem. wildcard
Defined:
globally; see XML source
Includes:
definition of elem. wildcard
Used:
never
table A rectangular table of any quantities.
Type:
anonymous complexType
Content:
complex, 8 attributes, 1 element
Defined:
globally; see XML source
Includes:
definition of 1 element
Used:
never
torsion A torsion angle ("dihedral") between 4 distinct atoms.
Type:
anonymous complexType (extension of torsionAngleType)
Content:
simple, 11 attributes
Defined:
globally; see XML source
Used:
at 2 locations
transform3 A transform in 3-space.
Type:
anonymous complexType (extension of matrix44Type)
Content:
simple, 4 attributes
Defined:
globally; see XML source
Used:
never
transitionState The transition state in a reaction.
Type:
anonymous complexType
Content:
complex, 4 attributes, 2 elements
Defined:
globally; see XML source
Includes:
definitions of 2 elements
Used:
at 1 location
unit A scientific unit.
Type:
anonymous complexType
Content:
complex, 7 attributes, 2 elements
Defined:
globally; see XML source
Includes:
definitions of 2 elements
Used:
at 1 location
unitList A container for several unit entries.
Type:
anonymous complexType
Content:
complex, 5 attributes, 2 elements
Defined:
globally; see XML source
Includes:
definitions of 2 elements
Used:
at 1 location
unitType The type of a scientific unit.
Type:
anonymous complexType
Content:
complex, 2 attributes, 2 elements
Defined:
globally; see XML source
Includes:
definitions of 2 elements
Used:
at 1 location
vector3 A vector in 3-space.
Type:
anonymous complexType (extension of vector3Type)
Content:
simple, 5 attributes
Defined:
globally; see XML source
Used:
never
xaxis The x-axis.
Type:
anonymous complexType
Content:
complex, 7 attributes, 1 element
Defined:
globally; see XML source
Includes:
definition of 1 element
Used:
at 1 location
yaxis The y-axis.
Type:
anonymous complexType
Content:
complex, 7 attributes, 1 element
Defined:
globally; see XML source
Includes:
definition of 1 element
Used:
at 1 location
zMatrix A zMatrix.
Type:
anonymous complexType
Content:
complex, 4 attributes, 3 elements
Defined:
globally; see XML source
Includes:
definitions of 3 elements
Used:
at 1 location
Simple Type Summary
angleUnitsType
 An enumeration of allowed angle units.
Defined:
globally; see XML source
Used:
at 1 location
atomIDType
 An identifier for an atom.
Defined:
globally; see XML source
Used:
at 5 locations
atomRefArrayType
 An array of atomRefs.
Defined:
globally; see XML source
Used:
at 6 locations
atomRefs2Type
 A reference to two distinct existing atoms in order.
Defined:
globally; see XML source
Used:
at 1 location
atomRefs3Type
 A reference to three distinct existing atoms in order.
Defined:
globally; see XML source
Used:
at 1 location
atomRefs4Type
 A reference to four distinct existing atoms in order.
Defined:
globally; see XML source
Used:
at 1 location
atomRefType
 A reference to an existing atom.
Defined:
globally; see XML source
Used:
at 1 location
bondRefArrayType
 An array of references to bonds.
Defined:
globally; see XML source
Used:
at 3 locations
bondRefType
 A reference to an existing bond.
Defined:
globally; see XML source
Used:
at 2 locations
box3Type
 A box in 3-space.
Defined:
globally; see XML source
Used:
at 1 location
chiralityType
 The chirality of a system or molecule.
Defined:
globally; see XML source
Used:
at 1 location
coordinateComponentArrayType
 An array of coordinateComponents for a single coordinate.
Defined:
globally; see XML source
Used:
at 8 locations
countArrayType
 Array of counts.
Defined:
globally; see XML source
Used:
at 1 location
countType
 A count multiplier for an object.
Defined:
globally; see XML source
Used:
at 1 location
dataTypeType
 an enumerated type for all dataTypes in STM.
Defined:
globally; see XML source
Used:
at 1 location
delimiterType
 A single non-whitespace character to separate components in arrays.
Defined:
globally; see XML source
Used:
at 1 location
dimensionType
 Allowed values for dimension Types in quantities.
Defined:
globally; see XML source
Used:
at 1 location
elementTypeArrayType
 An array of elementTypes.
Defined:
globally; see XML source
Used:
at 1 location
elementTypeType
 Allowed elementType values.
Defined:
globally; see XML source
Used:
at 2 locations
errorBasisType
 The basis of an error value.
Defined:
globally; see XML source
Used:
at 1 location
errorValueArrayType
 Array of error estimate values.
Defined:
globally; see XML source
Used:
at 1 location
errorValueType
 An estimate of the error in the value of a quantity.
Defined:
globally; see XML source
Used:
at 2 locations
floatArrayType
 An array of floats.
Defined:
globally; see XML source
Used:
at 2 locations
formalChargeArrayType
 Array of formalCharges.
Defined:
globally; see XML source
Used:
at 1 location
formalChargeType
 The formal charge on an object.
Defined:
globally; see XML source
Used:
at 2 locations
formulaType
 A concise representation for a molecular formula.
Defined:
globally; see XML source
Used:
at 2 locations
hydrogenCountArrayType
 Array of hydrogenCounts.
Defined:
globally; see XML source
Used:
at 1 location
hydrogenCountType
 The total number of hydrogen atoms bonded to an object.
Defined:
globally; see XML source
Used:
at 2 locations
idType
 A unique ID for an element.
Defined:
globally; see XML source
Used:
at 4 locations
isotopicSpinType
 A fractional representation of the spin of the nucleus.
Defined:
globally; see XML source
Used:
at 1 location
latticeType
 Allowed lattice types.
Defined:
globally; see XML source
Used:
at 1 location
line3Type
 An unbounded line in 3-space.
Defined:
globally; see XML source
Used:
at 1 location
matrix44Type
 A 4x4 transformation matrix ...
Defined:
globally; see XML source
Used:
at 1 location
matrixType
 Allowed matrix types.
Defined:
globally; see XML source
Used:
at 1 location
maxType
 The maximum INCLUSIVE value of a quantity.
Defined:
globally; see XML source
Used:
at 1 location
metadataType
 The name of the metadata.
Defined:
globally; see XML source
Used:
at 1 location
minType
 The minimum INCLUSIVE value of a quantity.
Defined:
globally; see XML source
Used:
at 1 location
moleculeRefType
 A reference to an existing molecule.
Defined:
globally; see XML source
Used:
at 1 location
namespaceRefType
 An XML QName with required prefix.
Defined:
globally; see XML source
Used:
at 24 locations
nonNegativeAngleType
 A non-signed angle.
Defined:
globally; see XML source
Used:
at 1 location
occupancyArrayType
 Array of atomic occupancies.
Defined:
globally; see XML source
Used:
at 1 location
occupancyType
 A floating point number between 0 and 1 inclusive Originally for crystallographic occupancy but re-usable for fractinal yield, etc.
Defined:
globally; see XML source
Used:
at 4 locations
orderArrayType
 An array of bond orders.
Defined:
globally; see XML source
Used:
at 1 location
orderType
 Bond order.
Defined:
globally; see XML source
Used:
at 2 locations
plane3Type
 An unbounded plane in 3-space.
Defined:
globally; see XML source
Used:
at 1 location
point3Type
 A point in 3-space.
Defined:
globally; see XML source
Used:
at 1 location
positiveNumberType
 A positive number.
Defined:
globally; see XML source
Used:
at 1 location
reactionFormatType
 The format of the reaction.
Defined:
globally; see XML source
Used:
at 1 location
reactionRoleType
 The role of the reaction within a reactionList.
Defined:
globally; see XML source
Used:
at 1 location
reactionTypeType
 The semantic type of the reaction.
Defined:
globally; see XML source
Used:
at 1 location
refType
 A reference to an existing object.
Defined:
globally; see XML source
Used:
at 3 locations
sizeType
 The size of an array.
Defined:
globally; see XML source
Used:
at 3 locations
spaceType
 Signifies real or reciprocal space.
Defined:
globally; see XML source
Used:
at 1 location
sphere3Type
 A sphere in 3-space.
Defined:
globally; see XML source
Used:
at 2 locations
stateType
 State of a substance or property.
Defined:
globally; see XML source
Used:
at 1 location
stereoType
 Bond stereochemistry as a string.
Defined:
globally; see XML source
Used:
at 1 location
torsionAngleType
 The type of a torsion angle.
Defined:
globally; see XML source
Used:
at 1 location
unitsType
 Scientific units.
Defined:
globally; see XML source
Used:
at 4 locations
vector3Type
 A vector in 3-space.
Defined:
globally; see XML source
Used:
at 3 locations
Attribute Group Summary
abbreviation
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
actionOrder
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
alternativeType
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
angleUnits
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
atomIDArray
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
atomMap
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
atomRef
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 3 locations
atomRef1Array
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
atomRef2Array
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
atomRefArray
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
atomRefs
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
atomRefs2
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
atomRefs3
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
atomRefs4
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 3 locations
atomSetRef
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
bondIDArray
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
bondMap
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
bondRef
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
bondRefs
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
box3
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
chirality
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
columns
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 3 locations
concise
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
constantToData
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
constantToSI
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
constraint
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
content
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
convention
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 102 locations
conventionValue
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
count
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 13 locations
countArray
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
dataType
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 7 locations
default
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
delimiter
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
dictRef
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 102 locations
dimensionality
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
dimensionBasis
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
duration
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
electronMap
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
elementType
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
elementTypeArray
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
end
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
endCondition
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
errorBasis
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 6 locations
errorValue
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 4 locations
errorValueArray
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
form
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
formalCharge
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 3 locations
formalChargeArray
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
format
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
formula
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
fractionDigits
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
from
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
ft
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
href
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 4 locations
hydrogenCount
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
hydrogenCountArray
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
id
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 107 locations
integral
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
irreducibleRepresentation
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
isotope
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
isotopeListRef
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
isotopeNumber
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
isotopeRef
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
kpoint
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
l
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
label
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
latticeType
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
length
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
linkType
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
lm
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
m
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
matrixType
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
max
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 5 locations
maxExclusive
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
maxInclusive
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
maxLength
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
maxValueArray
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
measurement
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
metadataType
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
min
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 5 locations
minExclusive
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
minInclusive
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
minLength
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
minValueArray
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
moleculeRef
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
multiplierToData
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
multiplierToSI
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
n
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
name
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 11 locations
number
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
objectClass
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
occupancy
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
occupancyArray
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
order
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
orderArray
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
parentSI
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
pattern
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
peakHeight
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
peakMultiplicity
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
peakShape
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
peakUnits
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
periodic
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
periodicity
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
pointGroup
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
power
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
preserve
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
ratio
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
reactionFormat
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 3 locations
reactionRole
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
reactionType
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
ref
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 45 locations
regionRefs
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
relatedEntryType
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
role
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 19 locations
rows
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 3 locations
serial
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
size
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 3 locations
spaceGroup
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
spaceType
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
spectrumType
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
sphere3
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
spin
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
spinMultiplicity
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
start
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
startCondition
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
state
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 8 locations
substanceListType
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
symbol
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
symmetryOriented
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
tautomeric
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
term
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
title
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 101 locations
to
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
totalDigits
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
type
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 10 locations
units
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 18 locations
unitType
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
value
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 4 locations
version
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
weight
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
whiteSpace
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
x2
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
x2Array
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
x3
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
x3Array
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
xFract
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
xFractArray
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
xMax
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
xMin
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
xUnits
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
xValue
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
xWidth
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
y2
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
y2Array
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
y3
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
y3Array
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
yFract
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
yFractArray
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
yield
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
yMax
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
yMin
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
yUnits
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
yValue
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
yWidth
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
z
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
z3
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 2 locations
z3Array
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
zFract
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
zFractArray
Content:
1 attribute
Defined:
globally; see XML source
Includes:
definition of 1 attribute
Used:
at 1 location
XML Source
<?xml version="1.0" encoding="UTF-8"?>
<xsd:schema elementFormDefault="qualified" targetNamespace="http://www.xml-cml.org/schema/cml2/react" xmlns="http://www.xml-cml.org/schema/cml2/react" xmlns:h="http://www.w3.org/1999/xhtml" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
<xsd:simpleType id="st.atomIDType" name="atomIDType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An identifier for an atom.</h:div>
<h:div class="description">
<h:p>
Of the form prefix:suffix where prefix and suffix
are purely alphanumeric (with _ and -) and prefix
is optional. This is similar to XML IDs (and we promote
this as good practice for atomIDs. Other punctuation and
whitespace is forbidden, so IDs from (say) PDB files are
not satisfactory.
</h:p>
<h:p>
The prefix is intended to form a pseudo-namespace so that
atom IDs in different molecules may have identical suffixes.
It is also useful if the prefix is the ID for the molecule
(though this clearly has its limitation). Atom IDs should not
be typed as XML IDs since they may not validate.
</h:p>
</h:div>
<h:div class="example" href="atomIDType1.xml"/>
</xsd:documentation>
<xsd:appinfo/>
</xsd:annotation>
<xsd:restriction base="xsd:string">
<xsd:pattern value="[A-Za-z_][A-Za-z0-9_\-]*(:[A-Za-z0-9_\-]+)?"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType id="st.countType" name="countType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A count multiplier for an object.</h:div>
<h:div class="description">
Many elements represent objects which can occur an arbitrary number of times in a scientific context. Examples are
<h:tt>action</h:tt>
,
<h:tt>object</h:tt>
or
<h:tt>molecule</h:tt>
s.
</h:div>
<h:div class="example" href="countType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:nonNegativeInteger"/>
</xsd:simpleType>
<xsd:simpleType id="st.idType" name="idType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A unique ID for an element.</h:div>
<h:div class="description">
<h:p>
This is not formally of type ID (an XML NAME which must start with a letter and contain only letters, digits and
<h:tt>.-_:</h:tt>
). It is recommended that IDs start with a letter, and contain no punctuation or whitespace. The function in XSLT will generate semantically void unique IDs.
</h:p>
<h:p>
It is difficult to ensure uniqueness when documents are merged. We suggest
namespacing IDs, perhaps using the containing elements as the base.
Thus
<h:tt>mol3:a1</h:tt>
could be a useful unique ID.
However this is still experimental.
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
<!--EBI-->
<!--<xsd:restriction base="xsd:QName"/>-->
<xsd:restriction base="xsd:string"/>
<!--EBI-->
</xsd:simpleType>
<xsd:simpleType id="st.namespaceRefType" name="namespaceRefType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An XML QName with required prefix.</h:div>
<h:div class="description">
<h:p>
A string referencing a dictionary, units, convention or other metadata.
</h:p>
<h:p>
The purpose is to allow authors to extend the vocabulary through their own namespaces without altering the schema. The prefix is mandatory. This convention is only used within STMML and related languages; it is NOT a generic URI.
</h:p>
</h:div>
<h:div class="example" href="namespaceRefType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="description">
<h:p>
The namespace prefix must start with an alpha character and can only contain alphanumeric and '_'. The suffix can have characters from the XML ID specification (alphanumeric, '_', '.' and '-'
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:pattern value="[A-Za-z][A-Za-z0-9_]*:[A-Za-z][A-Za-z0-9_\.\-]*"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType id="st.minType" name="minType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The minimum INCLUSIVE value of a quantity.</h:div>
<h:div class="description">
<h:p>
The minimum INCLUSIVE value of a sortable quantity such as
numeric, date or string. It should be ignored for dataTypes such as URL.
The use of
<h:tt>min</h:tt>
and
<h:tt>min</h:tt>
attributes can be used to give a range for the quantity.
The statistical basis of this range is not defined. The value of
<h:tt>min</h:tt>
is usually an observed
quantity (or calculated from observations). To restrict a value, the
<h:tt>
minExclusive
</h:tt>
type in a dictionary should be used.
</h:p>
<h:p>
The type of the minimum is the same as the quantity to which it refers - numeric,
date and string are currently allowed
</h:p>
</h:div>
<h:div class="example" href="maxType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:string"/>
</xsd:simpleType>
<xsd:simpleType id="st.maxType" name="maxType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The maximum INCLUSIVE value of a quantity.</h:div>
<h:div class="description">
<h:p>
The maximum INCLUSIVE value of a sortable quantity such as
numeric, date or string. It should be ignored for dataTypes such as URL.
The use of
<h:tt>min</h:tt>
and
<h:tt>max</h:tt>
attributes can be used to give a range for the quantity.
The statistical basis of this range is not defined. The value of
<h:tt>max</h:tt>
is usually an observed
quantity (or calculated from observations). To restrict a value, the
<h:tt>
maxExclusive
</h:tt>
type in a dictionary should be used.
</h:p>
<h:p>
The type of the maximum is the same as the quantity to which it refers - numeric,
date and string are currently allowed
</h:p>
</h:div>
<h:div class="example" href="maxType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:string"/>
</xsd:simpleType>
<xsd:simpleType id="st.unitsType" name="unitsType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Scientific units.</h:div>
<h:div class="description">
These will be linked to dictionaries of units with conversion information, using namespaced references (e.g.
<h:tt>si:m</h:tt>
). Distinguish carefully from _unitType_ which is an element describing a type of a unit in a _unitList_.
</h:div>
<h:div class="example" href="unit2.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="namespaceRefType"/>
</xsd:simpleType>
<xsd:simpleType id="st.positiveNumberType" name="positiveNumberType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A positive number.</h:div>
<h:div class="description">
Note that we also provide nonNegativeNumber with inclusive zero. The maximum number is (quite large) since 'unbounded' is more difficult to implement.
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:double">
<xsd:minExclusive value="0.0"/>
<xsd:maxInclusive value="1.0E+99"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType id="st.refType" name="refType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A reference to an existing object.</h:div>
<h:div class="description">
A reference to an existing element in the document. The target of the ref attribute must exist. The test for validity will normally occur in the element's _appinfo_. Any DOM Node created from this element will normally be a reference to another Node, so that if the target node is modified a the dereferenced content is modified. At present there are no deep copy semantics hardcoded into the schema.
</h:div>
</xsd:documentation>
</xsd:annotation>
<!--EBI modification-->
<!--<xsd:restriction base="xsd:QName"/>-->
<xsd:restriction base="xsd:string"/>
<!--EBI modification-->
</xsd:simpleType>
<xsd:simpleType id="st.atomRefs3Type" name="atomRefs3Type">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
A reference to three distinct existing atoms in order.
</h:div>
<h:div class="example" href="atomRefs31.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction>
<xsd:simpleType>
<xsd:list itemType="atomIDType"/>
</xsd:simpleType>
<xsd:length value="3"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType id="st.angleUnitsType" name="angleUnitsType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An enumeration of allowed angle units.</h:div>
<h:div class="description">May be obsolete.</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="degrees"/>
<xsd:enumeration value="radians"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType id="st.errorValueType" name="errorValueType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
An estimate of the error in the value of a quantity.
</h:div>
<h:div class="description">
An observed or calculated estimate of the error in the value of a numeric quantity. It should be ignored for dataTypes such as URL, date or string. The statistical basis of the errorValueType is not defined - it could be a range, an estimated standard deviation, an observed standard error, etc. This information can be added through _errorBasisType_.
</h:div>
<h:div class="example" href="scalar1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:float"/>
</xsd:simpleType>
<xsd:simpleType id="st.errorBasisType" name="errorBasisType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The basis of an error value.</h:div>
<h:div class="description">
Errors in values can be of several types and this simpleType
provides a small controlled vocabulary.
</h:div>
<h:div class="example" href="scalar1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:union>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="observedRange"/>
<xsd:enumeration value="observedStandardDeviation"/>
<xsd:enumeration value="observedStandardError"/>
<xsd:enumeration value="estimatedStandardDeviation"/>
<xsd:enumeration value="estimatedStandardError"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType>
<xsd:restriction base="namespaceRefType"/>
</xsd:simpleType>
</xsd:union>
</xsd:simpleType>
<xsd:simpleType id="st.dataTypeType" name="dataTypeType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">an enumerated type for all dataTypes in STM.</h:div>
<h:div class="description">
<h:p>
<h:tt>dataTypeType</h:tt>
represents an enumeration of allowed dataTypes
(at present identical with those in XML-Schemas (Part2- datatypes).
This means that implementers should be able to use standard XMLSchema-based
tools for validation without major implementation problems.
</h:p>
<h:p>
It will often be used an an attribute on
<h:a href="el.scalar">scalar</h:a>
,
<h:a href="el.array">array</h:a>
or
<h:a href="el.matrix">matrix</h:a>
elements.
</h:p>
</h:div>
<h:div class="description">
Note: the attribute xsi:type might be used to enforce the type-checking but I haven't worked this through yet.
</h:div>
<h:div class="example" href="dataTypeType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:union>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="xsd:string"/>
<xsd:enumeration value="xsd:boolean"/>
<xsd:enumeration value="xsd:float"/>
<xsd:enumeration value="xsd:double"/>
<xsd:enumeration value="xsd:decimal"/>
<xsd:enumeration value="xsd:duration"/>
<xsd:enumeration value="xsd:dateTime"/>
<xsd:enumeration value="xsd:time"/>
<xsd:enumeration value="xsd:date"/>
<xsd:enumeration value="xsd:gYearMonth"/>
<xsd:enumeration value="xsd:gYear"/>
<xsd:enumeration value="xsd:gMonthDay"/>
<xsd:enumeration value="xsd:gDay"/>
<xsd:enumeration value="xsd:gMonth"/>
<xsd:enumeration value="xsd:hexBinary"/>
<xsd:enumeration value="xsd:base64Binary"/>
<xsd:enumeration value="xsd:anyURI"/>
<xsd:enumeration value="xsd:QName"/>
<xsd:enumeration value="xsd:NOTATION"/>
<xsd:enumeration value="xsd:normalizedString"/>
<xsd:enumeration value="xsd:token"/>
<xsd:enumeration value="xsd:language"/>
<xsd:enumeration value="xsd:IDREFS"/>
<xsd:enumeration value="xsd:ENTITIES"/>
<xsd:enumeration value="xsd:NMTOKEN"/>
<xsd:enumeration value="xsd:NMTOKENS"/>
<xsd:enumeration value="xsd:Name"/>
<xsd:enumeration value="xsd:NCName"/>
<xsd:enumeration value="xsd:ID"/>
<xsd:enumeration value="xsd:IDREF"/>
<xsd:enumeration value="xsd:ENTITY"/>
<xsd:enumeration value="xsd:integer"/>
<xsd:enumeration value="xsd:nonPositiveInteger"/>
<xsd:enumeration value="xsd:negativeInteger"/>
<xsd:enumeration value="xsd:long"/>
<xsd:enumeration value="xsd:int"/>
<xsd:enumeration value="xsd:short"/>
<xsd:enumeration value="xsd:byte"/>
<xsd:enumeration value="xsd:nonNegativeInteger"/>
<xsd:enumeration value="xsd:unsignedLong"/>
<xsd:enumeration value="xsd:unsignedInt"/>
<xsd:enumeration value="xsd:unsignedShort"/>
<xsd:enumeration value="xsd:unsignedByte"/>
<xsd:enumeration value="xsd:positiveInteger"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType>
<xsd:restriction base="namespaceRefType"/>
</xsd:simpleType>
</xsd:union>
</xsd:simpleType>
<xsd:simpleType id="st.errorValueArrayType" name="errorValueArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Array of error estimate values.</h:div>
<h:div class="description">
An observed or calculated estimate of the error in the value of a numeric quantity. It should be ignored for dataTypes such as URL, date or string. The statistical basis of the errorValueType is not defined - it could be a range, an estimated standard deviation, an observed standard error, etc. This information can be added through _errorBasisType_.
</h:div>
<h:div class="example" href="scalar1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:list itemType="errorValueType"/>
</xsd:simpleType>
<xsd:simpleType id="st.floatArrayType" name="floatArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An array of floats.</h:div>
<h:div class="description">
An array of floats or other real numbers. Not used in STM Schema, but re-used by CML and other languages.
</h:div>
<h:div class="example" href="floatArrayType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:list itemType="xsd:float"/>
</xsd:simpleType>
<xsd:simpleType id="st.delimiterType" name="delimiterType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
A single non-whitespace character to separate components in arrays.
</h:div>
<h:div class="description">
<h:p>
Some STMML elements (such as
<h:a href="el.array">array</h:a>
) have
content representing concatenated values. The default separator is
whitespace (which can be normalised) and this should be used whenever
possible. However in some cases the values are empty, or contain whitespace or other
problematic punctuation, and a delimiter is required.
</h:p>
<h:p>
Note that the content string MUST start and end with the delimiter so
there is no ambiguity as to what the components are. Only printable
characters from the ASCII character set should be used, and character
entities should be avoided.
</h:p>
<h:p>
When delimiters are used to separate precise whitespace this should always
consist of spaces and not the other allowed whitespace characters
(newline, tabs, etc.). If the latter are important it is probably best to redesign
the application.
</h:p>
<h:p>
At present there is a controlled pattern of characters selected so as not to collide with common usage in XML document
</h:p>
</h:div>
<h:div class="example" href="delimiterType1.xml">
<h:em>The values in the array are</h:em>
"A", "B12", "" (empty string) and "D and E"
<h:em>note the spaces</h:em>
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:string">
<xsd:pattern value="[!$%^*@~;#,/|]"/>
<!--The below pattern is not validated by xmlSpy-->
<!--<xsd:pattern value="[\!\$\%\^\*\@\~\;\#\,\/\|]"/>-->
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType id="st.sizeType" name="sizeType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The size of an array.</h:div>
<h:div class="description">
The size of an array. Redundant, but serves as a check for processing software (useful if delimiters are used).
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:nonNegativeInteger"/>
</xsd:simpleType>
<xsd:simpleType id="st.elementTypeType" name="elementTypeType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Allowed elementType values.</h:div>
<h:div class="description">
<h:p>
The periodic table (up to
element number 118. In addition the following strings are allowed:
<h:ul>
<h:li>
<h:tt>Du</h:tt>
. ("dummy") This does not correspond to a "real" atom and can
support a point in space or within a chemical graph.
</h:li>
<h:li>
<h:tt>R</h:tt>
. ("R-group") This indicates that an atom or group of atoms could be attached at this point.
</h:li>
</h:ul>
</h:p>
</h:div>
<h:div class="example" href="elementTypeType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:union>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="Ac"/>
<xsd:enumeration value="Al"/>
<xsd:enumeration value="Ag"/>
<xsd:enumeration value="Am"/>
<xsd:enumeration value="Ar"/>
<xsd:enumeration value="As"/>
<xsd:enumeration value="At"/>
<xsd:enumeration value="Au"/>
<xsd:enumeration value="B"/>
<xsd:enumeration value="Ba"/>
<xsd:enumeration value="Bh"/>
<xsd:enumeration value="Bi"/>
<xsd:enumeration value="Be"/>
<xsd:enumeration value="Bk"/>
<xsd:enumeration value="Br"/>
<xsd:enumeration value="C"/>
<xsd:enumeration value="Ca"/>
<xsd:enumeration value="Cd"/>
<xsd:enumeration value="Ce"/>
<xsd:enumeration value="Cf"/>
<xsd:enumeration value="Cl"/>
<xsd:enumeration value="Cm"/>
<xsd:enumeration value="Co"/>
<xsd:enumeration value="Cr"/>
<xsd:enumeration value="Cs"/>
<xsd:enumeration value="Cu"/>
<xsd:enumeration value="Db"/>
<xsd:enumeration value="Dy"/>
<xsd:enumeration value="Er"/>
<xsd:enumeration value="Es"/>
<xsd:enumeration value="Eu"/>
<xsd:enumeration value="F"/>
<xsd:enumeration value="Fe"/>
<xsd:enumeration value="Fm"/>
<xsd:enumeration value="Fr"/>
<xsd:enumeration value="Ga"/>
<xsd:enumeration value="Gd"/>
<xsd:enumeration value="Ge"/>
<xsd:enumeration value="H">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Any isotope of hydrogen.</h:div>
<h:div class="description">
<h:p>
There are no special element symbols for D and T which should use the
<h:tt>isotope</h:tt>
attribute.
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="He"/>
<xsd:enumeration value="Hf"/>
<xsd:enumeration value="Hg"/>
<xsd:enumeration value="Ho"/>
<xsd:enumeration value="Hs"/>
<xsd:enumeration value="I"/>
<xsd:enumeration value="In"/>
<xsd:enumeration value="Ir"/>
<xsd:enumeration value="K"/>
<xsd:enumeration value="Kr"/>
<xsd:enumeration value="La"/>
<xsd:enumeration value="Li"/>
<xsd:enumeration value="Lr"/>
<xsd:enumeration value="Lu"/>
<xsd:enumeration value="Md"/>
<xsd:enumeration value="Mg"/>
<xsd:enumeration value="Mn"/>
<xsd:enumeration value="Mo"/>
<xsd:enumeration value="Mt"/>
<xsd:enumeration value="N"/>
<xsd:enumeration value="Na"/>
<xsd:enumeration value="Nb"/>
<xsd:enumeration value="Nd"/>
<xsd:enumeration value="Ne"/>
<xsd:enumeration value="Ni"/>
<xsd:enumeration value="No"/>
<xsd:enumeration value="Np"/>
<xsd:enumeration value="O"/>
<xsd:enumeration value="Os"/>
<xsd:enumeration value="P"/>
<xsd:enumeration value="Pa"/>
<xsd:enumeration value="Pb"/>
<xsd:enumeration value="Pd"/>
<xsd:enumeration value="Pm"/>
<xsd:enumeration value="Po"/>
<xsd:enumeration value="Pr"/>
<xsd:enumeration value="Pt"/>
<xsd:enumeration value="Pu"/>
<xsd:enumeration value="Ra"/>
<xsd:enumeration value="Rb"/>
<xsd:enumeration value="Re"/>
<xsd:enumeration value="Rf"/>
<xsd:enumeration value="Rh"/>
<xsd:enumeration value="Rn"/>
<xsd:enumeration value="Ru"/>
<xsd:enumeration value="S"/>
<xsd:enumeration value="Sb"/>
<xsd:enumeration value="Sc"/>
<xsd:enumeration value="Se"/>
<xsd:enumeration value="Sg"/>
<xsd:enumeration value="Si"/>
<xsd:enumeration value="Sm"/>
<xsd:enumeration value="Sn"/>
<xsd:enumeration value="Sr"/>
<xsd:enumeration value="Ta"/>
<xsd:enumeration value="Tb"/>
<xsd:enumeration value="Tc"/>
<xsd:enumeration value="Te"/>
<xsd:enumeration value="Th"/>
<xsd:enumeration value="Ti"/>
<xsd:enumeration value="Tl"/>
<xsd:enumeration value="Tm"/>
<xsd:enumeration value="U"/>
<xsd:enumeration value="Uun"/>
<xsd:enumeration value="Uuu"/>
<xsd:enumeration value="Uub"/>
<xsd:enumeration value="Uut"/>
<xsd:enumeration value="Uuq"/>
<xsd:enumeration value="Uup"/>
<xsd:enumeration value="Uuh"/>
<xsd:enumeration value="Uus"/>
<xsd:enumeration value="Uuo"/>
<xsd:enumeration value="V"/>
<xsd:enumeration value="W"/>
<xsd:enumeration value="Xe"/>
<xsd:enumeration value="Y"/>
<xsd:enumeration value="Yb"/>
<xsd:enumeration value="Zn"/>
<xsd:enumeration value="Zr"/>
<xsd:enumeration value="Dummy"/>
<xsd:enumeration value="Du">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A point or object with no chemical semantics.</h:div>
<h:div class="description">
<h:p>
Examples can be centroids, bond-midpoints, orienting "atoms" in small z-matrices.
</h:p>
<h:p>
Note "Dummy" has the same semantics but is now deprecated.
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="R">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
A point at which an atom or group might be attached.
</h:div>
<h:div class="description">
<h:p>
Examples are abbreviated organic functional groups, Markush representations, polymers, unknown atoms, etc. Semantics may be determined by the
<h:tt>role</h:tt>
attribute on the atom.
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:pattern value="[A-Za-z]+:[A-Za-z][A-Za-z0-9\-]+"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:union>
</xsd:simpleType>
<xsd:simpleType id="st.formalChargeType" name="formalChargeType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The formal charge on an object.</h:div>
<h:div class="description">
Used for electron-bookeeping. This has no relation to its calculated (fractional) charge or oxidation state.
</h:div>
<h:div class="example" href="formalChargeType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:integer"/>
</xsd:simpleType>
<xsd:simpleType id="st.hydrogenCountType" name="hydrogenCountType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
The total number of hydrogen atoms bonded to an object.
</h:div>
<h:div class="description">
The total number of hydrogen atoms bonded to an atom or contained in a molecule, whether explicitly included as atoms or not. It is an error to have hydrogen count less than the explicit hydrogen count. There is no default value and no assumptions about hydrogen Count can be made if it is not given. If hydrogenCount is given on every atom, then the values can be summed to give the total hydrogenCount for the (sub)molecule. Because of this hydrogenCount should not be used where hydrogen atoms bridge 2 or more atoms.
</h:div>
<h:div class="example" href="atom1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:nonNegativeInteger"/>
</xsd:simpleType>
<xsd:simpleType id="st.occupancyType" name="occupancyType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A floating point number between 0 and 1 inclusive</h:div>
<h:div class="description">
Originally for crystallographic occupancy but re-usable for fractinal yield, etc.
</h:div>
<h:div class="example" href="atom1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:float">
<xsd:minInclusive value="0"/>
<xsd:maxInclusive value="1"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType id="st.elementTypeArrayType" name="elementTypeArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An array of elementTypes.</h:div>
<h:div class="description">
Instances of this type will be used in array-style representation of atoms.
</h:div>
<h:div class="example" href="elementTypeArrayType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:list itemType="elementTypeType"/>
</xsd:simpleType>
<xsd:simpleType id="st.countArrayType" name="countArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Array of counts.</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:list itemType="countType"/>
</xsd:simpleType>
<xsd:simpleType id="st.formalChargeArrayType" name="formalChargeArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Array of formalCharges.</h:div>
<h:div class="description">
Used for electron-bookeeping. This has no relation to its calculated (fractional) charge or oxidation state.
</h:div>
<h:div class="example" href="formalChargeType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:list itemType="formalChargeType"/>
</xsd:simpleType>
<xsd:simpleType id="st.hydrogenCountArrayType" name="hydrogenCountArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Array of hydrogenCounts.</h:div>
<h:div class="description">
The total number of hydrogen atoms bonded to an atom or contained in a molecule, whether explicitly included as atoms or not. It is an error to have hydrogen count less than the explicit hydrogen count. There is no default value and no assumptions about hydrogen Count can be made if it is not given. If hydrogenCount is given on every atom, then the values can be summed to give the total hydrogenCount for the (sub)molecule. Because of this hydrogenCount should not be used where hydrogen atoms bridge 2 or more atoms.
</h:div>
<h:div class="example" href="atom1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:list itemType="hydrogenCountType"/>
</xsd:simpleType>
<xsd:simpleType id="st.occupancyArrayType" name="occupancyArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Array of atomic occupancies.</h:div>
<h:div class="description">
Primarily for crystallography. Values outside 0-1 are not allowed.
</h:div>
<h:div class="example" href="atom1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:list itemType="occupancyType"/>
</xsd:simpleType>
<xsd:simpleType id="st.coordinateComponentArrayType" name="coordinateComponentArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
An array of coordinateComponents for a single coordinate.
</h:div>
<h:div class="description">
An array of coordinateComponents for a single coordinate where these all refer to an X-coordinate (NOT x,y,z).Instances of this type will be used in array-style representation of 2-D or 3-D coordinates. Currently no machine validation. Currently not used in STMML, but re-used by CML (see example).
</h:div>
<h:div class="example" href="coordinateComponentArrayType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:list itemType="xsd:float"/>
</xsd:simpleType>
<xsd:simpleType id="st.atomRefArrayType" name="atomRefArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An array of atomRefs.</h:div>
<h:div class="description">
The atomRefs
cannot be schema- or schematron-validated. Instances of this type will
be used in array-style representation of bonds and atomParitys.
It can also be used for arrays of atomIDTypes such as in complex setereochemistry,
geometrical definitions, atom groupings, etc.
</h:div>
<h:div class="example" href="atomRefArrayType1.xml"/>
</xsd:documentation>
<xsd:appinfo/>
</xsd:annotation>
<xsd:list itemType="atomIDType"/>
</xsd:simpleType>
<xsd:simpleType id="st.atomRefType" name="atomRefType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A reference to an existing atom.</h:div>
<h:div class="example" href="atomRefType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="atomIDType"/>
</xsd:simpleType>
<xsd:simpleType id="st.atomRefs4Type" name="atomRefs4Type">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
A reference to four distinct existing atoms in order.
</h:div>
<h:div class="example" href="atomRefs41.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction>
<xsd:simpleType>
<xsd:list itemType="atomIDType"/>
</xsd:simpleType>
<xsd:length value="4"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType id="st.vector3Type" name="vector3Type">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A vector in 3-space.</h:div>
<h:div class="description">No constraints on magnitude (i.e. could be zero.</h:div>
<h:div class="example" href="vector31.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction>
<xsd:simpleType>
<xsd:list itemType="xsd:float"/>
</xsd:simpleType>
<xsd:length value="3"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType id="st.atomRefs2Type" name="atomRefs2Type">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
A reference to two distinct existing atoms in order.
</h:div>
<h:div class="example" href="atomRefs21.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction>
<xsd:simpleType>
<xsd:list itemType="atomIDType"/>
</xsd:simpleType>
<xsd:length value="2"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType id="st.bondRefArrayType" name="bondRefArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An array of references to bonds.</h:div>
<h:div class="description">
The references cannot (yet)
cannot be schema- or schematron-validated. Instances of this type will
be used in array-style representation of electron counts, etc.
It can also be used for arrays of bondIDTypes such as in complex stereochemistry,
geometrical definitions, bond groupings, etc.
</h:div>
</xsd:documentation>
<xsd:appinfo/>
</xsd:annotation>
<xsd:list itemType="bondRefType"/>
</xsd:simpleType>
<xsd:simpleType id="st.orderType" name="orderType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Bond order.</h:div>
<h:div class="description">
<h:p>
This is purely conventional and used
for bond/electron counting. There is no default value.
The emptyString attribute can be used to indicate a bond of
unknown or unspecified type. The interpretation of this is outside
the scope of CML-based algorithms. It may be accompanied by a
<h:tt>convention</h:tt>
attribute on the
<h:tt>bond</h:tt>
which links to a dictionary.
Example:
<h:tt>&lt;bond convention="ccdc:9" atomRefs2="a1 a2"/&gt;</h:tt>
could
represent a delocalised bond in the CCDC convention.
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:union>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="hbond">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Hydrogen bond.</h:div>
<h:div class="description">
Carries no semantics but will normally be between a hydrogen atom and an element with lone pairs.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="partial01">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Partial bond.</h:div>
<h:div class="description">
Can be used for a partial bond in a transition state, intermolecular interaction, etc. There is no numeric value associated and the bond order could be anywhere between 0 and single.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="S">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Single bond.</h:div>
<h:div class="description">synonymous with "1.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="1">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Single bond.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="partial12">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Intermediate between 1 and .</h:div>
<h:div class="description">
Could be used for a transition state or a delocalised system.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="D">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Double bond.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="2">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Double bond.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="partial23">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Intermediate between 2 and .</h:div>
<h:div class="description">
Could be used for a transition state or a delocalised system.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="T">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Triple bond.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="3">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Triple bond.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="A">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Aromatic bond.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType>
<xsd:restriction base="namespaceRefType"/>
</xsd:simpleType>
</xsd:union>
</xsd:simpleType>
<xsd:simpleType id="st.orderArrayType" name="orderArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An array of bond orders.</h:div>
<h:div class="description">See order.</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:list itemType="orderType"/>
</xsd:simpleType>
<xsd:simpleType id="st.dimensionType" name="dimensionType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Allowed values for dimension Types in quantities.</h:div>
<h:div class="description">
<h:p>
These are the 7 types prescribed by the SI system, together
with the "dimensionless" type. We intend to be somewhat uncoventional
and explore enhanced values of "dimensionless", such as "angle".
This may be heretical, but we find the present system impossible to implement
in many cases.
</h:p>
<h:p>
Used for constructing entries in a dictionary of units
</h:p>
</h:div>
<h:div class="example" href="dimensionType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="mass"/>
<xsd:enumeration value="length"/>
<xsd:enumeration value="time"/>
<xsd:enumeration value="current"/>
<xsd:enumeration value="amount"/>
<xsd:enumeration value="luminosity"/>
<xsd:enumeration value="temperature"/>
<xsd:enumeration value="dimensionless"/>
<xsd:enumeration value="angle">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An angl.</h:div>
<h:div class="description">
(formally dimensionless, but useful to have units).
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType id="st.bondRefType" name="bondRefType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A reference to an existing bond.</h:div>
<h:div class="general">
A reference to a bond may be made by atoms (e.g. for multicentre or pi-bonds), electrons (for annotating reactions or describing electronic properties) or possibly other bonds (no examples yet). The semantics are relatively flexible.
</h:div>
<h:div class="example" href="bond1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:string">
<xsd:pattern value="[A-Za-z0-9_\-]+(:[A-Za-z0-9_\-]+)?"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType id="st.formulaType" name="formulaType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A concise representation for a molecular formula.</h:div>
<h:div class="description">
This MUST adhere to a whitespaced syntax so that it is trivially machine-parsable. Each element is followed by its count, and the string is optionally ended by a formal charge. NO brackets or other nesting is allowed.
</h:div>
<h:div class="example" href="formulaType1.xml"/>
</xsd:documentation>
<xsd:appinfo/>
</xsd:annotation>
<xsd:restriction base="xsd:string">
<xsd:pattern value="\s*([A-Z][a-z]?\s+[1-9][0-9]*)(\s+[A-Z][a-z]?\s+[1-9][0-9]*)*(\s+[-|+]?[0-9]+)?\s*"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType id="st.isotopicSpinType" name="isotopicSpinType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
A fractional representation of the spin of the nucleus.
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:string">
<xsd:pattern value="\d{1,}(/\d)?"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType id="st.latticeType" name="latticeType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Allowed lattice types.</h:div>
<h:div class="description"/>
<h:div class="example" href="lattice3.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:union>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="primitive"/>
<xsd:enumeration value="full"/>
<xsd:enumeration value="aCentred">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">lattice with A centering.</h:div>
<h:div class="description">
A lattice which uses the translation operator {0, 0.5, 0.5}.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType>
<xsd:restriction base="namespaceRefType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">User-defined lattice-type.</h:div>
<h:div class="description">
This definition must be by reference to a namespaced dictionary entry.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:restriction>
</xsd:simpleType>
</xsd:union>
</xsd:simpleType>
<xsd:simpleType id="st.spaceType" name="spaceType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Signifies real or reciprocal space.</h:div>
<h:div class="description">
Likely to be used on types such as lattice, plane, point.
</h:div>
<h:div class="example" href="space1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:union>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="real"/>
<xsd:enumeration value="k-space">
<xsd:annotation>
<xsd:documentation>
<h:div class="description">A synonym for reciprocal.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="Fourier">
<xsd:annotation>
<xsd:documentation>
<h:div class="description">A synonym for reciprocal.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="reciprocal">
<xsd:annotation>
<xsd:documentation>
<h:div class="description"/>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType>
<xsd:restriction base="namespaceRefType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">User-defined space-type.</h:div>
<h:div class="description">No obvious possibilities, but who know.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:restriction>
</xsd:simpleType>
</xsd:union>
</xsd:simpleType>
<xsd:simpleType id="st.matrixType" name="matrixType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Allowed matrix types.</h:div>
<h:div class="description">
<h:p>
Many are square matrices. By default all elements must be included. For symmetric, antisymmetric and diagonal matrices some compression is possible by not reporting the identical or forced zero elements. These have their own subtypes, usually with UT or LT appended. Use these with caution as there is chance of confusion and you cannot rely on standard software to read these.
</h:p>
<h:p>
The matrix type fixes the order and semantics of the elements in the XML element but does not mandate any local syntax. Thus an application may insert newline characters after each row or use a &lt;row&gt; element.
</h:p>
</h:div>
<h:div class="example" href="matrix1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:union>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="rectangular">
<xsd:annotation>
<xsd:documentation>
<h:div class="description">
Rectangular with no semantic constraints and ordered rowwise (i.e. the column index runs fastest).
<h:pre>
1 2 3 4
0 3 5 6
</h:pre>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="square">
<xsd:annotation>
<xsd:documentation>
<h:div class="description">
Square with no semantic constraints.
<h:pre>
1 2 78
3 4 -1
-34 2 7
</h:pre>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="squareSymmetric">
<xsd:annotation>
<xsd:documentation>
<h:div class="description">
Square symmetric with all elements explicit.
<h:pre>
1 2 3
2 7 1
3 1 9
</h:pre>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="squareSymmetricLT">
<xsd:annotation>
<xsd:documentation>
<h:div class="description">
Square symmetric with the diagonal and lower triangle explicit and the upper triangle omitted. Rows are of length 1, 2, 3...
<h:pre>
1
2 7
3 1 9
</h:pre>
is equivalent to
<h:pre>
1 2 3
2 7 1
3 1 9
</h:pre>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="squareSymmetricUT">
<xsd:annotation>
<xsd:documentation>
<h:div class="description">
Square symmetric with the diagonal and upper triangle explicit. Rows are of length n, n-1, ... 2, 1
<h:pre>
1 7 9
2 -1
34
</h:pre>
is equivalent to
<h:pre>
1 7 9
7 2 -1
9 -1 34
</h:pre>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="squareAntisymmetric">
<xsd:annotation>
<xsd:documentation>
<h:div class="description">
Square antisymmetric with all elements explicit. The diagonal is necessarily zero.
<h:pre>
0 -2 3
2 0 1
-3 -1 0
</h:pre>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="squareAntisymmetricLT">
<xsd:annotation>
<xsd:documentation>
<h:div class="description">
Square symmetric with the lower triangle explicit and diagonal and upper triangle omitted. Rows are of length 1, 2,... n-1.
<h:pre>
-7
-9 1
</h:pre>
is equivalent to
<h:pre>
0 7 9
-7 0 -1
-9 1 0
</h:pre>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="squareAntisymmetricUT">
<xsd:annotation>
<xsd:documentation>
<h:div class="description">
Square symmetric with the upper triangle explicit and diagonal and lower triangle omitted. Rows are of length n-1, n-2,... 2,1.
<h:pre>
7 9
-1
</h:pre>
is equivalent to
<h:pre>
0 7 9
-7 0 -1
-9 1 0
</h:pre>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="diagonal">
<xsd:annotation>
<xsd:documentation>
<h:div class="description">
Symmetric. Elements are zero except on the diagonal. No compressed representation available (use
<h:tt>array</h:tt>
element).
</h:div>
<h:pre>
1 0 0
0 3 0
0 0 4
</h:pre>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="upperTriangular">
<xsd:annotation>
<xsd:documentation>
<h:div class="description">
Square. Elements are zero below the diagonal
<h:pre>
1 2 3 4
0 3 5 6
0 0 4 8
0 0 0 2
</h:pre>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="upperTriangularUT">
<xsd:annotation>
<xsd:documentation>
<h:div class="description">
Square. Elements below the diagonal are zero and omitted, and rows are of length n, n-1, ... , 2, 1.
<h:pre>
1 2 3 4
3 5 6
4 8
2
</h:pre>
is equivalent to
<h:pre>
1 2 3 4
0 3 5 6
0 0 4 8
0 0 0 2
</h:pre>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="lowerTriangular">
<xsd:annotation>
<xsd:documentation>
<h:div class="description">
Square. Elements are zero above the diagonal
<h:pre>
1 0 0
7 3 0
9 2 4
</h:pre>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="lowerTriangularLT">
<xsd:annotation>
<xsd:documentation>
<h:div class="description">
Square. Elements above the diagonal are zero and omitted, and rows are of length 1, 2, ...n.
<h:pre>
1
3 7
9 2 3
</h:pre>
is equivalent to
<h:pre>
1 0 0
3 7 0
9 2 3
</h:pre>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="unit">
<xsd:annotation>
<xsd:documentation>
<h:div class="description">
Square. Diagonal elements are 1 and off-diagonal are zero.
<h:pre>
1 0 0
0 1 0
0 0 1
</h:pre>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="unitary">
<xsd:annotation>
<xsd:documentation>
<h:div class="description">
Square. When multiplied by its transpose gives the unit matrix.
<h:pre>
0 -1 0
1 0 0
0 0 1
</h:pre>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="rowEigenvectors">
<xsd:annotation>
<xsd:documentation>
<h:div class="description">
Square. Each row corresponds to an eigenvector of a square matrix. Elements are real. The length of the eigenvectors is undefined, i.e. they are not required to be normalised to 1.
<h:pre>
0 -1 0
1 0 0
0 0 1
</h:pre>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="rotation22">
<xsd:annotation>
<xsd:documentation>
<h:div class="description">
The rotation is defined by the matrix premultiplyin a column vector (x, y) .
<h:pre>
0 -1
1 0
</h:pre>
produces (-y, x), i.e. a rotation of -90 degrees.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="rotationTranslation32">
<xsd:annotation>
<xsd:documentation>
<h:div class="description">
A third column defining the translation is added to a rotation22.
<h:pre>
0 -1 22
1 0 33
</h:pre>
produces (-y + 22, x + 33), i.e. a rotation of -90 degrees followed by a translation of (22, 33).
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="homogeneous33"/>
<xsd:enumeration value="rotation33"/>
<xsd:enumeration value="rotationTranslation43"/>
<xsd:enumeration value="homogeneous44"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType>
<xsd:restriction base="namespaceRefType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">User-defined matrix-type.</h:div>
<h:div class="description">
This definition must be by reference to a namespaced dictionary entry.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:restriction>
</xsd:simpleType>
</xsd:union>
</xsd:simpleType>
<xsd:simpleType id="st.metadataType" name="metadataType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The name of the metadata.</h:div>
<h:div class="description">
Metadata consists of name-value pairs (value is in the "content" attribute). The names are from a semi-restricted vocabulary, mainly Dublin Core. The content is unrestricted. The order of metadata has no implied semantics at present. Users can create their own metadata names using the namespaced prefix syntax (e.g. foo:institution). Ideally these names should be defined in an STMML dictionary.
</h:div>
<h:div class="curation">
2003-03-05: Added UNION to manage non-controlled name.
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:union>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="dc:coverage">
<xsd:annotation>
<xsd:documentation>
<h:div class="definition">
The extent or scope of the
content of the resource.
</h:div>
<h:div class="description">
Coverage will typically include
spatial location (a place name or geographic
coordinates), temporal period (a period label, date, or
date range) or jurisdiction (such as a named
administrative entity). Recommended best practice is to
select a value from a controlled vocabulary (for
example, the Thesaurus of Geographic Names [TGN]) and
that, where appropriate, named places or time periods
be used in preference to numeric identifiers such as
sets of coordinates or date ranges.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="dc:description">
<xsd:annotation>
<xsd:documentation>
<h:div class="definition">
An account of the content of the
resource.
</h:div>
<h:div class="description">
Description may include but is not
limited to: an abstract, table of contents, reference
to a graphical representation of content or a free-text
account of the content.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="dc:identifier">
<xsd:annotation>
<xsd:documentation>
<h:div class="definition">
An unambiguous reference to the
resource within a given context.
</h:div>
<h:div class="description">
Recommended best practice is to
identify the resource by means of a string or number
conforming to a formal identification system. Example
formal identification systems include the Uniform
Resource Identifier (URI) (including the Uniform
Resource Locator (URL)), the Digital Object Identifier
(DOI) and the International Standard Book Number
(ISBN).
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="dc:format">
<xsd:annotation>
<xsd:documentation>
<h:div class="definition">
The physical or digital
manifestation of the resource.
</h:div>
<h:div class="description">
Typically, Format may include the
media-type or dimensions of the resource. Format may be
used to determine the software, hardware or other
equipment needed to display or operate the resource.
Examples of dimensions include size and duration.
Recommended best practice is to select a value from a
controlled vocabulary (for example, the list of
Internet Media Types [MIME] defining computer media
formats).
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="dc:relation">
<xsd:annotation>
<xsd:documentation>
<h:div class="definition">
A reference to a related
resource.
</h:div>
<h:div class="description">
Recommended best practice is to
reference the resource by means of a string or number
conforming to a formal identification system.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="dc:rights">
<xsd:annotation>
<xsd:documentation>
<h:div class="definition">
Information about rights held in
and over the resource.
</h:div>
<h:div class="description">
Typically, a Rights element will
contain a rights management statement for the resource,
or reference a service providing such information.
Rights information often encompasses Intellectual
Property Rights (IPR), Copyright, and various Property
Rights. If the Rights element is absent, no assumptions
can be made about the status of these and other rights
with respect to the resource.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="dc:subject">
<xsd:annotation>
<xsd:documentation>
<h:div class="definition">
The topic of the content of the
resource.
</h:div>
<h:div class="description">
Typically, a Subject will be
expressed as keywords, key phrases or classification
codes that describe a topic of the resource.
Recommended best practice is to select a value from a
controlled vocabulary or formal classification
scheme.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="dc:title">
<xsd:annotation>
<xsd:documentation>
<h:div class="definition">A name given to the resource.</h:div>
<h:div class="description">
Typically, a Title will be a name by
which the resource is formally known.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="dc:type">
<xsd:annotation>
<xsd:documentation>
<h:div class="definition">
The nature or genre of the
content of the resource.
</h:div>
<h:div class="description">
Type includes terms describing
general categories, functions, genres, or aggregation
levels for content. Recommended best practice is to
select a value from a controlled vocabulary (for
example, the working draft list of Dublin Core Types
[DCT1]). To describe the physical or digital
manifestation of the resource, use the FORMAT
element.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="dc:contributor">
<xsd:annotation>
<xsd:documentation>
<h:div class="definition">
An entity responsible for making
contributions to the content of the resource.
</h:div>
<h:div class="description">
Examples of a Contributor include a
person, an organisation, or a service. Typically, the
name of a Contributor should be used to indicate the
entity.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="dc:creator">
<xsd:annotation>
<xsd:documentation>
<h:div class="definition">
An entity primarily responsible
for making the content of the resource.
</h:div>
<h:div class="description">
Examples of a Creator include a
person, an organisation, or a service. Typically, the
name of a Creator should be used to indicate the
entity.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="dc:publisher">
<xsd:annotation>
<xsd:documentation>
<h:div class="definition">
An entity responsible for making
the resource available.
</h:div>
<h:div class="description">
Examples of a Publisher include a
person, an organisation, or a service. Typically, the
name of a Publisher should be used to indicate the
entity.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="dc:source">
<xsd:annotation>
<xsd:documentation>
<h:div class="definition">
A Reference to a resource from
which the present resource is derived.
</h:div>
<h:div class="description">
The present resource may be derived
from the Source resource in whole or in part.
Recommended best practice is to reference the resource
by means of a string or number conforming to a formal
identification system.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="dc:language">
<xsd:annotation>
<xsd:documentation>
<h:div class="definition">
A language of the intellectual
content of the resource.
</h:div>
<h:div class="description">
Recommended best practice for the
values of the Language element is defined by RFC 1766
[RFC1766] which includes a two-letter Language Code
(taken from the ISO 639 standard [ISO639]), followed
optionally, by a two-letter Country Code (taken from
the ISO 3166 standard [ISO3166]). For example, 'en' for
English, 'fr' for French, or 'en-uk' for English used
in the United Kingdom.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="dc:date">
<xsd:annotation>
<xsd:documentation>
<h:div class="definition">
A date associated with an event
in the life cycle of the resource.
</h:div>
<h:div class="description">
Typically, Date will be associated
with the creation or availability of the resource.
Recommended best practice for encoding the date value
is defined in a profile of ISO 8601 [W3CDTF] and
follows the YYYY-MM-DD format.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="cmlm:safety">
<xsd:annotation>
<xsd:documentation>
<h:div class="definition">
Entry contains information
relating to chemical safety.
</h:div>
<h:div class="description">
Typically the content will be a
reference to a handbook, MSDS, threshhold or other
human-readable strin.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="cmlm:insilico">
<xsd:annotation>
<xsd:documentation>
<h:div class="definition">
Part or whole of the information
was computer-generated.
</h:div>
<h:div class="description">
Typically the content will be the
name of a method or a progra.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="cmlm:structure">
<xsd:annotation>
<xsd:documentation>
<h:div class="definition">3D structure included.</h:div>
<h:div class="description">details include.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="cmlm:reaction"/>
<xsd:enumeration value="cmlm:identifier"/>
<xsd:enumeration value="other"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType>
<xsd:restriction base="namespaceRefType"/>
</xsd:simpleType>
</xsd:union>
</xsd:simpleType>
<xsd:simpleType id="st.chiralityType" name="chiralityType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The chirality of a system or molecule.</h:div>
<h:div class="description">
This is being actively investigated by a IUPAC committee (2002) so the convention is likely to change. No formal default.
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="enantiomer"/>
<xsd:enumeration value="racemate"/>
<xsd:enumeration value="unknown"/>
<xsd:enumeration value="other"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType id="st.stateType" name="stateType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">State of a substance or property.</h:div>
<h:div class="description">
The state(s) of matter appropriate to a substance or property. It follows a partially controlled vocabulary. It can be extended through namespace codes to dictionaries.
</h:div>
<h:div class="example" href="stateType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:union>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="aqueous">
<xsd:annotation>
<xsd:documentation>
<h:div>An aqueous solutio.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="gas">
<xsd:annotation>
<xsd:documentation>
<h:div>
Gas or vapor. The default state for computation on isolated molecule.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="glass">
<xsd:annotation>
<xsd:documentation>
<h:div>A glassy stat.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="liquid">
<xsd:annotation>
<xsd:documentation>
<h:div>
Normally pure liquid (use solution where appropriate.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="nematic">
<xsd:annotation>
<xsd:documentation>
<h:div>The nematic phas.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="smectic">
<xsd:annotation>
<xsd:documentation>
<h:div>The smectic phas.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="solid">
<xsd:annotation>
<xsd:documentation>
<h:div>A soli.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="solidSolution">
<xsd:annotation>
<xsd:documentation>
<h:div>A solid solutio.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="solution">
<xsd:annotation>
<xsd:documentation>
<h:div>A (liquid) solutio.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType>
<xsd:restriction base="namespaceRefType"/>
</xsd:simpleType>
</xsd:union>
</xsd:simpleType>
<xsd:simpleType id="st.reactionFormatType" name="reactionFormatType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The format of the reaction.</h:div>
<h:div>
<h:p>
This is provided for machine-understanding of the format of the reaction steps and components.
</h:p>
<h:p>Semantics are semi-controlled.</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:union>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="reactantProduct">
<xsd:annotation>
<xsd:documentation>
<h:div>
<h:p>
The commonest representation with reactantList and productList.
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="cmlSnap">
<xsd:annotation>
<xsd:documentation>
<h:div>
<h:p>
A list of molecules representing snap shots on a reaction pathway.
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType>
<xsd:restriction base="namespaceRefType"/>
</xsd:simpleType>
</xsd:union>
</xsd:simpleType>
<xsd:simpleType id="st.reactionRoleType" name="reactionRoleType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The role of the reaction within a reactionList.</h:div>
<h:div class="description">Semantics are semi-controlled.</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:union>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="complete">
<xsd:annotation>
<xsd:documentation>
<h:div>
<h:p>
On reactionList signifies that the children are the complete description of the reaction.
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="overall">
<xsd:annotation>
<xsd:documentation>
<h:div>
<h:p>
The overall reaction in a multi-step reaction. Normally this would be the first reaction in a reactionList and the individual steps are held in a following sibling reactionList.
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="rateDeterminingStep">
<xsd:annotation>
<xsd:documentation>
<h:div>
<h:p>
The rate-determining step in a multi-step reaction. This implies also that the reaction has a role of step.
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="step">
<xsd:annotation>
<xsd:documentation>
<h:div>
<h:p>
A step in a multi-step reaction. This reaction will normally be a child of reactionList.
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="steps">
<xsd:annotation>
<xsd:documentation>
<h:div>
<h:p>a reactionList containing steps</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType>
<xsd:restriction base="namespaceRefType">
<xsd:annotation>
<xsd:documentation>
<h:div>
<h:p>
Examples could be "myDict:step1", "foo:chainPropagation", etc.
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:restriction>
</xsd:simpleType>
</xsd:union>
</xsd:simpleType>
<xsd:simpleType id="st.reactionTypeType" name="reactionTypeType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The semantic type of the reaction.</h:div>
<h:div>
<h:p>
This is provided for machine-understanding of the topology or logic of the reaction steps and components (i.e. not for a general classification for which
<h:tt>label</h:tt>
is more appropriate.)
</h:p>
<h:p>
Semantics are semi-controlled. Some terms are appropriate to multistep reactions, and can be used with or without explicit steps.
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:union>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="chainReaction">
<xsd:annotation>
<xsd:documentation>
<h:div>
<h:p>
A reaction in which one or more reactive reaction intermediates (frequently radicals) are continuously regenerated, usually through a repetitive cycle of elementary steps (the 'propagation step') (IUPAC GoldBook).
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="initiation">
<xsd:annotation>
<xsd:documentation>
<h:div>
<h:p>
A reaction or process generating free radicals (or some other reactive
reaction intermediates) which then induce a chain reaction. For example,
in the chlorination of alkanes by a radical mechanism the initiation step is
the dissociation of molecular chlorine.
IUPAC Compendium of Chemical Terminology 2nd Edition (1997).
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="termination">
<xsd:annotation>
<xsd:documentation>
<h:div>
<h:p>
The steps in a chain reaction in which reactive intermediates are destroyed
or rendered inactive, thus ending the chain.
IUPAC Compendium of Chemical Terminology 2nd Edition (1997)
.
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="reversible">
<xsd:annotation>
<xsd:documentation>
<h:div>
<h:p>
A reaction which can proceed in the forward direction as readily as in the reverse direction (IUPAC GoldBook).
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType>
<xsd:restriction base="namespaceRefType"/>
</xsd:simpleType>
</xsd:union>
</xsd:simpleType>
<xsd:simpleType id="st.sphere3Type" name="sphere3Type">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A sphere in 3-space.</h:div>
<h:div class="description">
Defined by 4 real numbers, conventionally a point3 at the centre of the sphere and a nonNegative scalar for the radius.
</h:div>
<h:div class="example" href="sphere31.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction>
<xsd:simpleType>
<xsd:list itemType="xsd:float"/>
</xsd:simpleType>
<xsd:length value="4"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType id="st.box3Type" name="box3Type">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A box in 3-space.</h:div>
<h:div class="description">
Defined by 6 real numbers (x1 y1 z1 x2 y2 z2). By default these are Cartesian coordinates (with units specified elsewhere - responsibility of schema creator.) If there is a means of specifying oblique axes (e.g. crystallographic cell) the box may be a parallelipiped. The components are grouped in threes ans separated by a semicolon to avoid problems of guessing the convention.
</h:div>
<h:div class="example" href="box31.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction>
<xsd:simpleType>
<xsd:list itemType="xsd:float"/>
</xsd:simpleType>
<xsd:length value="6"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType id="st.moleculeRefType" name="moleculeRefType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A reference to an existing molecule.</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="idType"/>
</xsd:simpleType>
<xsd:simpleType id="st.nonNegativeAngleType" name="nonNegativeAngleType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A non-signed angle.</h:div>
<h:div class="description">
Re-used by _angle_. Note that we also provide positiveAngleType (e.g. for cell angles) and torsionAngleType for _torsion_.
</h:div>
<h:div class="example" href="nonNegativeAngleType.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:float">
<xsd:minInclusive value="0.0"/>
<xsd:maxInclusive value="180.0"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType id="st.stereoType" name="stereoType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Bond stereochemistry as a string.</h:div>
<h:div class="description">
This is purely conventional. There is no default value.
The emptyString attribute can be used to indicate a bond of
unknown or unspecified type. The interpretation of this is outside
the scope of CML-based algorithms. It may be accompanied by a
<h:tt>convention</h:tt>
attribute which links to a dictionary.
</h:div>
<h:div class="example" href="bond1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="C">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A cis bond.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="T">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A trans bond.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="W">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A wedge bond.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="H">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A hatch bond.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">empty or missing.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType id="st.line3Type" name="line3Type">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An unbounded line in 3-space.</h:div>
<h:div class="description">
Defined by 6 real numbers, conventionally an arbitrary point on the line and a vector3. There is no significance to the point (i.e. it is not the "end of the line") and there are an infinite number of ways of representing the line.
</h:div>
<h:div class="example" href="line31.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction>
<xsd:simpleType>
<xsd:list itemType="xsd:float"/>
</xsd:simpleType>
<xsd:length value="6"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType id="st.plane3Type" name="plane3Type">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An unbounded plane in 3-space.</h:div>
<h:div class="description">
Defined by 4 real numbers, conventionally a vector3 normal to the plane and a signed scalar representing the distance to the origin. The vector must not be of zero length (and need not be normalized.
</h:div>
<h:div class="example" href="plane31.xml">
<h:p>
The first three numbers are the vector, followed by the distance
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction>
<xsd:simpleType>
<xsd:list itemType="xsd:float"/>
</xsd:simpleType>
<xsd:length value="4"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType id="st.point3Type" name="point3Type">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A point in 3-space.</h:div>
<h:div class="description">The 3 components can have any signed value.</h:div>
<h:div class="example" href="point31.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction>
<xsd:simpleType>
<xsd:list itemType="xsd:float"/>
</xsd:simpleType>
<xsd:length value="3"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType id="st.torsionAngleType" name="torsionAngleType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The type of a torsion angle.</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:float">
<xsd:minInclusive value="-360.0"/>
<xsd:maxInclusive value="360.0"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType id="st.matrix44Type" name="matrix44Type">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A 4x4 transformation matrix</h:div>
<h:div class="description">...</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction>
<xsd:simpleType>
<xsd:list itemType="xsd:float"/>
</xsd:simpleType>
<xsd:length value="16"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:attributeGroup id="attGp.title" name="title">
<xsd:attribute id="att.title" name="title" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A title on an element.</h:div>
<h:div class="description">No controlled value.</h:div>
<h:div class="example" href="title1.xml"/>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.id" name="id">
<xsd:attribute id="att.id" name="id" type="idType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
An attribute providing a unique ID for an element.
</h:div>
<h:div class="description"/>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.convention" name="convention">
<xsd:attribute id="att.convention" name="convention" type="namespaceRefType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A reference to a convention.</h:div>
<h:div class="description">
There is no controlled vocabulary for conventions, but the author must ensure that the semantics are openly available and that there are mechanisms for implementation. The convention is inherited by all the subelements,
so that a convention for
<h:tt>molecule</h:tt>
would by default extend to its
<h:tt>bond</h:tt>
and
<h:tt>atom</h:tt>
children. This can be overwritten
if necessary by an explicit
<h:tt>convention</h:tt>
.
<h:p>
It may be useful to create conventions with namespaces (e.g.
<h:tt>iupac:name</h:tt>
).
Use of
<h:tt>convention</h:tt>
will normally require non-STMML semantics, and should be used with
caution. We would expect that conventions prefixed with "ISO" would be useful,
such as ISO8601 for dateTimes.
</h:p>
<h:p>
There is no default, but the conventions of STMML or the related language (e.g. CML) will be assumed.
</h:p>
</h:div>
<h:div class="example" href="convGroup1.xml" id="ex"/>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.dictRef" name="dictRef">
<xsd:attribute id="att.dictRef" name="dictRef" type="namespaceRefType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A reference to a dictionary entry.</h:div>
<h:div class="description">
Elements in data instances such as _scalar_ may have a
<h:tt>dictRef</h:tt>
attribute to point to an entry in a dictionary. To avoid excessive use of (mutable) filenames and URIs we recommend a namespace prefix, mapped to a namespace URI in the normal manner. In this case, of course, the namespace URI must point to a real XML document containing _entry_ elements and validated against STMML Schema.
<h:p>
Where there is concern about the dictionary becoming separated from the document the dictionary entries can be physically included as part of the data instance and the normal XPointer addressing mechanism can be used.
</h:p>
<h:p>
This attribute can also be used on _dictionary_ elements to define the namespace prefix
</h:p>
</h:div>
<h:div class="example" href="dictRefGroup1.xml"/>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.min" name="min">
<xsd:attribute id="att.min" name="min" type="minType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
The minimum value allowed for an element or attribute.
</h:div>
<h:div class="description"/>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.max" name="max">
<xsd:attribute id="att.max" name="max" type="maxType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
Maximum value allowed for an element or attribute.
</h:div>
<h:div class="description"/>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.units" name="units">
<xsd:attribute id="att.units" name="units" type="unitsType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Scientific units on an element.</h:div>
<h:div class="description">
These must be taken from a dictionary of units. There should be some mechanism for validating the type of the units against the possible values of the element.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.start" name="start">
<xsd:attribute id="att.start" name="start" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The start time.</h:div>
<h:div class="description">
The start time in any allowable XSD representation of date, time or dateTime. This will normally be a clock time or date.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.startCondition" name="startCondition">
<xsd:attribute id="att.startCondition" name="startCondition" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The start condition.</h:div>
<h:div class="description">
This can describe the condition(s) that has to be met before an action can begin, such as in a recipe. Semantics are unexplored but could be used to control robotic operations.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.duration" name="duration">
<xsd:attribute id="att.duration" name="duration" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The duration of the action.</h:div>
<h:div class="description">Semantics undefined.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.end" name="end">
<xsd:attribute id="att.end" name="end" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The end time.</h:div>
<h:div class="description">
The start time in any allowable XSD representation of date, time or dateTime. This will normally be a clock time or date.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.endCondition" name="endCondition">
<xsd:attribute id="att.endCondition" name="endCondition" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The end condition.</h:div>
<h:div class="description">
<h:p>
At present a human-readable string describing some condition when the
ac tion should end. As XML develops it may be possible to add machine-processable
semantics in this field.
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.type" name="type">
<xsd:attribute id="att.type" name="type" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Type of the object.</h:div>
<h:div class="description">
A qualifier which may affect the semantics of the object.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.actionOrder" name="actionOrder">
<xsd:attribute id="att.actionOrder" name="order">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
Describes whether child elements are sequential or parallel.
</h:div>
<h:div class="description">There is no default.</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="sequential"/>
<xsd:enumeration value="parallel"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.count" name="count">
<xsd:attribute id="att.count" name="count" type="positiveNumberType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The count of the object.</h:div>
<h:div class="description">
No fixed semantics or default, normally integral. It is presumed that the element can be multiplied by the count value.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.ref" name="ref">
<xsd:attribute id="att.ref" name="ref" type="refType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A reference to an element of given type.</h:div>
<h:div class="description">
<h:tt>ref</h:tt>
modifies an element into a reference to an existing element of that type within the document. This is similar to a pointer and it can be thought of a strongly typed hyperlink. It may also be used for "subclassing" or "overriding" elements.
<br xmlns=""/>
When referring to an element most of the "data" such as attribute values and element content will be on the full instantiated element. Therefore ref (and possibly id) will normally be the only attributes on the pointing element. However there may be some attributes (title, count, etc.) which have useful semantics, but these are element-specific
</h:div>
<h:div class="example" href="refGroup1.xml"/>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.alternativeType" name="alternativeType">
<xsd:attribute id="att.alternativeType" name="type">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The type of an alternative.</h:div>
<h:div class="general">
This adds semantics to an _alternative_ and might be used by an RDF or related engine.
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:simpleType>
<xsd:union>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="synonym"/>
<xsd:enumeration value="quasi-synonym"/>
<xsd:enumeration value="acronym"/>
<xsd:enumeration value="abbreviation"/>
<xsd:enumeration value="homonym"/>
<xsd:enumeration value="identifier"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType>
<xsd:restriction base="namespaceRefType"/>
</xsd:simpleType>
</xsd:union>
</xsd:simpleType>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.atomRefs3" name="atomRefs3">
<xsd:attribute id="att.atomRefs3" name="atomRefs3" type="atomRefs3Type">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A list of three references to atoms.</h:div>
<h:div class="description">
Typically used for defining angles,
but could also be used to define a three-centre bond.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.angleUnits" name="angleUnits">
<xsd:attribute id="att.angleUnits" name="units" type="angleUnitsType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Restricts units to radians or degrees.</h:div>
<h:div class="description"/>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.errorValue" name="errorValue">
<xsd:attribute id="att.errorValue" name="errorValue" type="errorValueType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Value of the error.</h:div>
<h:div class="description">
Reports the author's estimate of the error in a scalar value. Only meaningful for dataTypes mapping to real number.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.errorBasis" name="errorBasis">
<xsd:attribute id="att.errorBasis" name="errorBasis" type="errorBasisType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Basis of the error estimate.</h:div>
<h:div class="description"/>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.role" name="role">
<xsd:attribute id="att.role" name="role" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Role of the object.</h:div>
<h:div class="description">
How the object functions or its position in the architecture. No controlled vocabulary.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.name" name="name">
<xsd:attribute id="att.name" name="name" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Name of the object.</h:div>
<h:div class="description">
A string by which the object is known. Often a required attribute. The may or may not be a semi-controlled vocabulary.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.dataType" name="dataType">
<xsd:attribute id="att.dataType" name="dataType" type="dataTypeType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The data type of the object.</h:div>
<h:div class="description">
Normally applied to scalar/array objects but may extend to more complex one.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.errorValueArray" name="errorValueArray">
<xsd:attribute id="att.errorValueArray" name="errorValueArray" type="errorValueArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Array of error values.</h:div>
<h:div class="description">
Reports the author's estimate of the error in an array of values. Only meaningful for dataTypes mapping to real number.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.minValueArray" name="minValueArray">
<xsd:attribute id="att.minValueArray" name="minValueArray" type="floatArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Minimum values for numeric _matrix_ or _array.</h:div>
<h:div class="description">
A whitespace-separated lists of the same length as the array in the parent element.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.maxValueArray" name="maxValueArray">
<xsd:attribute id="att.maxValueArray" name="maxValueArray" type="floatArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Maximum values for numeric _matrix_ or _array.</h:div>
<h:div class="description">
A whitespace-separated list of the same length as the array in the parent element.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.delimiter" name="delimiter">
<xsd:attribute id="att.delimiter" name="delimiter" type="delimiterType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A delimiter character for arrays and matrices.</h:div>
<h:div class="description">
By default array components ('elements' in the non-XML sense) are whitespace-separated. This fails for components with embedded whitespace or missing completely:
<h:pre>
Example:
In the protein database ' CA' and 'CA' are different atom types, and and array could be:
&lt;array delimiter="/" dictRef="pdb:atomTypes"&gt;/ N/ CA/CA/ N/&lt;/array&gt;
</h:pre>
Note that the array starts and ends with the delimiter, which must be chosen to avoid accidental use. There is currently no syntax for escaping delimiters.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.size" name="size">
<xsd:attribute id="att.size" name="size" type="sizeType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The size of an array or matrix.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.elementType" name="elementType">
<xsd:attribute id="att.elementType" name="elementType" type="elementTypeType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The identity of a chemical element.</h:div>
<h:div class="description">Normally mandatory on _atom_, _isotope_, etc.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.formalCharge" name="formalCharge">
<xsd:attribute id="att.formalCharge" name="formalCharge" type="formalChargeType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The formalCharge on the object.</h:div>
<h:div class="description">
NOT the calculated charge or oxidation state. No formal default, but assumed to be zero if omitted. It may become good practice to include it.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.hydrogenCount" name="hydrogenCount">
<xsd:attribute id="att.hydrogenCount" name="hydrogenCount" type="hydrogenCountType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Number of hydrogens.</h:div>
<h:div class="description">
The total number of hydrogens bonded to the atom or molecule. It is preferable to include hydrogens explicitly, and where this is done their count represents the minimum (and may thus override this attribute). It is dangerous to use this attribute for electron-deficient molecules (e.g. diborane) or hydrogen bonds. There is NO DEFAULT and the absence of this attribute must not be given any meaning.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.isotope" name="isotope">
<xsd:attribute id="att.isotope" name="isotope" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The isotope for an element.</h:div>
<h:div class="description">
A real number describing the isotope. Probably obsolet.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.isotopeNumber" name="isotopeNumber">
<xsd:attribute id="att.isotopeNumber" name="isotopeNumber" type="xsd:positiveInteger">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The integer number for an isotope.</h:div>
<h:div class="description">
The number representing the isotope. By default it does not point to a fuller description of the isotope (use isotopeRef).
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.isotopeRef" name="isotopeRef">
<xsd:attribute id="att.isotopeRef" name="isotopeRef" type="xsd:QName">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Reference to a fuller description of the isotope.</h:div>
<h:div class="general">
The description may be found in an external collection (e.g. IUPAC) or within the current document.
</h:div>
<h:div class="example" href="isotope2.xml"/>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.isotopeListRef" name="isotopeListRef">
<xsd:attribute id="att.isotopeListRef" name="isotopeListRef" type="xsd:QName">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
Reference to a description of the isotopic composition of an atom.
</h:div>
<h:div class="description">
Used when more than one atom shares the same isotopic composition (e.g. when H/D have been scrambled over some or all of the atoms in a molecule..
</h:div>
<h:div class="example" href="isotope1.xml"/>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.occupancy" name="occupancy">
<xsd:attribute id="att.occupancy" name="occupancy" type="occupancyType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Occupancy for an atom.</h:div>
<h:div class="description">
Normally only found in crystallography. Defaults to 1.0. The occupancy is required to calculate the molecular formaula from the atoms.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.spinMultiplicity" name="spinMultiplicity">
<xsd:attribute id="att.spinMultiplicity" name="spinMultiplicity" type="xsd:positiveInteger">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Spin multiplicity.</h:div>
<h:div class="description">
Normally for a molecule. This attribute gives the spin multiplicity of the molecule and is independent of any atomic information. No default, and it may take any positive integer value (though values are normally between 1 and 5.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.x2" name="x2">
<xsd:attribute id="att.x2" name="x2" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">x2 coordinate for an object.</h:div>
<h:div class="description">
Used for displaying the object in 2 dimensions. Unrelated to the 3-D coordinates for the object. The orientation of the axes matters as it can affect the chirality of object.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.y2" name="y2">
<xsd:attribute id="att.y2" name="y2" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">y2 coordinate for an object.</h:div>
<h:div class="description">
Used for displaying the object in 2 dimensions. Unrelated to the 3-D coordinates for the object. The orientation of the axes matters as it can affect the chirality of object.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.x3" name="x3">
<xsd:attribute id="att.x3" name="x3" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The x coordinate of a 3 dimensional object.</h:div>
<h:div class="summary">
The default units are Angstrom. (The provision for other units is weak at present.) Objects are always described with a right-handed coordinate system.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.y3" name="y3">
<xsd:attribute id="att.y3" name="y3" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The y coordinate of a 3 dimensional object.</h:div>
<h:div class="summary">
The default units are Angstrom. (The provision for other units is weak at present.) Objects are always described with a right-handed coordinate system.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.z3" name="z3">
<xsd:attribute id="att.z3" name="z3" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The z coordinate of a 3 dimensional object.</h:div>
<h:div class="summary">
The default units are Angstrom. (The provision for other units is weak at present.) Objects are always described with a right-handed coordinate system.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.xFract" name="xFract">
<xsd:attribute id="att.xFract" name="xFract" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Fractional x coordinate.</h:div>
<h:div class="description">
normally xFract, yFract and zFract should all be present or absent. If present a _crystal_ element should also occur.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.yFract" name="yFract">
<xsd:attribute id="att.yFract" name="yFract" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Fractional y coordinate.</h:div>
<h:div class="description">
normally xFract, yFract and zFract should all be present or absent. If present a _crystal_ element should also occur.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.zFract" name="zFract">
<xsd:attribute id="att.zFract" name="zFract" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Fractional y coordinate.</h:div>
<h:div class="description">
normally xFract, yFract and zFract should all be present or absent. If present a _crystal_ element should also occur.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.elementTypeArray" name="elementTypeArray">
<xsd:attribute id="att.elementTypeArray" name="elementType" type="elementTypeArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The identity of a chemical element.</h:div>
<h:div class="description">Normally mandatory on _atom_, _isotope_, etc.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.countArray" name="countArray">
<xsd:attribute id="att.countArray" name="countArray" type="countArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Array of object counts.</h:div>
<h:div class="description">
No fixed semantics or default, normally integral. It is presumed that the element can be multiplied by the count value.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.formalChargeArray" name="formalChargeArray">
<xsd:attribute id="att.formalChargeArray" name="formalCharge" type="formalChargeArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An array of formalCharges.</h:div>
<h:div class="description">
Used in CML2 Array mode. NOT the calculated charge or oxidation state. No formal defaults, but assumed to be zero if omitted. It may become good practice to include it.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.hydrogenCountArray" name="hydrogenCountArray">
<xsd:attribute id="att.hydrogenCountArray" name="hydrogenCount" type="hydrogenCountArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Array of hydrogenCounts.</h:div>
<h:div class="description">
Normally used in CML2 array mode. The total number of hydrogens bonded to the atom or molecule. It is preferable to include hydrogens explicitly, and where this is done their count represents the minimum (and may thus override this attribute). It is dangerous to use this attribute for electron-deficient molecules (e.g. diborane) or hydrogen bonds. There is NO DEFAULT and the absence of this attribute must not be given any meaning.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.occupancyArray" name="occupancyArray">
<xsd:attribute id="att.occupancyArray" name="occupancy" type="occupancyArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Array of occupancies.</h:div>
<h:div class="description">
Normally only found in crystallography. Defaults to 1.0. The occupancy is required to calculate the molecular formula from the atoms.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.x2Array" name="x2Array">
<xsd:attribute id="att.x2Array" name="x2" type="coordinateComponentArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">array of x2 coordinate.</h:div>
<h:div class="description">
Normally used in CML2 array mode. Used for displaying the object in 2 dimensions. Unrelated to the 3-D coordinates for the object. The orientation of the axes matters as it can affect the chirality of object.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.y2Array" name="y2Array">
<xsd:attribute id="att.y2Array" name="y2" type="coordinateComponentArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">array of y2 coordinate.</h:div>
<h:div class="description">
Normally used in CML2 array mode. Used for displaying the object in 2 dimensions. Unrelated to the 3-D coordinates for the object. The orientation of the axes matters as it can affect the chirality of object.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.x3Array" name="x3Array">
<xsd:attribute id="att.x3Array" name="x3" type="coordinateComponentArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An array of x3 coordinate.</h:div>
<h:div class="summary">Normally used in CML2 array mode.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.y3Array" name="y3Array">
<xsd:attribute id="att.y3Array" name="y3" type="coordinateComponentArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An array of y3 coordinate.</h:div>
<h:div class="summary">Normally used in CML2 array mode.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.z3Array" name="z3Array">
<xsd:attribute id="att.z3Array" name="z3" type="coordinateComponentArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An array of z3 coordinate.</h:div>
<h:div class="summary">Normally used in CML2 array mode.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.xFractArray" name="xFractArray">
<xsd:attribute id="att.xFractArray" name="xFract" type="coordinateComponentArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Array of fractional x coordinate.</h:div>
<h:div class="description">
normally xFract, yFract and zFract should all be present or absent. If present a _crystal_ element should also occur.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.yFractArray" name="yFractArray">
<xsd:attribute id="att.yFractArray" name="yFract" type="coordinateComponentArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Array of fractional y coordinate.</h:div>
<h:div class="description">
normally xFract, yFract and zFract should all be present or absent. If present a _crystal_ element should also occur.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.zFractArray" name="zFractArray">
<xsd:attribute id="att.zFractArray" name="zFract" type="coordinateComponentArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Array of fractional z coordinate.</h:div>
<h:div class="description">
normally xFract, yFract and zFract should all be present or absent. If present a _crystal_ element should also occur.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.atomIDArray" name="atomIDArray">
<xsd:attribute id="att.atomIDArray" name="atomID" type="atomRefArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An array of atom IDs.</h:div>
<h:div class="description">Normally an attribute of an array-based element.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.atomRef" name="atomRef">
<xsd:attribute id="att.atomRef" name="atomRef" type="atomRefType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A reference to an atom.</h:div>
<h:div class="description">Used by bond, electron, etc.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.n" name="n">
<xsd:attribute id="att.n" name="n" type="xsd:nonNegativeInteger">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The principal quantum number.</h:div>
<h:div class="description">Takes values 1, 2, 3, etc.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.l" name="l">
<xsd:attribute id="att.l" name="l" type="xsd:nonNegativeInteger">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The secondary quantum number.</h:div>
<h:div class="description">takes values 0, 1, etc.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.m" name="m">
<xsd:attribute id="att.m" name="m" type="xsd:integer">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The azimuthal quantum number.</h:div>
<h:div class="description">takes values -1, 0, 1, etc.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.symbol" name="symbol">
<xsd:attribute id="att.symbol" name="symbol" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A symbol.</h:div>
<h:div class="description">Currently only used on _atomicBasisFunction_.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.lm" name="lm">
<xsd:attribute id="att.lm" name="lm">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">symbolic represention of l amd m.</h:div>
<h:div class="description">takes avlues of s, p, px, dxy, dx2y2, f, etc.</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="s"/>
<xsd:enumeration value="p"/>
<xsd:enumeration value="px"/>
<xsd:enumeration value="py"/>
<xsd:enumeration value="pz"/>
<xsd:enumeration value="d"/>
<xsd:enumeration value="dxy"/>
<xsd:enumeration value="dyz"/>
<xsd:enumeration value="dxz"/>
<xsd:enumeration value="dx2y2"/>
<xsd:enumeration value="dz2"/>
<xsd:enumeration value="f"/>
<xsd:enumeration value="g"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.atomRefs4" name="atomRefs4">
<xsd:attribute id="att.atomRefs4" name="atomRefs4" type="atomRefs4Type">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A list of 4 references to atoms.</h:div>
<h:div class="description">
Typically used for defining torsions and atomParities,
but could also be used to define a four-centre bond.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.kpoint" name="kpoint">
<xsd:attribute id="att.kpoint" name="kpoint" type="vector3Type">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The k vector.</h:div>
<h:div class="description">The k-vector with 3 components.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.weight" name="weight">
<xsd:attribute id="att.weight" name="weight" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Weight of the element.</h:div>
<h:div class="description">
Currently the weight of the kPoint, derived from the symmetry such as the inverse of the multiplicity in real space. Thus a point at 0,0,0 in monoclinic space might be 0.25. The lowest value possible is probably 1/48.0 (in m3m).
</h:div>
<h:div class="curation">2003-09-15 (added at suggestion of Jon Wakelin).</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.label" name="label">
<xsd:attribute id="att.label" name="label" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A label.</h:div>
<h:div class="description">
The semantics of label are not defined in the schema but are normally commonly used standard or semi-standard text strings. This attribute has the the same semantics as the more common _label_ elemen.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.atomRefs2" name="atomRefs2">
<xsd:attribute id="att.atomRefs2" name="atomRefs2" type="atomRefs2Type">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">References to two different atoms.</h:div>
<h:div class="description">
Available for any reference to atoms but normally will be the normal reference attribute on the bond element. The order of atoms is preserved and may matter for some conventions (e.g. wedge/hatch or donor bonds.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.atomRefs" name="atomRefs">
<xsd:attribute id="att.atomRefs" name="atomRefs" type="atomRefArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A reference to a list of atoms.</h:div>
<h:div class="description">Used by bonds, electrons, atomSets, etc.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.bondRefs" name="bondRefs">
<xsd:attribute id="att.bondRefs" name="bondRefs" type="bondRefArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A reference to a list of bonds.</h:div>
<h:div class="description">Used by electrons, bondSets, etc.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.order" name="order">
<xsd:attribute id="att.order" name="order" type="orderType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The order of the bond.</h:div>
<h:div class="description">
There is NO default. This order is for bookkeeping only and is not related to length, QM calculations or other experimental or theoretical calculations.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.bondIDArray" name="bondIDArray">
<xsd:attribute id="att.bondIDArray" name="bondID" type="bondRefArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The IDs for an array of bond.</h:div>
<h:div class="general">Required in CML2 array mode.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.atomRef1Array" name="atomRef1Array">
<xsd:attribute id="att.atomRef1Array" name="atomRef1" type="atomRefArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The first atoms in each bond.</h:div>
<h:div class="description">
Currently only used in bondArray in CML2 array mode.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.atomRef2Array" name="atomRef2Array">
<xsd:attribute id="att.atomRef2Array" name="atomRef2" type="atomRefArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The second atoms in each bond.</h:div>
<h:div class="general">Only used in bondArray in CML2 array mode.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.orderArray" name="orderArray">
<xsd:attribute id="att.orderArray" name="order" type="orderArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The order of the bond.</h:div>
<h:div class="description">
There is NO default. This order is for bookkeeping only and is not related to length, QM calculations or other experimental or theoretical calculations.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.atomRefArray" name="atomRefArray">
<xsd:attribute id="att.atomRefArray" name="atomRefArray" type="atomRefArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An array of references to atoms.</h:div>
<h:div class="description">Typical use would be to atoms defining a plane.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.conventionValue" name="conventionValue">
<xsd:attribute id="att.conventionValue" name="conventionValue" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The value of an element with a _convention_.</h:div>
<h:div class="description">
When convention is used this attribute must be present and element content must be empty.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.z" name="z">
<xsd:attribute id="att.z" name="z" type="xsd:nonNegativeInteger">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The number of molecules per cell.</h:div>
<h:div class="description">
Molecules are defined as the _molecule_ which directly contains the _crystal_ element.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.objectClass" name="objectClass">
<xsd:attribute id="att.objectClass" name="objectClass" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The class of an object.</h:div>
<h:div class="description">
The type of this information. This is not controlled, but examples might include:
<h:ul>
<h:li>label</h:li>
<h:li>summary</h:li>
<h:li>note</h:li>
<h:li>usage</h:li>
<h:li>qualifier</h:li>
</h:ul>
It might be used to control display or XSL filtering.
</h:div>
<h:div class="note">
The attribute is named 'objectClass' to avoid clashes with other class attributes and inappropriate conversion to foo.getClass().
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.href" name="href">
<xsd:attribute id="att.href" name="href" type="xsd:anyURI">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">address of a resource.</h:div>
<h:div class="description">
Links to another element in the same or other file. For dictionary/@dictRef requires the prefix and the physical URI
address to be contained within the same file. We can anticipate that
better mechanisms will arise - perhaps through XMLCatalogs.
At least it works at present.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.dimensionBasis" name="dimensionBasis">
<xsd:attribute id="att.dimensionBasis" name="dimensionBasis" type="dimensionType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The basis of the dimension.</h:div>
<h:div class="description">
Normally taken from the seven SI types but possibly expandable.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.power" name="power">
<xsd:attribute id="att.power" name="power" type="xsd:float" use="required">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The power to which a dimension should be raised.</h:div>
<h:div class="description">
Normally an integer. Must be included, even if unity.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.preserve" name="preserve">
<xsd:attribute id="att.preserve" name="preserve" type="xsd:boolean">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Is the dimension preserved during algebra.</h:div>
<h:div class="dimension">
Experimental. The idea is to support concepts like volume/volume where alebraically these cancel out. preserve="yes" is intending to support preservation during derivation of new unitTypes.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.bondRef" name="bondRef">
<xsd:attribute id="att.bondRef" name="bondRef" type="bondRefType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A reference to a bond.</h:div>
<h:div class="description">used by electron, etc.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.rows" name="rows">
<xsd:attribute id="att.rows" name="rows" type="sizeType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Number of rows.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.columns" name="columns">
<xsd:attribute id="att.columns" name="columns" type="sizeType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Number of columns.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.unitType" name="unitType">
<xsd:attribute id="att.unitType" name="unitType" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A reference to the type of a unit.</h:div>
<h:div class="description">
Used in defining the unit and doing symbolic algebra on the dimensionality.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.minExclusive" name="minExclusive">
<xsd:attribute id="att.minExclusive" name="minExclusive" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">minimum exclusive value.</h:div>
<h:div class="description">by analogy with xsd:schema.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.minInclusive" name="minInclusive">
<xsd:attribute id="att.minInclusive" name="minInclusive" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">minimum inclusive value.</h:div>
<h:div class="description">by analogy with xsd:schema.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.maxExclusive" name="maxExclusive">
<xsd:attribute id="att.maxExclusive" name="maxExclusive" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">maximum exclusive value.</h:div>
<h:div class="description">by analogy with xsd:schema.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.maxInclusive" name="maxInclusive">
<xsd:attribute id="att.maxInclusive" name="maxInclusive" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">minimum inclusive value.</h:div>
<h:div class="description">by analogy with xsd:schem.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.totalDigits" name="totalDigits">
<xsd:attribute id="att.totalDigits" name="totalDigits" type="xsd:positiveInteger">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">total digits in a scalar.</h:div>
<h:div class="description">based on xsd:schema.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.fractionDigits" name="fractionDigits">
<xsd:attribute id="att.fractionDigits" name="fractionDigits" type="xsd:nonNegativeInteger">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Number of digits after the point.</h:div>
<h:div class="description">
This is used in dictionaries to define precision. However it might be replaced by xsd:facet.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.length" name="length">
<xsd:attribute id="att.length" name="length" type="xsd:nonNegativeInteger">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Length of a scalar.</h:div>
<h:div class="description">Probably will be replaced with xsd:schema tool.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.minLength" name="minLength">
<xsd:attribute id="att.minLength" name="minLength" type="xsd:nonNegativeInteger">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">minimum length of a scalar.</h:div>
<h:div class="description">by analogy with xsd:schema.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.maxLength" name="maxLength">
<xsd:attribute id="att.maxLength" name="maxLength" type="xsd:positiveInteger">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">maximum length of a scalar.</h:div>
<h:div class="description">by analogy with xsd:schem.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.whiteSpace" name="whiteSpace">
<xsd:attribute id="att.whiteSpace" name="whiteSpace" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Whitespace.</h:div>
<h:div class="description">Attached to entry. This may be obsolete.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.pattern" name="pattern">
<xsd:attribute id="att.pattern" name="pattern" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Pattern constraint.</h:div>
<h:div class="description">Based on xsd:schema.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.term" name="term">
<xsd:attribute id="att.term" name="term" type="xsd:string" use="required">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A term in a dictionary.</h:div>
<h:div class="description">
The term should be a noun or nounal phrase, with a separate definition and further description.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.value" name="value">
<xsd:attribute id="att.value" name="value" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Value of a scalar object.</h:div>
<h:div class="description">
The value must be consistent with the dataType of the object.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.default" name="default">
<xsd:attribute id="att.default" name="default" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">default value in an enumeration.</h:div>
<h:div class="description">
A non-whitespace string (value is irrelevant) indicates that the content of this enumeration is the default value (usually of a scalar). It is an error to have more than one default. If the scalar in an instance document has no value (i.e. is empty or contains only whitespace) its value is given by the default. If the scalar in the instance is empty and no enumerations have a default attribute, an application may throw an error.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.concise" name="concise">
<xsd:attribute id="att.concise" name="concise" type="formulaType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A concise formula.</h:div>
<h:div class="general">
The string represents an (unstructured) formula i.e. no submolecules. Recommended to use the format "H 2 O 1", etc.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.version" name="version">
<xsd:attribute id="att.version" name="version" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The version of the identifier.</h:div>
<h:div class="general">
The IChI or other identifier may be dependent on the date of release and this attribute is highly recommended.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.tautomeric" name="tautomeric">
<xsd:attribute id="att.tautomeric" name="tautomeric" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Indicates whether the structure is a tautomer.</h:div>
<h:div class="general">
Currently used with IChI _identifier_ element. Semantics, vocabulary and usage are application-dependent.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.number" name="number">
<xsd:attribute id="att.number" name="number" type="xsd:nonNegativeInteger">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A number determined by context</h:div>
<h:div class="description">
Used for isotope number in isotope, and rotational symmetry number in symmetry for calculation of entropy, etc.
</h:div>
<h:div class="curation">2003-03-30: added number attribut.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.spin" name="spin">
<xsd:attribute id="att.spin" name="spin" type="isotopicSpinType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The spin of a system.</h:div>
<h:div class="description">
Supports fractional values. Currently the spin of a nucleus. The normal fraction representing the spin of the isotope.
</h:div>
<h:div class="example" href="spin1.xml"/>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.latticeType" name="latticeType">
<xsd:attribute id="att.latticeType" name="latticeType" type="latticeType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The primitivity of a lattice.</h:div>
<h:div class="description">
No default. The semantics of this are software-dependent (i.e. this Schema does not check for consistency between spacegroups, symmetry operators, etc.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.spaceType" name="spaceType">
<xsd:attribute id="att.spaceType" name="spaceType" type="spaceType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The spaceType of the lattice.</h:div>
<h:div class="description">
Usually real or reciprocal. No default. The semantics of this are software-dependent (i.e. this Schema does not check for consistency for unitTypes, etc.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.periodic" name="periodic">
<xsd:attribute default="true" id="att.periodic" name="periodic" type="xsd:boolean">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Is the axis periodic.</h:div>
<h:div class="description">
Any or all of the axes may be periodic or aperiodic. An example could be a surface where 2 periodic axes (not necessarily orthogonal) are used to describe the coordinates in the surface, perhaps representing lattice vectors of a 3D crystal or 2D layer. The third vector is orthogonal and represents coordinates normal to the surface. In this case only the direction, not the magnitude of the vector is important.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.from" name="from">
<xsd:attribute id="att.from" name="from" type="idType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The base of a link.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.to" name="to">
<xsd:attribute id="att.to" name="to" type="idType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The target of a link.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.linkType" name="linkType">
<xsd:attribute id="att.linkType" name="linkType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The type of the link.</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="extended">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A container for locators.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="locator">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A link to an element.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="arc">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A labelled link.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.matrixType" name="matrixType">
<xsd:attribute id="att.matrixType" name="matrixType" type="matrixType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Type of matrix.</h:div>
<h:div class="description">
Mainly square, but extensible through the _xsd:union_ mechanis.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.content" name="content">
<xsd:attribute id="att.content" name="content" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">content of metadata.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.metadataType" name="metadataType">
<xsd:attribute id="att.metadataType" name="name" type="metadataType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The metadata type.</h:div>
<h:div class="description">
This is likely to be the Dublin Core name or something similar. The use of "type" is an infelicitous misnomer and we shall try to remove it.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.serial" name="serial">
<xsd:attribute id="att.serial" name="serial" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Serial number or other id.</h:div>
<h:div class="summary">
Currently only on module. Modules with the same _role_ attribute can be distinguished by _serial_. This is often an integer but other schemes may be used.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.formula" name="formula">
<xsd:attribute id="att.formula" name="formula" type="formulaType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Simple chemical formula.</h:div>
<h:div class="general">
This attribute should only be used for simple formulae (i.e. without brackets or other nesting for which a _formula_ child element should be used. The attribute might be used as a check on the child elements or for ease of representation. Essentially the same as _concise_ attribute on _formula.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.chirality" name="chirality">
<xsd:attribute id="att.chirality" name="chirality" type="chiralityType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The chirality of a system or molecule.</h:div>
<h:div class="description">
This is being actively investigated by a IUPAC committee (2002) so the convention is likely to change. No formal default.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.symmetryOriented" name="symmetryOriented">
<xsd:attribute id="att.symmetryOriented" name="symmetryOriented" type="xsd:boolean">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Is the molecule oriented to the symmetry</h:div>
<h:div class="description">
No formal default, but a molecule is assumed to be oriented according to any _symmetry_ children. This is required for crystallographic data, but some systems for isolated molecules allow specification of arbitrary Cartesian or internal coordinates, which must be fitted or refined to a prescribed symmetry. In this case the attribute value is false.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.constraint" name="constraint">
<xsd:attribute id="att.constraint" name="constraint" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Constraint on a parameter.</h:div>
<h:div class="description">
Semantics not yet finalised. We anticipate "fixed", "none" and symbolic relationships to other parameters.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.peakHeight" name="peakHeight">
<xsd:attribute id="att.peakHeight" name="peakHeight" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Height of a peak.</h:div>
<h:div class="description">
For 1-dimensional data (e.g. y vs x) hould use the same units as the appropriate axis (e.g. y).
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.peakMultiplicity" name="peakMultiplicity">
<xsd:attribute id="att.peakMultiplicity" name="peakMultiplicity">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Multiplicity of a peak.</h:div>
<h:div class="description">Uses a semi-controlled vocabulary.</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:simpleType>
<xsd:union>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="singlet">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A single maximum within the peak rang.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="doublet">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
Two maxima (not necessarily equal) within the peak rang.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="triplet">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
Three maxima (not necessarily equal) within the peak rang.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="quartet">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
Four maxima (not necessarily equal) within the peak rang.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="quintet">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
Five maxima (not necessarily equal) within the peak rang.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="sextuplet">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
Six maxima (not necessarily equal) within the peak rang.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="multiplet">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
Several maxima (not necessarily equal) within the peak rang.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType>
<xsd:restriction base="namespaceRefType">
<xsd:annotation>
<xsd:documentation>
<h:div>User contributed vocabulary of type foo:ba.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:restriction>
</xsd:simpleType>
</xsd:union>
</xsd:simpleType>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.peakShape" name="peakShape">
<xsd:attribute id="att.peakShape" name="peakShape">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Shape of a peak.</h:div>
<h:div class="description">
Semi-controlled vocabulary such as broad or sharp.
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:simpleType>
<xsd:union>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="sharp">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A sharp peak.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="broad">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A broad peak.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="shoulder">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
A brodening of a peak suggesting the presence of a smaller incompletely resolved component.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType>
<xsd:restriction base="namespaceRefType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">User contributed vocabulary of type foo:bar.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:restriction>
</xsd:simpleType>
</xsd:union>
</xsd:simpleType>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.integral" name="integral">
<xsd:attribute id="att.integral" name="integral" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Area under a peak.</h:div>
<h:div class="description">
Unfortunately units are usually arbitrary and not related to the x- and y- axis units, and in this case _peakUnits_ should be use.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.peakUnits" name="peakUnits">
<xsd:attribute id="att.peakUnits" name="peakUnits" type="unitsType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Units for a peak or peak integral.</h:div>
<h:div class="description">
For 2-dimensional spectra the units represent the observation. For an integral they are usually arbitrary and not related to the x- and y- axis units. Thus NMR spectra may use hydrogen count as the units for the peak area.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.xMin" name="xMin">
<xsd:attribute id="att.xMin" name="xMin" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Minimum yValue.</h:div>
<h:div class="description">
Annotates x-axis data with a minimum value. This need not be algorithmically deducible from the data and is typically used for the extent of a _peak_ or _peakGroup_. It uses xUnits or the same units as the data. There may or may not be a _xMax_ attribute but if so xMin should be less than or equals to it.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.xMax" name="xMax">
<xsd:attribute id="att.xMax" name="xMax" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Maximum yValue.</h:div>
<h:div class="description">
Annotates x-axis data with a maximum value. This need not be algorithmically deducible from the data and is typically used for the extent of a _peak_ or _peakGroup_. It uses xUnits or the same units as the data. There may or may not be a _xMin_ attribute but if so xMax should be greater than or equals to it.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.xValue" name="xValue">
<xsd:attribute id="att.xValue" name="xValue" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Value along an x axis.</h:div>
<h:div class="description">
Annotates x-axis data with a value. It is typically used for the location of a _peak_ or _peakGroup_. It uses xUnits or the same units as the data.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.xWidth" name="xWidth">
<xsd:attribute id="att.xWidth" name="xWidth" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An unsigned interval along an x axis.</h:div>
<h:div class="description">
It is typically used for the width of a _peak_ or _peakGroup_ but could be used for any range. It uses xUnits or the same units as the data.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.xUnits" name="xUnits">
<xsd:attribute id="att.xUnits" name="xUnits" type="unitsType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Units for x axis.</h:div>
<h:div class="description">
All x-axis data must have unambiguous units. Ideally the data and _xMin_ or _xValue_ should share the same units but different xUnits can be used as long as it is clear..
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.yMin" name="yMin">
<xsd:attribute id="att.yMin" name="yMin" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Minimum yValue.</h:div>
<h:div class="description">
Annotates y-axis data with a minimum value. This need not be algorithmically deducible from the data and is typically used for the extent of a _peak_ or _peakGroup_. It uses yUnits or the same units as the data. There may or may not be a _yMax_ attribute but if so yMin should be less than or equal to it.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.yMax" name="yMax">
<xsd:attribute id="att.yMax" name="yMax" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Maximum yValue.</h:div>
<h:div class="description">
Annotates y-axis data with a maximum value. This need not be algorithmically deducible from the data and is typically used for the extent of a _peak_ or _peakGroup_. It uses yUnits or the same units as the data. There may or may not be a _yMin_ attribute but if so yMax should be greater than or equals to it.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.yValue" name="yValue">
<xsd:attribute id="att.yValue" name="yValue" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Value along a y axis.</h:div>
<h:div class="description">
Annotates y-axis data with a value. It is typically used for the location of a _peak_ or _peakGroup_. It uses yUnits or the same units as the data.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.yWidth" name="yWidth">
<xsd:attribute id="att.yWidth" name="yWidth" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An unsigned interval along a y axis.</h:div>
<h:div class="description">
It is typically used for the width of a _peak_ or _peakGroup_ but could be used for any range. It uses yUnits or the same units as the data.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.yUnits" name="yUnits">
<xsd:attribute id="att.yUnits" name="yUnits" type="unitsType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Units for y axis.</h:div>
<h:div class="description">
All y-axis data must have unambiguous units. Ideally the data and _yMin_ or _yValue_ should share the same units but different yUnits can be used as long as it is clear.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.form" name="form">
<xsd:attribute id="att.form" name="form" type="namespaceRefType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A reference to a functional form.</h:div>
<h:div class="description">Currently used for potential.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.state" name="state">
<xsd:attribute id="att.state" name="state" type="stateType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The physical state of the substance.</h:div>
<h:div class="description">No fixed semantics or default.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.reactionFormat" name="reactionFormat">
<xsd:attribute id="att.reactionFormat" name="format" type="reactionFormatType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Format of the reaction component.</h:div>
<h:div class="description">
Indicates how the components of reactionScheme, reactionStepList, etc. should be processed. No controlled vocabulary. One example is format="cmlSnap" asserts that the processor can assume that the reactants and products can be rendered using the CMLSnap design. Note that the reaction can be interpreted without reference to the format, which is primarily a processing instruction.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.reactionRole" name="reactionRole">
<xsd:attribute id="att.reactionRole" name="role" type="reactionRoleType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Role of the reaction.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.reactionType" name="reactionType">
<xsd:attribute id="att.reactionType" name="type" type="reactionTypeType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Type of the reaction.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.atomMap" name="atomMap">
<xsd:attribute id="att.atomMap" name="atomMap" type="xsd:QName">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
A reference to a map providing mappings between atoms
</h:div>
<h:div class="description">
The map will normally be contained within the same document and referenced by its ID. It will contain a list of links with from and to attributes linking atoms. The topology of the linking is defined by the application - it could be overlay of molecular fragments, reactant/product mapping, etc. The reserved phrase "USE_IDS" assume that the sets of atoms are of equal size and have 1:1 mapping between each id. This is another way of saying that the atoms mapped by a given ID are "the same atom".
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.electronMap" name="electronMap">
<xsd:attribute id="att.electronMap" name="electronMap" type="xsd:QName">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
A reference to a map providing mappings between electrons
</h:div>
<h:div class="description">
The map will normally be contained within the same document and referenced by its ID. It will contain a list of links with from and to attributes linking electrons. The topology of the linking is defined by the application - it could be reactant/product mapping, etc. The reserved phrase "USE_IDS" assume that the sets of electrons are of equal size and have 1:1 mapping between each id. This is another way of saying that the electrons mapped by a given ID are "the same electron".
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.bondMap" name="bondMap">
<xsd:attribute id="att.bondMap" name="bondMap" type="xsd:QName">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
A reference to a map providing mappings between bonds
</h:div>
<h:div class="description">
The map will normally be contained within the same document and referenced by its ID. It will contain a list of links with from and to attributes linking bonds. The topology of the linking is defined by the application - it could be overlay of molecular fragments, reactant/product mapping, etc. The reserved phrase "USE_IDS" assume that the sets of bonds are of equal size and have 1:1 mapping between each id. This is another way of saying that the bonds mapped by a given ID are "the same bond".
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.yield" name="yield">
<xsd:attribute id="att.yield" name="yield" type="occupancyType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Yield of a reaction or reactionStep.</h:div>
<h:div class="description">
Yields can be given on either element. They should lie in the range 0 to 1 inclusive (i.e. percentages will need to be converted). Software may use yield to calculate amounts of substances created during a reaction or series of reactions.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.ratio" name="ratio">
<xsd:attribute id="att.ratio" name="ratio" type="occupancyType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A ratio in the range 0 to 1.</h:div>
<h:div class="description">
Currently used for ratios between brached reactions but re-usable for other concepts.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.sphere3" name="sphere3">
<xsd:attribute id="att.sphere3" name="sphere3" type="sphere3Type">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A sphere.</h:div>
<h:div class="description">
Currently describes a region. Any point falling within the sphere or on its surface is within the region.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.box3" name="box3">
<xsd:attribute id="att.box3" name="box3" type="box3Type">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A parallelipiped box.</h:div>
<h:div class="description">
By default the box uses isometric Cartesians axes but can also be linked to lattice Vector. Any point falling within the box or on a boundary is within the regio.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.atomSetRef" name="atomSetRef">
<xsd:attribute id="att.atomSetRef" name="atomSetRef" type="refType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An atomSet describing the region.</h:div>
<h:div class="description">
Any point falling within atomOffset of any atom in the set lies within the region. This means the region could consist of disjoint fragments.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.regionRefs" name="regionRefs">
<xsd:attribute id="att.regionRefs" name="regionRefs" type="refType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A list of regions creating a union.</h:div>
<h:div class="description">
The union of a series of regions produces a larger region (possibly disjoint). Any point belonging to any of the referenced regions is a member of this region.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.relatedEntryType" name="relatedEntryType">
<xsd:attribute id="att.relatedEntryType" name="type">
<xsd:simpleType>
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Type of relatedEntry.</h:div>
<h:div class="description">
Type represents a the type of relationship in a relatedEntry element.
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:union>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="parent"/>
<xsd:enumeration value="partitiveParent"/>
<xsd:enumeration value="child"/>
<xsd:enumeration value="partitiveChild"/>
<xsd:enumeration value="related"/>
<xsd:enumeration value="synonym"/>
<xsd:enumeration value="quasi-synonym"/>
<xsd:enumeration value="antonym"/>
<xsd:enumeration value="homonym"/>
<xsd:enumeration value="see"/>
<xsd:enumeration value="seeAlso"/>
<xsd:enumeration value="abbreviation"/>
<xsd:enumeration value="acronym"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType>
<xsd:restriction base="namespaceRefType"/>
</xsd:simpleType>
</xsd:union>
</xsd:simpleType>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.moleculeRef" name="moleculeRef">
<xsd:attribute id="att.moleculeRef" name="moleculeRef" type="moleculeRefType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A reference to a molecule.</h:div>
<h:div class="description">Used by spectrum, etc.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.spectrumType" name="spectrumType">
<xsd:attribute id="att.spectrumType" name="type">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The type of the spectrum.</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:simpleType>
<xsd:union>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="infrared">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An infrared spectrum.</h:div>
<h:div class="description">
The measurement should denote transmittance or absorbanc.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="massSpectrum">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A "simple" mass spectrum.</h:div>
<h:div class="description">
This excludes experiments such as GC/MS, MS/MS, etc. though these could be constructed out of individual spectra with some care. The spectrum may be continuous (
<h:tt>data</h:tt>
or a
<h:tt>peakList</h:tt>
).
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="NMR">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An NMR spectrum.</h:div>
<h:div class="description">
This can include any experiment which creates a "1D" or "2D" data array. The symmetry of the spectrum can be specified but the details of the NMR experiment (COSY, NOESY, etc.) are not part of CMLSpect. They can be described though the normal
<h:tt>dictRef</h:tt>
mechanism.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="UV/VIS">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
A spectrum somewhere in the UV VIS region of the spectrum.
</h:div>
<h:div class="description">
The measurement should denote transmittance or absorbance.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType>
<xsd:restriction base="namespaceRefType"/>
</xsd:simpleType>
</xsd:union>
</xsd:simpleType>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.format" name="format">
<xsd:attribute id="att.format" name="format">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Format of a spectrum.</h:div>
<h:div class="description">
The data structure of the spectrum. (Not the format of the data). This describes how the data structure is to be interpreted.
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:simpleType>
<xsd:union>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="1D">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">one dimensional spectru.</h:div>
<h:div class="description">
Data are represented by two _array_s, one representing the independent variable (e.g. wavelength, mass number) and the other the measured dependent variable (absorption, intensity, etc.). This can normally be plotted directly with the independent variable as the x-axis. The order of the points is not necessarily significant and may be increasing or decreasing.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="2Dsymm">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Two dimensional spectru.</h:div>
<h:div class="description">
Data are represented by a single symmetric _matrix_ with both axes identical (i.e. the same independent variable). A typical example is a "2D 1HNMR spectrum". The dependent variable is represented by the matrix elements. This can normally be plotted as a square symmentric about a diagonal.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="2Dasymm">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Two dimensional spectrum with different axe.</h:div>
<h:div class="description">
Data are represented by non-square _matrix_ with independent axes. A typical example is a "2D 1H 13C NMR spectrum". The dependent variable is represented by the matrix elements. .
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType>
<xsd:restriction base="namespaceRefType"/>
</xsd:simpleType>
</xsd:union>
</xsd:simpleType>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.measurement" name="measurement">
<xsd:attribute id="att.measurement" name="measurement">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Type of spectral measurement.</h:div>
<h:div class="description">
The nature of the measured data. This is not an exhaustive list and should only be used if it affects the storage or immediate processing.
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:simpleType>
<xsd:union>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="transmittance">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
Data are transmittance, so "peaks" are usually troughs.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="absorbance">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Data are absorbanc.</h:div>
<h:div class="description">so "peaks" are normally peaks.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType>
<xsd:restriction base="namespaceRefType"/>
</xsd:simpleType>
</xsd:union>
</xsd:simpleType>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.ft" name="ft">
<xsd:attribute default="none" id="att.ft" name="ft">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Domain of an FT spectrum.</h:div>
<h:div class="description">
Indicates whether a spectrum is raw FID or has been transforme.
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:simpleType>
<xsd:union>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="raw">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
Data are raw, so will normally require transforming.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="transformed">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
Data have been transformed. This value indicates that an FT experiment and transformation have been performe.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="none">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
This was not known to be an FT experiment. (It may have been, but the author or abstracter omitted to mention it).
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType>
<xsd:restriction base="namespaceRefType"/>
</xsd:simpleType>
</xsd:union>
</xsd:simpleType>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.substanceListType" name="substanceListType">
<xsd:attribute id="att.substanceListType" name="type">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Type of the substanceList.</h:div>
<h:div class="description">Extension is allowed through the "other" value.</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="solution"/>
<xsd:enumeration value="mixture"/>
<xsd:enumeration value="other"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.pointGroup" name="pointGroup">
<xsd:attribute id="att.pointGroup" name="pointGroup" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A point group.</h:div>
<h:div class="description">
No fixed semantics, though Schoenflies is recommended over Hermann-Mauguin. We may provide a controlled-extensible list in the future.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.spaceGroup" name="spaceGroup">
<xsd:attribute id="att.spaceGroup" name="spaceGroup" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A space group.</h:div>
<h:div class="description">
No fixed semantics, though Hermann-Mauguin or Hall is recommended over Schoenflies. We may provide a controlled-extensible list in the future.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.irreducibleRepresentation" name="irreducibleRepresentation">
<xsd:attribute id="att.irreducibleRepresentation" name="irreducibleRepresentation" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A symmetry species.</h:div>
<h:div class="description">
No fixed semantics, though we may provide a controlled-extensible list in the future.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.dimensionality" name="dimensionality">
<xsd:attribute id="att.dimensionality" name="dimensionality" type="xsd:positiveInteger">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Dimensionality of a coordinate system.</h:div>
<h:div class="summary">
Note that this means that coordinates of higher dimensionality are ignored or an error is flagged. Thus z3 and dimensionality='2' are incompatible. At present higher dimensionalities than 3 (cf. Wondratschek) are not supported. The labelling of the axes id not controlled. ?? should we have an explicit attribute for labelling convention?.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.periodicity" name="periodicity">
<xsd:attribute id="att.periodicity" name="periodicity" type="xsd:positiveInteger">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Periodicity of the system.</h:div>
<h:div class="summary">
This represents the number of dimensions (or coordinate axes) along periodic behaviour occurs and can be supported by symmetry operators or other transformations. Periodicity must never exceed dimensionality.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.abbreviation" name="abbreviation">
<xsd:attribute id="att.abbreviation" name="abbreviation" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Abbreviation.</h:div>
<h:div class="description">Abbreviation for units, terms, etc.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.parentSI" name="parentSI">
<xsd:attribute id="att.parentSI" name="parentSI" type="namespaceRefType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
A dictRef like reference to the id of the parent SI unit.
</h:div>
<h:div class="description">
This parent should occur in this or another dictionary and be accessible through the dictRef mechanism. This attribute is forbidden for SI Units themselves. The mechanism holds for base SI units (7) and all compound (derived) units made by combinations of base Units.
</h:div>
<h:div class="example" href="unit3.xml"/>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.multiplierToSI" name="multiplierToSI">
<xsd:attribute id="att.multiplierToSI" name="multiplierToSI" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Multiplier to generate SI equivalent.</h:div>
<h:div class="description">
The factor by which the non-SI unit should be multiplied to convert a quantity to its representation in SI Units. This is applied *before* _constantToSI_. Necessarily unity for SI unit.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.constantToSI" name="constantToSI">
<xsd:attribute id="att.constantToSI" name="constantToSI" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Additive constant to generate SI equivalent.</h:div>
<h:div class="description">
The amount to add to a quantity in non-SI units to convert its representation to SI Units. This is applied *after* multiplierToSI. It is necessarily zero for SI units.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.multiplierToData" name="multiplierToData">
<xsd:attribute default="1.0" id="att.multiplierToData" name="multiplierToData" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The scale by which to multiply the raw data.</h:div>
<h:div class="description">
The scale is applied *before* adding the constant.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:attributeGroup id="attGp.constantToData" name="constantToData">
<xsd:attribute default="0.0" id="att.constantToData" name="constantToData" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The constant to add to the raw data.</h:div>
<h:div class="description">add *after* applying any multiplier.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:attributeGroup>
<xsd:element id="el.abundance" name="abundance">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The abundance of an isotope.</h:div>
<h:div class="description">
The abundance of an isotope in an isotopeList. Values are expressed in percentages.
</h:div>
<h:div class="example" href="isotope1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:simpleContent>
<xsd:extension base="xsd:float">
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="min"/>
<xsd:attributeGroup ref="max"/>
<xsd:attributeGroup ref="units"/>
</xsd:extension>
</xsd:simpleContent>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.action" name="action">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
An action which might occur in scientific data or narrative.
</h:div>
<h:div class="description">
An action which might occur in scientific data or narrative. The definition is deliberately vague, intending to collect examples of possible usage. Thus an action could be addition of materials, measurement, application of heat or radiation. The content model is unrestricted. _action_ iself is normally a child of _actionList_.
<h:p>
The start, end and duration attributes should be interpreted as
</h:p>
<h:ul>
<h:li>
XSD dateTimes and XSD durations. This allows precise recording of time of day, etc, or duration after start of actionList. A
<h:tt>convention="xsd"</h:tt>
attribute should be used to enforce XSD.
</h:li>
<h:li>
a numerical value, with a units attribute linked to a dictionary.
</h:li>
<h:li>
a human-readable string (unlikely to be machine processable)
</h:li>
</h:ul>
<h:p>
<h:tt>startCondition</h:tt>
and
<h:tt>endCondition</h:tt>
values are not constrained, which allows XSL-like
<h:tt>test</h:tt>
attribute values. The semantics of the conditions are yet to be defined and at present are simply human readable.
</h:p>
<h:p>
The order of the
<h:tt>action</h:tt>
elements in the document may, but will not always, define
the order that they actually occur in.
</h:p>
<h:p>
A delay can be shown by an
<h:tt>action</h:tt>
with no content. Repeated actions or
actionLists are indicated through the count attribute.
</h:p>
</h:div>
<h:div class="example" href="action1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType mixed="true">
<xsd:sequence maxOccurs="unbounded" minOccurs="0">
<xsd:any processContents="lax"/>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="units"/>
<xsd:attributeGroup ref="start"/>
<xsd:attributeGroup ref="startCondition"/>
<xsd:attributeGroup ref="duration"/>
<xsd:attributeGroup ref="end"/>
<xsd:attributeGroup ref="endCondition"/>
<xsd:attributeGroup ref="type"/>
<xsd:attributeGroup ref="actionOrder"/>
<xsd:attributeGroup ref="count">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">Number of times the action should be repeated.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
<xsd:attributeGroup ref="ref"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.actionList" name="actionList">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A container for a group of actions.</h:div>
<h:div class="description">
<h:tt>ActionList</h:tt>
contains a series of
<h:tt>action</h:tt>
s or
nested
<h:tt>actionList</h:tt>
s.
</h:div>
<h:div class="example" href="actionList1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType mixed="true">
<xsd:sequence maxOccurs="unbounded" minOccurs="0">
<xsd:any processContents="lax"/>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="start"/>
<xsd:attributeGroup ref="startCondition"/>
<xsd:attributeGroup ref="duration"/>
<xsd:attributeGroup ref="end"/>
<xsd:attributeGroup ref="endCondition"/>
<xsd:attributeGroup ref="units"/>
<xsd:attributeGroup ref="count"/>
<xsd:attributeGroup ref="type"/>
<xsd:attributeGroup ref="actionOrder"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.alternative" name="alternative">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An alternative name for an entry.</h:div>
<h:div class="description">
At present a child of _entry_ which represents an alternative string that refers to the concept. There is a partial controlled vocabulary in _alternativeType_ with values such as :
<h:ul>
<h:li>synonym</h:li>
<h:li>acronym</h:li>
<h:li>abbreviation</h:li>
</h:ul>
</h:div>
<h:div class="example" href="alternative1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:simpleContent>
<xsd:extension base="xsd:string">
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="alternativeType"/>
</xsd:extension>
</xsd:simpleContent>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.amount" name="amount">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The amount of a substance.</h:div>
<h:div class="description">
The
<h:tt>units</h:tt>
attribute is mandatory and can be customised to support mass, volumes, moles, percentages, or rations (e.g. ppm).
</h:div>
<h:div class="example" href="amount1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:simpleContent>
<xsd:extension base="xsd:float">
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup id="att.amount.units" ref="units"/>
</xsd:extension>
</xsd:simpleContent>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.angle" name="angle">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An angle between three atoms.</h:div>
<h:div class="description">
<h:p>It can be used for:</h:p>
<h:ul>
<h:li>
Recording experimentally determined bond angles (e.g. in
a crystallographic paper).
</h:li>
<h:li>
Providing the angle component for internal coordinates (e.g.
z-matrix).
</h:li>
</h:ul>
</h:div>
<h:div class="example" href="angle1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:simpleContent>
<xsd:extension base="nonNegativeAngleType">
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="atomRefs3"/>
<xsd:attributeGroup ref="angleUnits"/>
<xsd:attributeGroup ref="errorValue"/>
<xsd:attributeGroup ref="errorBasis"/>
<xsd:attributeGroup ref="min"/>
<xsd:attributeGroup ref="max"/>
<xsd:attributeGroup ref="ref"/>
</xsd:extension>
</xsd:simpleContent>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.annotation" name="annotation">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
A documentation container similar to annotation in XML Schema.
</h:div>
<h:div class="description">
A documentation container similar to
<h:tt>annotation</h:tt>
in XML Schema. At present this is experimental and designed to be used for dictionaries, units, etc. One approach is to convert these into XML Schemas when the
<h:tt>documentation</h:tt>
and
<h:tt>appinfo</h:tt>
children will emerge in their correct position in the derived schema.
<h:p>
It is possible that this may develop as a useful tool for annotating components
of complex objects such as molecules.
</h:p>
</h:div>
<h:div class="example" href="annotation1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType mixed="true">
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="documentation"/>
<xsd:element ref="appinfo"/>
</xsd:choice>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.appinfo" name="appinfo">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A container similar to appinfo in XML Schema.</h:div>
<h:div class="description">
A container for machine processable documentation for an entry. This is likely to be platform and/or language specific. It is possible that XSLT, RDF or XBL will emerge as generic languages. See _annotation_ and _documentation_ for further information.
</h:div>
<h:div class="example" href="appinfo1.xml">
<h:p>
An example in XSLT where an element _foo_ calls a bespoke template
</h:p>
.
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType mixed="true">
<xsd:sequence maxOccurs="unbounded" minOccurs="0">
<xsd:any processContents="lax"/>
</xsd:sequence>
<xsd:attributeGroup ref="role">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">
Allows a processor to inspect the role of the appinfo and process accordingly.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.arg" name="arg">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An argument for a function.</h:div>
<h:div class="description">
Arguments can be typed and have explicit or free values.
</h:div>
<h:div class="example" href="potential1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="atom"/>
<xsd:element ref="scalar"/>
<xsd:element ref="array"/>
<xsd:element ref="matrix"/>
<xsd:element ref="expression"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="name"/>
<xsd:attributeGroup ref="dataType"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.array" name="array">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
A homogenous 1 dimensional array of similar object.
</h:div>
<h:div class="description">
These can be encoded as strings (i.e. XSD-like datatypes) and are concatenated as string content. The size of the array should always be &gt;= 1. The default delimiter is whitespace. The _normalize-space()_ function of XSLT could be used to normalize all whitespace to single spaces and this should not affect the value of the array elements. To extract the elements __java.lang.StringTokenizer__ could be used. If the elements themselves contain whitespace then a different delimiter must be used and is identified through the
<h:tt>delimiter</h:tt>
attribute. This method is mandatory if it is required to represent empty strings. If a delimiter is used it MUST start and end the array - leading and trailing whitespace is ignored. Thus
<h:tt>size+1</h:tt>
occurrences of the delimiter character are required. If non-normalized whitespace is to be encoded (e.g. newlines, tabs, etc) you are recommended to translate it character-wise to XML character entities.
<h:p>
Note that normal Schema validation tools cannot validate the elements
of
<h:b>array</h:b>
(they are defined as
<h:tt>string</h:tt>
) However if the string is
split, a temporary schema
can be constructed from the type and used for validation. Also the type
can be contained in a dictionary and software could decide to retrieve this
and use it for validation.
</h:p>
<h:p>
When the elements of the
<h:tt>array</h:tt>
are not simple scalars
(e.g.
<h:a href="el.scalar">scalar</h:a>
s with a value and an error, the
<h:tt>scalar</h:tt>
s should be used as the elements. Although this is
verbose, it is simple to understand. If there is a demand for
more compact representations, it will be possible to define the
syntax in a later version.
</h:p>
</h:div>
<h:div class="example" href="array1.xml">
<h:p>
the
<h:tt>size</h:tt>
attribute is not mandatory but provides a useful validity
check):
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:simpleContent>
<xsd:extension base="xsd:string">
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="dataType"/>
<xsd:attributeGroup ref="errorValueArray"/>
<xsd:attributeGroup ref="errorBasis"/>
<xsd:attributeGroup ref="minValueArray"/>
<xsd:attributeGroup ref="maxValueArray"/>
<xsd:attributeGroup ref="units"/>
<xsd:attributeGroup ref="delimiter"/>
<xsd:attributeGroup ref="size"/>
<xsd:attributeGroup ref="ref"/>
</xsd:extension>
</xsd:simpleContent>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.atom" name="atom">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An atom.</h:div>
<h:div documentation="general">Usually within an _atomArray_.</h:div>
<h:div class="example" href="atom1.xml"/>
</xsd:documentation>
<xsd:appinfo/>
</xsd:annotation>
<xsd:complexType>
<xsd:choice>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:annotation>
<xsd:documentation>
<h:div class="general">
<h:p>The main content model of the atom.</h:p>
<h:ul>
<h:li>
<h:b>name</h:b>
can be used for atom labels, etc. More than one name can be used if required.
</h:li>
<h:li>
<h:b>scalar</h:b>
contains any scalar properties of the atom (examples are chemical shift, B-value, etc.) linked through
<h:tt>dictRef</h:tt>
(CmlDictRefType).
</h:li>
<h:li>
<h:b>array</h:b>
contains any properties of the atom describable by a homogeneous array linked through
<h:tt>dictRef</h:tt>
(CmlDictRefType).
</h:li>
<h:li>
<h:b>matrix</h:b>
contains any properties of the atom describable by a homogeneous matrix linked through
<h:tt>dictRef</h:tt>
(CmlDictRefType). An example is the polarizability tensor
</h:li>
<h:li>
<h:b>atomParity</h:b>
(CmlAtomParityElement) the required way of defining atom-based chirality
</h:li>
<h:li>
<h:b>electron</h:b>
a away of associating electron(s) with the atom
</h:li>
</h:ul>
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:element ref="name"/>
<xsd:element ref="label"/>
<xsd:element ref="atomType"/>
<xsd:element ref="array"/>
<xsd:element ref="matrix"/>
<xsd:element ref="scalar"/>
<xsd:element ref="atomParity"/>
<xsd:element ref="electron"/>
</xsd:choice>
</xsd:choice>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="count">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">
Most useful in _formula_ but possibly useful in _atomArray_ where coordinates and connectivity is not defined. No formal default, but assumed to be 1.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
<xsd:attributeGroup ref="elementType"/>
<xsd:attributeGroup ref="formalCharge"/>
<xsd:attributeGroup ref="hydrogenCount"/>
<xsd:attributeGroup ref="isotope"/>
<xsd:attributeGroup ref="isotopeNumber"/>
<xsd:attributeGroup ref="isotopeRef"/>
<xsd:attributeGroup ref="isotopeListRef"/>
<xsd:attributeGroup ref="occupancy"/>
<xsd:attributeGroup ref="spinMultiplicity"/>
<xsd:attributeGroup ref="x2"/>
<xsd:attributeGroup ref="y2"/>
<xsd:attributeGroup ref="x3"/>
<xsd:attributeGroup ref="y3"/>
<xsd:attributeGroup ref="z3"/>
<xsd:attributeGroup ref="xFract"/>
<xsd:attributeGroup ref="yFract"/>
<xsd:attributeGroup ref="zFract"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="role">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">
This can be used to describe the purpose of atoms whose _elementType_s are __dummy__ or __locant__. Vocabulary not controlled.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.atomArray" name="atomArray">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A container for a list of atoms.</h:div>
<h:div class="description">
A child of _molecule_ and contains _atom_ information. There are two strategies:
<h:ul>
<h:li>
Create individual _atom_ elements under _atomArray_ (in any order). This gives the greatest flexibility but is the most verbose.
</h:li>
<h:li>
Create
<h:tt>*Array</h:tt>
attributes (e.g. of _elementTypeArrayType_ under _atomArray_. This requires all arrays to be of identical lengths with explicit values for all atoms in every array. This is NOT suitable for complexType atom children such as _atomParity_. It also cannot be checked as easily by schema- and schematron validation. The _atomIDArray_ attribute is mandatory. It is allowed (though not yet recommended) to add _*Array_ children such as _floatArray_
</h:li>
</h:ul>
The attributes are directly related to the scalar attributes under _atom_ which should be consulted for more info.
</h:div>
<h:div class="example" href="atomArray1.xml">
<h:p>
Example - these are exactly equivalent representations
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="atom"/>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="elementTypeArray"/>
<xsd:attributeGroup ref="countArray"/>
<xsd:attributeGroup ref="formalChargeArray"/>
<xsd:attributeGroup ref="hydrogenCountArray"/>
<xsd:attributeGroup ref="occupancyArray"/>
<xsd:attributeGroup ref="x2Array"/>
<xsd:attributeGroup ref="y2Array"/>
<xsd:attributeGroup ref="x3Array"/>
<xsd:attributeGroup ref="y3Array"/>
<xsd:attributeGroup ref="z3Array"/>
<xsd:attributeGroup ref="xFractArray"/>
<xsd:attributeGroup ref="yFractArray"/>
<xsd:attributeGroup ref="zFractArray"/>
<xsd:attributeGroup ref="atomIDArray"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.atomicBasisFunction" name="atomicBasisFunction">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An atomicBasisFunction.</h:div>
<h:div class="description">
<h:p>
An atomic atomicBasisFunction which can be linked to atoms, eigenvalues/vectors etc. Normally contained within _basisSet_
</h:p>
<h:p>
Normally these are atom-centered functions, but they can also serve as "ghost" functions which are centered on points. IN CCML these can be dummy atoms so that the atomRef mechanism can still be used.
</h:p>
<h:p>
This information is required to interpret the eignevector components and map them onto the atom list. However this mapping is normally implicit in the program and so it may be necessary to generate
<h:tt>basisSet</h:tt>
information for some programs before XML technology can be automatically used to link the components of the CCML document.
</h:p>
</h:div>
<h:div class="example" href="atomicBasisFunction1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<!--<xsd:choice minOccurs="0" maxOccurs="unbounded"/>-->
<xsd:choice minOccurs="0">
<xsd:element ref="gradient"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="atomRef">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">
The atom owning this atomicBasisFunction. This reference is required to tie the reported eigenvector components to the list of atoms.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="n"/>
<xsd:attributeGroup ref="l"/>
<xsd:attributeGroup ref="m"/>
<xsd:attributeGroup ref="symbol"/>
<xsd:attributeGroup ref="lm"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.atomParity" name="atomParity">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The stereochemistry round an atom centre.</h:div>
<h:div class="description">
It follows the convention of the MIF format, and uses 4 distinct atoms to define the chirality. These can be any atoms (though they are normally bonded to the current atom). There is no default order and the order is defined by the atoms in the atomRefs4 attribute. If there are only 3 ligands, the current atom should be included in the 4 atomRefs.
<h:p>
The value of the parity is a signed number. (It can only be zero if two or more atoms are coincident or the configuration is planar). The sign is the sign of the chiral volume created by the four atoms (a1, a2, a3, a4):
</h:p>
<h:pre>
| 1 1 1 1 |
| x1 x2 x3 x4 |
| y1 y2 y3 y4 |
| z1 z2 z3 z4 |
</h:pre>
<h:p>
Note that
<h:tt>atomParity</h:tt>
cannot be used with the *Array syntax for
atoms.
</h:p>
</h:div>
<h:div class="example" href="atomParity1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:simpleContent>
<xsd:extension base="xsd:float">
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="atomRefs4"/>
</xsd:extension>
</xsd:simpleContent>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.atomSet" name="atomSet">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A set of references to atoms.</h:div>
<h:div class="description">
An atomSet consists of a number of unique references to atoms throught their ids. atomSets need not be related to molecules (which are generally created by aggregation of explicit atoms). Two or more atomSets may reference the same atom, and atomSets may be empty.
<h:p>
atomSets have many potential uses such as:
<h:ul>
<h:li>identifying functional groups</h:li>
<h:li>results of substructure matching</h:li>
<h:li>
identifying atoms with particular roles in a calculation
</h:li>
</h:ul>
</h:p>
<h:p>
The atomSet may be referenced from elsewhere in the document and you are encouraged to use locally unique id attributes on atomSets.
</h:p>
</h:div>
<h:div class="example" href="atomSet1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:simpleContent>
<xsd:extension base="atomRefArrayType">
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="size"/>
</xsd:extension>
</xsd:simpleContent>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.atomType" name="atomType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An atomType.</h:div>
<h:div class="description">
<h:p>
atomTypes are used in a wide variety of ways in computational chemistry. They are normally labels added to existing atoms (or dummy atoms) in the molecule and have a number of defined properties. These properties are usually in addition to those deducible from the elementType of the atom. AtomTypes usually depend on the chemical or geometrical environment of the atom and are frequently assigned by algorithms with chemical perception. However they are often frequently set or "tweaked" by humans initiating a program run.
</h:p>
<h:p>
AtomTypes on an atom have no formal relation to its
<h:tt>elementType</h:tt>
, which only describe the number of protons in the nucleus. It is not unknown (though potentially misleading) to use an "incompatible" atomType to alter the computational properties of an atom (e.g. pretend this K+ is a Ca++ to increase its effective charge).
<h:tt>atomTypes</h:tt>
will also be required to describe pseudoAtoms such as "halogen" (generic) or "methyl group" (unified atom). Atoms in computations can therefore have an
<h:tt>atomTypeRef</h:tt>
attribute.
</h:p>
<h:p>
An atomType contains numeric or other quantities associated with it (charges, masses, use in force-fields, etc.) and also description of any perception algorithms (chemical and/or geometrical) which could be used to compute or constrain it. This is still experimental.
</h:p>
<h:p>
atomTypes are referred to by their mandatory
<h:tt>name</h:tt>
attribute. An atom referes to one or more atomTypes through atomType/@ref children
</h:p>
</h:div>
<h:div class="example" href="atomType1.xml"/>
<h:div class="note">examples not yet teste.</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="molecule"/>
<xsd:element ref="atom"/>
<xsd:element ref="label"/>
</xsd:choice>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="scalar"/>
<xsd:element ref="array"/>
<xsd:element ref="matrix"/>
<xsd:element ref="property"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="name">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">
The name will usually be namespaced as 'gulp:si', 'tripos:c.3', etc. It must occur except for atomType/@re.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="atomRef"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.atomTypeList" name="atomTypeList">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A container for one or more atomTypes.</h:div>
<h:div class="description">It can contain several atomTypes.</h:div>
<h:div class="example" href="atomTypeList1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="metadataList"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="name"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="atomType"/>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="ref"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.band" name="band">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A band or Brillouin zone.</h:div>
<h:div class="description">Not yet finalise.</h:div>
<h:div class="example" href="band1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="array">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Band energies associated with this kpoin.</h:div>
<h:div class="description">The energy units must be give.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:element>
</xsd:sequence>
<xsd:attributeGroup ref="kpoint"/>
<xsd:attributeGroup ref="weight"/>
<xsd:attributeGroup ref="label"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.bandList" name="bandList">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A container for bands.</h:div>
<h:div class="description">Experimental.</h:div>
<h:div class="example" href="band1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="band"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.basisSet" name="basisSet">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A container for one or more atomicBasisFunctions.</h:div>
<h:div class="description">This can contain several orbitals.</h:div>
<h:div class="example" href="basisSet1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="metadataList"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="name"/>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="atomicBasisFunction"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="role"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.bond" name="bond">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A bond between atoms, or between atoms and bonds.</h:div>
<h:div class="description">
_bond_ is a child of _bondArray_ and contains bond information. Bond must refer to at least two atoms (normally using _atomRefs2_) but may also refer to more for multicentre bonds. Bond is often EMPTY but may contain _electron_, _length_ or _bondStereo_ elements.
</h:div>
<h:div class="example" href="bond1.xml"/>
</xsd:documentation>
<xsd:documentation>
<h:div class="validation" href="cmlCore.val.bond.xml"/>
</xsd:documentation>
<xsd:appinfo>
<comment xmlns="">
Validate Bonds
</comment>
<template id="val-bond" match="bond" xmlns="">
<comment>Atom Refs for 2-atom bond</comment>
<variable name="at1" select="substring-before(normalize-space(@atomRefs2),' ')"/>
<variable name="at2" select="substring-after(normalize-space(@atomRefs2),' ')"/>
<comment>Are atoms distinct?</comment>
<if test="$at1 = $at2">
<call-template name="error">
<with-param name="error">
BOND (
<value-of select="@id"/>
): ATOMS not distinct:
<value-of select="$at1"/>
</with-param>
</call-template>
</if>
<comment>Do both atoms exist in current molecule context?</comment>
<if test="not(key('atoms', $at1))">
<call-template name="error">
<with-param name="error">
BOND (
<value-of select="@id"/>
): ATOMREF not found:
<value-of select="$at1"/>
</with-param>
</call-template>
</if>
<if test="not(key('atoms', $at2))">
<call-template name="error">
<with-param name="error">
BOND (
<value-of select="@id"/>
): ATOMREF not found:
<value-of select="$at2"/>
</with-param>
</call-template>
</if>
</template>
</xsd:appinfo>
</xsd:annotation>
<xsd:complexType id="bond.content.id">
<xsd:choice>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="bondType"/>
<xsd:element ref="electron">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">One or more electrons associated with the bond.</h:div>
<h:div class="description">
The _bondRef_ on the _electron_ should point to the id on the bond. We may relax this later and allow reference by context.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element ref="bondStereo">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The stereo convention for the bond.</h:div>
<h:div class="general">only one convention allowed.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:element>
</xsd:choice>
</xsd:choice>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="atomRefs2"/>
<xsd:attributeGroup ref="atomRefs">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">
This is designed for multicentre bonds (as in delocalised systems or electron-deficient centres. The semantics are experimental at this stage. As an example, a B-H-B bond might be described as
&lt;bond atomRefs="b1 h2 b2"/.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
<xsd:attributeGroup ref="bondRefs">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">
This is designed for pi-bonds and other systems where formal valence bonds are not drawn to atoms. The semantics are experimental at this stage. As an example, a Pt-|| bond (as the Pt-ethene bond in Zeise's salt) might be described as &lt;bond atomRefs="pt1" bondRefs="b32"/.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
<xsd:attributeGroup ref="order"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.bondArray" name="bondArray">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A container for a number of bonds.</h:div>
<h:div class="description">
_bondArray_ is a child of _molecule_ and contains _bond_ information. There are two strategies:
<h:ul>
<h:li>
Create individual
<h:tt>bond</h:tt>
elements under
<h:tt>bondArray</h:tt>
(in any order). This gives the greatest flexibility but is the most verbose.
</h:li>
<h:li>
Create
<h:tt>*Array</h:tt>
attributes (e.g. of
<h:tt>orderArrayType</h:tt>
under
<h:tt>bondArray</h:tt>
. This requires all arrays to be of identical lengths with explicit values for all bonds in every array. This is NOT suitable for complexType bond children such as _bondStereo_ nor can IDs be added to bonds.. It also cannot be checked as easily by schema- and schematron validation. The _atomRef1Array_ and _atomRef2Array_ attributes are then mandatory. It is allowed (though not yet recommended) to add _*Array_ children such as _floatArray_
</h:li>
</h:ul>
<h:p>
The attributes are directly related to the scalar attributes under _atom_ which should be consulted for more info.
</h:p>
</h:div>
<h:div class="example" href="bondArray1.xml">
<h:p>
Example - these are exactly equivalent representations
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:choice>
<xsd:element maxOccurs="unbounded" ref="bond"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="array"/>
</xsd:choice>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="bondIDArray"/>
<xsd:attributeGroup ref="atomRef1Array"/>
<xsd:attributeGroup ref="atomRef2Array"/>
<xsd:attributeGroup ref="orderArray"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.bondSet" name="bondSet">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A set of references to bonds.</h:div>
<h:div class="description">
An bondSet consists of a number of unique references to bonds throught their ids. bondSets need not be related to molecules (which are generally created by aggregation of explicit bonds). Two or more bondSets may reference the same bond, and bondSets may be empty.
<h:p>
bondSets have many potential uses such as:
<h:ul>
<h:li>identifying functional groups</h:li>
<h:li>results of substructure matching</h:li>
<h:li>
identifying bonds with particular roles in a calculation
</h:li>
</h:ul>
</h:p>
<h:p>
The bondSet may be referenced from elsewhere in the document and you are encouraged to use locally unique id attributes on bondSets.
</h:p>
</h:div>
<h:div class="example" href="bondSet1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:simpleContent>
<xsd:extension base="bondRefArrayType">
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="size"/>
</xsd:extension>
</xsd:simpleContent>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.bondStereo" name="bondStereo">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
A container supporting cis trans wedge hatch and other stereochemistry.
</h:div>
<h:div class="description">
<h:p>
An explict list of atomRefs must be given, or it must be a child of
<h:tt>bond</h:tt>
. There are no implicit conventions such as E/Z. This will be extended to other types of stereochemistry.
</h:p>
<h:p>At present the following are supported:</h:p>
<h:ul>
<h:li>
No atomRefs attribute.
<h:b>Deprecated, but probably unavoidable</h:b>
.
This must be a child of
<h:tt>bond</h:tt>
where it picks up the two atomRefs
in the
<h:tt>atomRefs2</h:tt>
attribute. Possible values are C/T (which only makes sense
if there is exactly one ligand at each end of the bond) and W/H. The latter
should be raplaced by
<h:tt>atomParity</h:tt>
wherever possible. Note that W/H makes
no sense without 2D atom coordinates.
</h:li>
<h:li>
<h:b>atomRefs4 attribute</h:b>
. The 4 atoms represent a cis or trans configuration.
This may or may not be a child of
<h:tt>bond</h:tt>
; if so the second and third atomRefs
should be identical with the two atomRefs in the bond. This structure can be used
to guide processors in processing stereochemistry and is recommended, since there is
general agreement on the semantics. The semantics of
<h:tt>bondStereo</h:tt>
not related to
bonds is less clear (e.g. cumulenes, substituted ring nuclei) etc.It is
currently an error to have more than one
<h:tt>bondStereo</h:tt>
referring to the same ordered
4-atom list
</h:li>
<h:li>
<h:b>atomRefs attribute</h:b>
. There are other stereochemical conventions such as cis/trans
for metal complexes which require a variable number of reference atoms. This allows
users to create their own - at present we do not see CML creating exhaustive tables.
For example cis/trans square-planar complexes might require 4 (or 5) atoms for their
definition, octahedral 6 or 7, etc. In principle this is very powerful and could
supplement or replace the use of
<h:i>cis-</h:i>
,
<h:i>mer-</h:i>
, etc.
</h:li>
</h:ul>
<h:p>
the
<h:tt>atomRefs</h:tt>
and
<h:tt>atomRefs4</h:tt>
attributes cannot be used
simultaneously.
</h:p>
</h:div>
<h:div class="example" href="bondStereo1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:simpleContent>
<xsd:extension base="stereoType">
<xsd:attributeGroup ref="atomRefs4"/>
<xsd:attributeGroup ref="atomRefArray"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="conventionValue"/>
</xsd:extension>
</xsd:simpleContent>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.bondType" name="bondType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The type of a bond.</h:div>
<h:div class="description">
Bond types are used to describe the behaviour of bonds in forcefields, functional groups, reactions and many other domains. They are not as well formalised as atomTypes and we provide less semantic support. BondTypes are referred to by their mandatory _name_ attribute.
</h:div>
<h:div class="example" href="bondType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="molecule"/>
<xsd:element ref="bond"/>
<xsd:element ref="label"/>
</xsd:choice>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="scalar"/>
<xsd:element ref="array"/>
<xsd:element ref="matrix"/>
<xsd:element ref="property"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="name">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">
The bondType name. The name will usually be namespaced as 'gulp:si', 'tripos:c.3', etc. It must occur except when the ref attribute is give.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.bondTypeList" name="bondTypeList">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A container for one or more bondTypes.</h:div>
<h:div class="description">_bondTypeList_ can contain several bondTypes.</h:div>
<h:div class="example" href="bondTypeList1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="metadataList"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="name"/>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="bondType"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="ref"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.cml" name="cml">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A general container for CML elements.</h:div>
<h:div class="description">
Often the root of the CML (sub)document. Has no explicit function but serves to hold the dictionaries, namespace, and can alert CML processors and search/XMLQuery tools that there is chemistry in the document. Can contain any content, but usually a list of molecules and other CML components. Can be nested.
</h:div>
<h:div class="example" href="cml1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence maxOccurs="unbounded" minOccurs="0">
<xsd:annotation>
<xsd:documentation>
<h:div class="description">No specific restrictions..</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:any processContents="lax"/>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.conditionList" name="conditionList">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
A container for one or more experimental condition.
</h:div>
<h:div class="description">
This can contain several conditions. These include (but are not limited to) intensive physical properties (temperature, pressure, etc.), apparatus (test-tube, rotary evaporator, etc.). Actions can be represented elsewhere by stmml:actionList and solvents or other substances by cml:substanceList.
</h:div>
<h:div class="example" href="conditionList1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="metadataList"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="name"/>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="scalar"/>
<xsd:element ref="list"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="role"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.crystal" name="crystal">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A crystallographic cell.</h:div>
<h:div class="description">
Required if fractional coordinates are provided for a molecule. There are precisely SIX child
<h:tt>scalar</h:tt>
s to represent the cell lengths and angles in that order. There are no default values; the spacegroup is also included.
</h:div>
<h:div class="example" href="crystal1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
All 6 cell parameters must be given, even where angles are fixed by symmetry. The order is fixed as a,b,c,alpha,gamma,beta and software can neglect any title or dictRef attributes. Error estimates can be given if required. Any units can be used, but the defaults are Angstrom (10^-10 m) and degrees.
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:element maxOccurs="6" minOccurs="6" ref="scalar"/>
<xsd:element minOccurs="0" ref="symmetry"/>
</xsd:sequence>
<xsd:attributeGroup ref="z"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.definition" name="definition">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The definition for an entry.</h:div>
<h:div class="description">
The definition should be a short nounal phrase defining the subject of the entry. Definitions should not include commentary, implementations, equations or formulae (unless the subject is one of these) or examples.
<h:p>
The definition can be in any markup language, but normally XHTML will be used,
perhaps with links to other XML namespaces such as CML for chemistry.
</h:p>
</h:div>
<h:div class="example" href="definition1.xml">
<h:em>From the IUPAC Dictionary of Medicinal Chemistry</h:em>
<h:br/>
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType mixed="true">
<xsd:sequence maxOccurs="unbounded" minOccurs="0">
<xsd:any processContents="lax"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.description" name="description">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Descriptive information.</h:div>
<h:div class="description">
This can occur in objects which require textual comment such as entry.
<h:p>
Entries should have at least one separate
<h:a href="el.definition">definition</h:a>
s.
<h:tt>description</h:tt>
is then used for most of the other information, including
examples. The
<h:tt>class</h:tt>
attribute has an uncontrolled vocabulary and
can be used to clarify the purposes of the
<h:tt>description</h:tt>
elements.
</h:p>
</h:div>
<h:div class="example" href="description1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType mixed="true">
<xsd:sequence maxOccurs="unbounded" minOccurs="0">
<xsd:any processContents="lax"/>
</xsd:sequence>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="objectClass"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.dictionary" name="dictionary">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A dictionary.</h:div>
<h:div class="description">
A dictionary is a container for _entry_ elements. Dictionaries can also contain unit-related information. The dictRef attribute on a dictionary element sets a namespace-like prefix allowing the dictionary to be referenced from within the document. In general dictionaries are referenced from an element using the __dictRef__ attribute.
</h:div>
<h:div class="example" href="dictionary1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="unitList"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="annotation"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="description"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="entry"/>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="href"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.dimension" name="dimension">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A dimension supporting scientific unit.</h:div>
<h:div class="description">
This will be primarily used within the definition of units.
</h:div>
<h:div class="example" href="dimension1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence/>
<xsd:attributeGroup ref="dimensionBasis"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="name"/>
<xsd:attributeGroup ref="power"/>
<xsd:attributeGroup ref="preserve"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.documentation" name="documentation">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Documentation in the annotation of an entry.</h:div>
<h:div class="description">
<h:p>
A container similar to
<h:tt>documentation</h:tt>
in XML Schema. This is NOT part of the textual content of an entry but is designed to support the transformation of dictionary entrys into schemas for validation. This is experimental and should only be used for dictionaries, units, etc. One approach is to convert these into XML Schemas when the
<h:tt>documentation</h:tt>
and
<h:tt>appinfo</h:tt>
children will emerge in their correct position in the derived schema.
</h:p>
<h:p>
Do NOT confuse documentation with the description or the definition which are part of the content
of the dictionary
</h:p>
<h:p>
If will probably only be used when there is significant appinfo
in the entry or where the entry defines an XSD-like datatype of an element in the document.
</h:p>
</h:div>
<h:div class="example" href="documentation1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType mixed="true">
<xsd:sequence maxOccurs="unbounded" minOccurs="0">
<xsd:any processContents="lax"/>
</xsd:sequence>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="title"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.eigen" name="eigen">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An element to hold eigenstuff.</h:div>
<h:div class="description">
Holds an array of eigenvalues and a matrix of eigenvector.
</h:div>
<h:div class="example" href="eigen1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element minOccurs="0" ref="array"/>
<xsd:element minOccurs="0" ref="matrix"/>
</xsd:sequence>
<xsd:attributeGroup ref="units"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="type"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.electron" name="electron">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An electron.</h:div>
<h:div class="description">
Since there is very little use of electrons in current chemical information this is a fluid concept. I expect it to be used for electron counting, input and output of theochem operations, descriptions of orbitals, spin states, oxidation states, etc. Electrons can be associated with atoms, bonds and combinations of these. At present there is no hardcoded semantics. However, _atomRef_ and similar attributes can be used to associate electrons with atoms or bond.
</h:div>
<h:div class="example" href="electron1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="atomRef"/>
<xsd:attributeGroup ref="atomRefs"/>
<xsd:attributeGroup ref="bondRef"/>
<xsd:attributeGroup ref="bondRefs"/>
<xsd:attributeGroup ref="count"/>
<xsd:attributeGroup ref="ref"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.entry" name="entry">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A dictionary entry.</h:div>
<h:div class="desacription">
The original design for validation with attribute-based constraints is ponderous and fragile. In future constraints will be added through
<h:tt>appinfo</h:tt>
in
<h:tt>annotation</h:tt>
. We shall develop this further in the near future.
</h:div>
<h:div class="curation">2003-03-30: added metadataList to content mode.</h:div>
<h:div class="example" href="entry1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="metadataList"/>
<xsd:element ref="alternative"/>
<xsd:element ref="annotation"/>
<xsd:element ref="definition"/>
<xsd:element ref="description"/>
<xsd:element ref="enumeration"/>
<xsd:element ref="relatedEntry"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dataType"/>
<xsd:attributeGroup ref="rows"/>
<xsd:attributeGroup ref="columns"/>
<xsd:attributeGroup ref="unitType"/>
<xsd:attributeGroup ref="minExclusive"/>
<xsd:attributeGroup ref="minInclusive"/>
<xsd:attributeGroup ref="maxExclusive"/>
<xsd:attributeGroup ref="maxInclusive"/>
<xsd:attributeGroup ref="totalDigits"/>
<xsd:attributeGroup ref="fractionDigits"/>
<xsd:attributeGroup ref="length"/>
<xsd:attributeGroup ref="minLength"/>
<xsd:attributeGroup ref="maxLength"/>
<xsd:attributeGroup ref="units"/>
<xsd:attributeGroup ref="whiteSpace"/>
<xsd:attributeGroup ref="pattern"/>
<xsd:attributeGroup ref="term"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.enumeration" name="enumeration">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An enumeration of value.</h:div>
<h:div class="description">
An enumeration of string values. Used where a dictionary entry constrains the possible values in a document instance. The dataTypes (if any) must all be identical and are defined by the dataType of the containing element.
</h:div>
<h:div class="example" href="enumeration1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element minOccurs="0" ref="annotation"/>
</xsd:sequence>
<xsd:attributeGroup ref="value"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="default"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.expression" name="expression">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An expression that can be evaluated.</h:div>
<h:div class="description">
Experimental. This is essentially a mathematical function, expressed currently in reverse Polish notation but we expect to move to MathML.
</h:div>
<h:div class="example" href="potential1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="parameter"/>
<xsd:element ref="operator"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="dataType"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.formula" name="formula">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A molecular formula.</h:div>
<h:div class="description">
<h:p>
It is
defined by
<h:tt>atomArray</h:tt>
s each with a list of elementTypes and their
counts (or default=1). All other information in the
<h:tt>atomArray</h:tt>
is ignored.
<h:tt>formula</h:tt>
are nestable so that aggregates (e.g. hydrates,
salts, etc.) can be described. CML does not require that formula information
is consistent with (say) crystallographic information; this allows for
experimental variance.
</h:p>
<h:p>
An alternative briefer representation is also available through the
<h:tt>conciseForm</h:tt>
. This must include whitespace round all elements and
their counts, which must be explicit.
</h:p>
</h:div>
<h:div class="example" href="formula1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:choice>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="formula"/>
<xsd:element ref="atomArray"/>
</xsd:choice>
</xsd:choice>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="count">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">Allows for fractional components.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
<xsd:attributeGroup ref="formalCharge">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">This allows a charge to be added to the formul.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
<xsd:attributeGroup ref="concise"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.gradient" name="gradient">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A gradient.</h:div>
<h:div class="description">
A container for a quantity or quantities representing the gradient of other quantities. At present just takes a scalar child.
</h:div>
<h:div class="example" href="gradient1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="scalar"/>
<xsd:element ref="array"/>
<xsd:element ref="matrix"/>
<xsd:element ref="property"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.identifier" name="identifier">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A structured identifier.</h:div>
<h:div class="description">
<h:p>
Supports compund identifiers such as IChI. At present uses the V0.9 IChI XML representation verbatim but will almost certainly change with future IChIs.
</h:p>
<h:p>
The inclusion of elements from other namespaces causes problems with validation. The content model is deliberately LAX but the actual elements in IChI will fail the validation as they are not declared in CML.
</h:p>
For simple scalar values the value attribute can be used with empty content. Where an identifier has several components a series of label elements can be used.
</h:div>
<h:div class="curation">2003-07-10: Fixed count on identifier children..</h:div>
<h:div class="curation">2003-03-12: Added isotopic and atoms..</h:div>
<h:div class="example" href="identifier1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence maxOccurs="unbounded" minOccurs="0">
<xsd:any processContents="lax"/>
</xsd:sequence>
<xsd:attributeGroup ref="value"/>
<xsd:attributeGroup ref="version"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="tautomeric"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.isotope" name="isotope">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A specific isotope.</h:div>
<h:div class="description">
Defines an isotope in terms of exact mass and spin. Differentiate from isotopeList which defines a mixture of isotope.
</h:div>
<h:div class="example" href="isotope1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element minOccurs="0" ref="abundance"/>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="number"/>
<xsd:attributeGroup ref="spin"/>
<xsd:attributeGroup ref="elementType"/>
<xsd:attributeGroup ref="ref"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.isotopeList" name="isotopeList">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A container for one or more isotopes.</h:div>
<h:div class="description">
Can contain several isotopes. These may be related in several ways. This allows the definition of natural abundance and averged enrichment.
</h:div>
<h:div class="example" href="isotopeList1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="isotope"/>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="ref"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.label" name="label">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A text string qualifying an object.</h:div>
<h:div class="description">
A label can be used to identify or distinguish elements, add keywords or classifications and similar processes. It is usually interpretable by domain-aware humans (e.g. C3'-endo, but not a34561). It is usually either built in a semantically rich fashion (e.g. C2'-alpha-H) or belongs to a controlled vocabulary. It is possibly accessed by software in a domain-specific manner. It differs from
<h:tt>description</h:tt>
which is free text. The distinction between titles, names and labels is fuzzy, but we think this is worth making. Labels may be necesssary to identify objects within programs, while names are more likely to be reserved for database searches. Titles are likely to be freer text and not recommended for precise object retrieval.
</h:div>
<h:div class="note">
Labels should not contain whitespace. Punctuation marks are often necessary, but should not be gratuitously used. Punctuation clashing with XML character entities should be avoided; if this is not possible it should be escaped.
</h:div>
<h:div class="example" href="label1.xml">
<h:em>From IUPAC Dictionary of Medicinal Chemistry</h:em>
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence maxOccurs="unbounded" minOccurs="0">
<xsd:any processContents="lax"/>
</xsd:sequence>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="value"/>
<xsd:attributeGroup ref="objectClass"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.lattice" name="lattice">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A lattice of dimension 3 or less.</h:div>
<h:div class="description">
Lattice is a general approach to describing periodic systems. It can have variable dimensionality or periodicity, and could be finite.
</h:div>
<h:div class="note">
_lattice_ is more general than _crystal_ in cmlCore which is used primarily for reporting crystallographic experiments.`A lattice can be described by latticeVectors, cell axes and angles, or metric tensors, etc. (only axes/angles are allowed under
<h:tt>crystal</h:tt>
). The dimensionality is enforced through a _system_ parent element.
</h:div>
<h:div class="example" href="lattice3.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:choice>
<xsd:element maxOccurs="6" minOccurs="3" ref="scalar">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
All appropriate cell parameters must be given, even where angles are fixed by symmetry. The order is fixed as a,b,c,alpha,beta,gamma and software can neglect any title or dictRef attributes. Error estimates can be given if required. Any units can be used, but the defaults are Angstrom (10^-10 m) and degrees. To be developed for lower dimensionality.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element maxOccurs="3" ref="latticeVector"/>
<xsd:element ref="matrix"/>
</xsd:choice>
<xsd:element minOccurs="0" ref="symmetry"/>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="latticeType"/>
<xsd:attributeGroup ref="spaceType"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.latticeVector" name="latticeVector">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A vector3 representing a lattice axis.</h:div>
<h:div class="description">
a
<h:tt>lattice</h:tt>
can be represented by 1-3 non-linearly dependent latticeVectors. If the dimensionality is less than 3 latticeVectors are the preferred method. Similarly, if the axes show a mixture of periodicity and non-periodicity latticeVectors can support this. The number of periodic vectors must correspond with the periodicity attribute on a
<h:tt>system</h:tt>
element.
<h:p>
The vector must not be zero and units must be given. (Zero vectors must not be used to reduce dimensionality).
</h:p>
<h:p>A lattice vector defaults to periodic.</h:p>
.
</h:div>
<h:div class="description">
Any or all of the axes may be periodic or aperiodic. An example could be a surface where 2 periodic axes (not necessarily orthogonal) are used to describe the coordinates in the surface, perhaps representing lattice vectors of a 3D crystal or 2D layer. The third vector is orthogonal and represents coordinates normal to the surface. In this case only the direction, not the magnitude of the vector is importan.
</h:div>
<h:div class="example" href="latticeVector1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:simpleContent>
<xsd:extension base="vector3Type">
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="units"/>
<xsd:attributeGroup ref="periodic"/>
</xsd:extension>
</xsd:simpleContent>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.length" name="length">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A length between two atoms.</h:div>
<h:div class="general">
This is either an experimental measurement or used to build up internal coordinates (as in a z-matrix) (only one allowed). We expect to move length as a child of _molecule_ and remove it from here.
</h:div>
<h:div class="example" href="length1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:simpleContent>
<xsd:extension base="xsd:float">
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="atomRefs2"/>
<xsd:attributeGroup ref="units"/>
<xsd:attributeGroup ref="errorValue"/>
<xsd:attributeGroup ref="errorBasis"/>
<xsd:attributeGroup ref="min"/>
<xsd:attributeGroup ref="max"/>
<xsd:attributeGroup ref="ref"/>
</xsd:extension>
</xsd:simpleContent>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.line3" name="line3">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A line in 3-space.</h:div>
<h:div class="description">A line characterised by one or two endpoints.</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:simpleContent>
<xsd:extension base="line3Type">
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="units"/>
</xsd:extension>
</xsd:simpleContent>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.link" name="link">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An internal or external link to other objects.</h:div>
<h:div class="description">
<h:p>
<h:b>
Semantics are similar to XLink, but simpler and only a subset is implemented.
</h:b>
This is intended to make the instances easy to create and read, and software
relatively easy to implement. The architecture is:
</h:p>
<h:ul>
<h:li>
<h:b>
A single element (
<h:tt>link</h:tt>
) used for all linking purposes.
</h:b>
</h:li>
<h:li>
<h:b>
The link types are determined by the
<h:tt>type</h:tt>
attribute and can be:
</h:b>
.
<h:ul>
<h:li>
<h:b>locator</h:b>
. This points to a single target and must carry either a
<h:tt>ref</h:tt>
or
<h:tt>href</h:tt>
attribute.
<h:tt>locator</h:tt>
links are usually children of an extended link.
<h:li>
<h:b>arc</h:b>
. This is a 1:1 link with both ends (
<h:tt>from</h:tt>
and
<h:tt>to</h:tt>
) defined.
</h:li>
<h:li>
<h:b>extended</h:b>
. This is usually a parent of several locator links and serves
to create a grouping of link ends (i.e. a list of references in documents).
</h:li>
Many-many links can be built up from arcs linking extended elements
</h:li>
</h:ul>
<h:p>
All links can have optional
<h:tt>role</h:tt>
attributes. The semantics of this are not defined;
you are encouraged to use a URI as described in the XLink specification.
</h:p>
<h:p>There are two address spaces:</h:p>
<h:ul>
<h:li>
The
<h:tt>href</h:tt>
attribute on locators behaves in the same way as
<h:tt>href</h:tt>
in
HTML and is of type
<h:tt>xsd:anyURI</h:tt>
. Its primary use is to use XPointer to reference
elements outside the document.
</h:li>
<h:li>
The
<h:tt>ref</h:tt>
attribute on locators and the
<h:tt>from</h:tt>
and
<h:tt>to</h:tt>
attributes on
<h:tt>arc</h:tt>
s refer to IDs (
<h:em>without</h:em>
the '#' syntax).
</h:li>
</h:ul>
<h:p>
Note: several other specific linking mechanisms are defined elsewhere in STM.
<h:a href="el.relatedEntry">relatedEntry</h:a>
should be used in dictionaries, and
<h:a href="st.dictRef">dictRef</h:a>
should be used to link to dictionaries. There are no required uses of
<h:tt>link</h:tt>
in STMML
but we have used it to map atoms, electrons and bonds in reactions in CML
</h:p>
</h:li>
</h:ul>
<h:p>
<h:b>Relation to XLink</h:b>
.
At present (2002) we are not aware of generic XLink
processors from which we would benefit, so the complete implementation brings little
extra value.
Among the simplifications from Xlink are:
</h:p>
<h:ul>
<h:li>
<h:tt>type</h:tt>
supports only
<h:tt>extended</h:tt>
,
<h:tt>locator</h:tt>
and
<h:tt>arc</h:tt>
</h:li>
<h:li>
<h:tt>label</h:tt>
is not supported and
<h:tt>id</h:tt>
s are used as targets of links.
</h:li>
<h:li>
<h:tt>show</h:tt>
and
<h:tt>actuate</h:tt>
are not supported.
</h:li>
<h:li>
<h:tt>xlink:title</h:tt>
is not supported (all STM elements can have a
<h:tt>title</h:tt>
attribute).
</h:li>
<h:li>
<h:tt>xlink:role</h:tt>
supports any string (i.e. does not have to be a namespaced resource).
This mechanism can, of course, still be used and we shall promote it where STM
benefits from it
</h:li>
<h:li>
The
<h:tt>to</h:tt>
and
<h:tt>from</h:tt>
attributes point to IDs rather than labels
</h:li>
<h:li>The xlink namespace is not used</h:li>
<h:li>
It is not intended to create independent linkbases, although some collections of
links may have this property and stand outside the documents they link to
</h:li>
</h:ul>
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:any maxOccurs="unbounded" minOccurs="0"/>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="from"/>
<xsd:attributeGroup ref="to"/>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="role">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">
The role of the link. Xlink adds semantics through a
URI; we shall not be this strict. We shall not normally use this mechanism
and use dictionaries instead.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
<xsd:attributeGroup ref="href">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">
The target of the (locator) link, outside the document.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
<xsd:attributeGroup ref="linkType"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.list" name="list">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A generic container with no implied semantics.</h:div>
<h:div class="description">
A generic container with no implied semantics. It just contains things and can have attributes which bind conventions to it. It could often act as the root element in an STM document.
</h:div>
<h:div class="example" href="list1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:any maxOccurs="unbounded" minOccurs="0" processContents="lax"/>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="type"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.map" name="map">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A container for links</h:div>
<h:div class="description">
There has been some confusion between map and link. At present we are trying to develop link as the primary link and map as the container.
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="link"/>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.matrix" name="matrix">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A rectangular matrix of any quantities.</h:div>
<h:div class="description">
<h:p>
By default
<h:tt>matrix</h:tt>
represents
a rectangular matrix of any quantities
representable as XSD or STMML dataTypes. It consists of
<h:tt>rows*columns</h:tt>
elements, where
<h:tt>columns</h:tt>
is the
fasting moving index. Assuming the elements are counted from 1 they are
ordered
<h:tt>
V[1,1],V[1,2],...V[1,columns],V[2,1],V[2,2],...V[2,columns],
...V[rows,1],V[rows,2],...V[rows,columns]
</h:tt>
</h:p>
<h:p>
By default whitespace is used to separate matrix elements; see
<h:a href="el.array">array</h:a>
for details. There are NO characters or markup
delimiting the end of rows; authors must be careful!. The
<h:tt>columns</h:tt>
and
<h:tt>rows</h:tt>
attributes have no default values; a row vector requires
a
<h:tt>rows</h:tt>
attribute of 1.
</h:p>
<h:p>
<h:tt>matrix</h:tt>
also supports many types of square matrix, but at present we
require all elements to be given, even if the matrix is symmetric, antisymmetric
or banded diagonal. The
<h:tt>matrixType</h:tt>
attribute allows software to
validate and process the type of matrix.
</h:p>
</h:div>
<h:div class="example" href="matrix1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:simpleContent>
<xsd:extension base="xsd:string">
<xsd:attributeGroup ref="dataType"/>
<xsd:attributeGroup ref="delimiter"/>
<xsd:attributeGroup ref="rows"/>
<xsd:attributeGroup ref="columns"/>
<xsd:attributeGroup ref="units"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="matrixType"/>
<xsd:attributeGroup ref="errorValueArray"/>
<xsd:attributeGroup ref="errorBasis"/>
<xsd:attributeGroup ref="minValueArray"/>
<xsd:attributeGroup ref="maxValueArray"/>
</xsd:extension>
</xsd:simpleContent>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.mechanism" name="mechanism">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The mechanism of a reaction.</h:div>
<h:div class="description">
<h:p>
In some cases this may be a simple textual description or reference within a controlled vocabulary. In others it may describe the complete progress of the reaction, including topological or cartesian movement of atoms, bonds and electrons and annotation with varying quantities (e.g. energies).
</h:p>
<h:p>
For named reaction mechanisms ("Diels-Alder", "ping-pong", "Claisen rearrangement", etc.) the
<h:tt>name</h:tt>
element should be used. For classification (e.g. "hydrolysis"), the
<h:tt>label</h:tt>
may be more appropriate.
</h:p>
<h:p>
In more detailed cases the mechanism refers to components of the
<h:tt>reaction</h:tt>
element. Thus bond23 might be cleaved while bond19 is transformed (mapped) to bond99. The
<h:tt>mechanismComponent</h:tt>
can be used to refer to components and add annotation. This is still experimental.
</h:p>
</h:div>
<h:div class="description">
<h:p>
IUPAC Compendium of Chemical Terminology 2nd Edition (1997) describes a mechanism as:
<h:blockquote>
A detailed description of the process leading from the reactants to the
products of a reaction, including a characterization as complete as possible
of the composition, structure, energy and other properties of reaction
intermediates, products and transition states. An acceptable mechanism of
a specified reaction (and there may be a number of such alternative mechanisms
not excluded by the evidence) must be consistent with the reaction
stoichiometry, the rate law and with all other available experimental data,
such as the stereochemical course of the reaction. Inferences concerning
the electronic motions which dynamically interconvert successive species
along the reaction path (as represented by curved arrows, for example) are
often included in the description of a mechanism.
It should be noted that for many reactions all this information is not
available and the suggested mechanism is based on incomplete experimental
data. It is not appropriate to use the term mechanism to describe a
statement of the probable sequence in a set of stepwise reactions. That
should be referred to as a reaction sequence, and not a mechanism.
</h:blockquote>
</h:p>
<h:p>
CMLReact provides reactionScheme and annotions to describe the reaction sequence and both it and
<h:tt>mechanism</h:tt>
could co-occur within a reactionScheme container.
</h:p>
</h:div>
<h:div class="example" href="mechanism1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="name"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="label"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="description"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="mechanismComponent"/>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.mechanismComponent" name="mechanismComponent">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
An information component within a reaction mechanism.
</h:div>
<h:div class="description">
<h:p>
Information components can represent both physical constituents of the reaction or abstract concepts (types of bond cleavage, thermodynamics, etc.). There are several ways that components of the reaction can be annotated and/or quantified. One approach will be to refer to specific bonds and atoms through their ids and use mechanismComponent to describe their role, properties, etc. Another is to use mechanismComponent to identify types of bond formed/broken without reference to actual atoms and bonds (initially through the
<h:tt>name</h:tt>
element). Yet another will be to include information on the reaction profile.
</h:p>
<h:p>This is still experimental.</h:p>
</h:div>
<h:div class="example" href="mechanismComponent1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:any maxOccurs="unbounded" minOccurs="0" processContents="lax"/>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.metadata" name="metadata">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A general container for metadata.</h:div>
<h:div class="description">
<h:p>
A general container for metadata, including at least
Dublin Core (DC) and CML-specific metadata
</h:p>
<h:p>
In its simple form each element provides a name and content in a similar
fashion to the
<h:tt>meta</h:tt>
element in HTML.
<h:tt>metadata</h:tt>
may have simpleContent
(i.e. a string for adding further information - this is not controlled).
</h:p>
</h:div>
<h:div class="example" href="metadata1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:simpleContent>
<xsd:extension base="xsd:string">
<xsd:attributeGroup ref="content"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="metadataType"/>
<xsd:attributeGroup ref="title"/>
</xsd:extension>
</xsd:simpleContent>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.metadataList" name="metadataList">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A general container for metadata elements.</h:div>
<h:div class="description">
MetadataLists can have local roles (e.g. a bibliographic reference could be a single meteadatList with, say, 3-6 components). The role attribute is used in an uncontrolled manner for this. MetadataLists can also be nested, but metadata and metadataList children should not occur on the same level of the hierarchy.
</h:div>
<h:div class="example" href="metadata1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="metadataList"/>
<xsd:element ref="metadata"/>
</xsd:choice>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="name"/>
<xsd:attributeGroup ref="role"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.module" name="module">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A module in a calculation.</h:div>
<h:div class="description">
<h:p>
Many programs are based on discrete modules which produce chunks of output. There are also conceptual chunks such as initialisation, calculation and summary/final which often have finer submodules such as cycle, iteration, snapshot, etc. There is no controlled vocabulary but a typical structure is shown in the example. One of the challenges of CCML is to find communality between different programs and to use agreed abstractions for the modules.
</h:p>
</h:div>
<h:div class="example" href="module1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:any maxOccurs="unbounded" minOccurs="0" processContents="lax"/>
</xsd:sequence>
<xsd:attributeGroup ref="serial"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="role">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">
The module can have a program-specific name through its title or dictRef (e.g. "MINIM", "l201") and a generic role ("dynamicsCalculation", "equilibration", etc.). In general role will be controlled by CCML.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.molecule" name="molecule">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A container for atoms, bonds and submolecules.</h:div>
<h:div class="description">
<h:p>
<h:tt>molecule</h:tt>
is a container for atoms, bonds and submolecules along
with properties such as crystal and non-builtin properties. It should either
contain
<h:tt>molecule</h:tt>
or *Array for atoms and bonds. A molecule
can be empty (e.g. we just know its name, id, etc.)
</h:p>
<h:p>
"Molecule" need not represent a chemically meaningful molecule. It
can contain atoms with bonds (as in the solid-sate) and it could
simply carry a name (e.g. "taxol") without formal representation
of the structure. It can contain "sub molecules", which are often
discrete subcomponents (e.g. guest-host).
</h:p>
<h:p>
Molecule can contain a &lt;list&gt; element to contain data
related to the molecule.
Within this can be string/float/integer and other nested lists
</h:p>
</h:div>
<h:div class="example" href="molecule1.xml"/>
</xsd:documentation>
<xsd:documentation>
<h:div class="curation">
Revised content model to allow any order of lengths, angles, torsions 2003-01-01..
</h:div>
</xsd:documentation>
<xsd:documentation>
<h:div class="curation">Added role attribute 2003-03-19..</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
The float|integer|string children are for compatibility with CML-1 and are deprecated. scalar|array|matrix should be used instead.
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="metadataList"/>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="formula"/>
<xsd:element ref="name"/>
<xsd:element ref="label"/>
<xsd:element ref="identifier"/>
<xsd:element ref="symmetry"/>
</xsd:choice>
<xsd:element minOccurs="0" ref="crystal"/>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="molecule"/>
<xsd:sequence>
<xsd:element ref="atomArray"/>
<xsd:element minOccurs="0" ref="bondArray"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="electron"/>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="zMatrix"/>
<xsd:element ref="length"/>
<xsd:element ref="angle"/>
<xsd:element ref="torsion"/>
</xsd:choice>
</xsd:sequence>
</xsd:choice>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="scalar"/>
<xsd:element ref="array"/>
<xsd:element ref="matrix"/>
<xsd:element ref="list"/>
<xsd:element ref="propertyList"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="formula"/>
<xsd:attributeGroup ref="count"/>
<xsd:attributeGroup ref="chirality"/>
<xsd:attributeGroup ref="formalCharge"/>
<xsd:attributeGroup ref="spinMultiplicity"/>
<xsd:attributeGroup ref="symmetryOriented"/>
<xsd:attributeGroup ref="role">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">
<h:p>
No formal semantics (yet). The role describes the purpose of the molecule element at this stage in the information. Examples can be "conformation", "dynamicsStep", "vibration", "valenceBondIsomer", etc. This attribute may be used by applications to determine how to present a set of molecule elements.
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.name" name="name">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A string identifying a object.</h:div>
<h:div class="description">
<h:tt>name</h:tt>
is used for chemical names (formal and trivial) for molecules and also for identifiers such as CAS registry and RTECS. It can also be used for labelling atoms. It should be used in preference to the
<h:tt>title</h:tt>
attribute because it is repeatable and can be linked to a dictionary.
<h:p>
Constraining patterns can be described in the dictionary and used to validate
<h:tt>name</h:tt>
s.
</h:p>
</h:div>
<h:div class="example" href="name1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:simpleContent>
<xsd:extension base="xsd:string">
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
</xsd:extension>
</xsd:simpleContent>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.object" name="object">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
An object which might occur in scientific data or narrative.
</h:div>
<h:div class="description">
Deliberately vague. Thus an instrument might be built from sub component objects, or a program could be composed of smaller modules (objects).
<h:tt>object</h:tt>
could be used to encapsulate graphical primitives (e.g. in reaction schemes, drawings of apparatus, etc.). Unrestricted content model.
</h:div>
<h:div class="example" href="object1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType mixed="true">
<xsd:sequence maxOccurs="unbounded" minOccurs="0">
<xsd:any processContents="lax"/>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="name"/>
<xsd:attributeGroup ref="type"/>
<xsd:attributeGroup ref="count"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.observation" name="observation">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An observation or occurrence.</h:div>
<h:div class="description">
A container for any events that need to be recorded, whether planned or not. They can include notes, measurements, conditions that may be referenced elsewhere, etc. There are no controlled semantics.
</h:div>
<h:div class="example" href="observation1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType mixed="true">
<xsd:sequence maxOccurs="unbounded" minOccurs="0">
<xsd:any processContents="lax"/>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="type"/>
<xsd:attributeGroup ref="count"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.operator" name="operator">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An operator within an expression.</h:div>
<h:div class="description">
Experimental. An operator acts on one or more arguments (at present the number is fixed by the type). The formulation is reverse Polish so the result (with its dataType) is put on a stack for further use.
</h:div>
<h:div class="example" href="potential1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<!--<xsd:choice minOccurs="0" maxOccurs="unbounded"/>-->
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="type"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.parameter" name="parameter">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A parameter describing the computation.</h:div>
<h:div class="description">
<h:p>
A parameter is a broad concept and can describe numeric quantities, objects, keywords, etc. The distinction between keywords and parameters is often fuzzy. ("MINIM" might mean "minimize", while "MINIM=3" might require three iterations to be run. It may help to think of control keywords as boolean parameters.
</h:p>
<h:p>
Numeric parameters can describe values in molecules, forcefields or other objects. Often the parameters will be refined or otherwise varied during the calculation. Some parameters may be fixed at particulat values or relaxed at different stages in the calculation. Parameters can have errors, gradients and other indications of uncertainty.
</h:p>
<h:p>
String/character parameters are often abbreviated in program input, and this is supported through the
<h:tt>regex</h:tt>
and
<h:tt>ignoreCase</h:tt>
attributes.
</h:p>
<h:p>
Parameters will usually be defined separately from the objects and use the
<h:tt>ref</h:tt>
attribute to reference them.
</h:p>
<h:p>
Parameters can be used to describe additional constraints. This will probably require the development of a microlanguage and until then may use program-specific mecxhanisms. A common approach will be to use an array of values (or objects) to represent different input values for (parts of) the calculation. Thus a conformational change could be specified by an array of several torsion angles.
</h:p>
<h:p>
A parameter will frequently have a
<h:tt>dictRef</h:tt>
pointing to a dictionary which may have more information about how the parameter is to be used or the values it can take.
</h:p>
<h:p>
The allowable content of
<h:tt>parameter</h:tt>
s may be shown by a "template" in the
<h:tt>appinfo</h:tt>
; this is stil experimental.
</h:p>
</h:div>
<h:div class="example" href="parameter1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="scalar"/>
<xsd:element ref="array"/>
<xsd:element ref="matrix"/>
<xsd:element ref="property"/>
<xsd:element ref="expression"/>
</xsd:choice>
<xsd:choice minOccurs="0">
<xsd:element ref="gradient"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="value">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">
This is a shorthand for a single scalar value of the parameter. It should only be used with the
<h:tt>ref</h:tt>
attribute as it inherits all the dataTyping of the referenced element. It must not be used for defining new parameters as it has no mechanism for units and dataTyping. [This may change?].
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
<xsd:attributeGroup ref="constraint"/>
<xsd:attributeGroup ref="name"/>
<xsd:attributeGroup ref="role">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">
<h:p>
Used to define concepts such as independent and dependent variables
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.parameterList" name="parameterList">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A container for one or more parameters.</h:div>
<h:div class="description">parameterList can contain several parameters.</h:div>
<h:div class="example" href="parameterList1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="metadataList"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="name"/>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="parameter"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="role"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.particle" name="particle">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An object in space carrying a set of properties.</h:div>
<h:div class="description">
<h:tt>particles</h:tt>
have many of the characteristics of
<h:tt>atom</h:tt>
s but without at atomic nucleus. It does not have an elementType and cannot be involved in bonding, etc. It has coordinates, may carry charge and might have a mass. It represents some aspect of a computational model and should not be used for purely geometrical concepts such as centroid. Examples of particles are "shells" (e.g. in GULP) which are linked to atoms for modelling polarizability or lonepairs and approximations to multipoles. Properties such as charge, mass should be scalar/array/matrix children.
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:any maxOccurs="unbounded" minOccurs="0" processContents="lax"/>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="type">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">
Used in a similar manner to
<h:tt>atomType</h:tt>
. Examples might be "lonePair", "polarizable Oxygen", etc.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
<xsd:attributeGroup ref="x3"/>
<xsd:attributeGroup ref="y3"/>
<xsd:attributeGroup ref="z3"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.peak" name="peak">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A peak; annotated by human or machine.</h:div>
<h:div class="description">
<h:p>
A
<h:tt>peak</h:tt>
can describe:
<h:ul>
<h:li>
A single point in a spectrum. Usually a maximum but could be a shoulder, inflexion or indeed any point of interest.
</h:li>
<h:li>
A continuous range of values within a spectrum, defined by maximum and minimum values on either/both axes
</h:li>
</h:ul>
</h:p>
</h:div>
<h:div class="description">
The units should always be given. (The raw spectral data may unfortunately use different units and no assumptions should be made).
</h:div>
<h:div class="example" href="peak1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element minOccurs="0" ref="metadataList">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
Allows
<h:i>inter alia</h:i>
the provenance of the peak assignment to be recorde.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="atom"/>
<xsd:element ref="bond"/>
<xsd:element ref="molecule"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="peakHeight"/>
<xsd:attributeGroup ref="peakMultiplicity"/>
<xsd:attributeGroup ref="peakShape"/>
<xsd:attributeGroup ref="integral"/>
<xsd:attributeGroup ref="peakUnits"/>
<xsd:attributeGroup ref="xMin"/>
<xsd:attributeGroup ref="xMax"/>
<xsd:attributeGroup ref="xValue"/>
<xsd:attributeGroup ref="xWidth"/>
<xsd:attributeGroup ref="xUnits"/>
<xsd:attributeGroup ref="yMin"/>
<xsd:attributeGroup ref="yMax"/>
<xsd:attributeGroup ref="yValue"/>
<xsd:attributeGroup ref="yWidth"/>
<xsd:attributeGroup ref="yUnits"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.peakGroup" name="peakGroup">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A list of closely related peaks or peakGroups.</h:div>
<h:div class="description">
Distinguish between
<h:tt>peakList</h:tt>
(primarily a navigational container) and
<h:tt>peakGroup</h:tt>
where the peaks (or groups) have some close relation not shared by all peaks. All descendants must use consistent units.
</h:div>
<h:div class="example" href="peakGroup1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element minOccurs="0" ref="metadataList">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
Allows
<h:i>inter alia</h:i>
the provenance of the peak assignment to be recorde.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="peak"/>
<xsd:element ref="peakGroup"/>
<xsd:element ref="atom"/>
<xsd:element ref="bond"/>
<xsd:element ref="molecule"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="peakHeight"/>
<xsd:attributeGroup ref="peakMultiplicity"/>
<xsd:attributeGroup ref="peakShape"/>
<xsd:attributeGroup ref="integral"/>
<xsd:attributeGroup ref="peakUnits"/>
<xsd:attributeGroup ref="xMin"/>
<xsd:attributeGroup ref="xMax"/>
<xsd:attributeGroup ref="xValue"/>
<xsd:attributeGroup ref="xWidth"/>
<xsd:attributeGroup ref="xUnits"/>
<xsd:attributeGroup ref="yMin"/>
<xsd:attributeGroup ref="yMax"/>
<xsd:attributeGroup ref="yValue"/>
<xsd:attributeGroup ref="yWidth"/>
<xsd:attributeGroup ref="yUnits"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.peakList" name="peakList">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A list of peaks or peakGroups.</h:div>
<h:div class="description">
Distinguish between
<h:tt>peakList</h:tt>
(primarily a navigational container) and
<h:tt>peakGroup</h:tt>
where the peaks (or groups) have some close relation not shared by all peaks. All peaks and peakGroups should use the same units.
</h:div>
<h:div class="example" href="peakList1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element minOccurs="0" ref="metadataList">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
Allows
<h:i>inter alia</h:i>
the provenance of the peak assignment to be recorde.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="peak"/>
<xsd:element ref="peakGroup"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="ref"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.plane3" name="plane3">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A plane in 3-space.</h:div>
<h:div class="description">An oriented plane of indefinite extent.</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:simpleContent>
<xsd:extension base="plane3Type">
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="units"/>
</xsd:extension>
</xsd:simpleContent>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.point3" name="point3">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A point in 3-space.</h:div>
<h:div class="description"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:simpleContent>
<xsd:extension base="point3Type">
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="units"/>
</xsd:extension>
</xsd:simpleContent>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.potential" name="potential">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An explicit potential.</h:div>
<h:div class="description">
This represents the actual function for the potential (i.e. with explicit values) rather than the functional form, which will normally be referenced from this.
</h:div>
<h:div class="example" href="potential1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="arg"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="form"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.potentialForm" name="potentialForm">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The functional form of a potential.</h:div>
<h:div class="description">
This has generic arguments and parameters rather than explicit ones. It is essentially a mathematical function, expressed currently in reverse Polish notation.
</h:div>
<h:div class="example" href="potential1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="arg"/>
</xsd:choice>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="parameter"/>
</xsd:choice>
<xsd:choice minOccurs="0">
<xsd:element ref="expression"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="name"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.potentialList" name="potentialList">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A container for explicit potentials.</h:div>
<h:div class="description">Experimental.</h:div>
<h:div class="example" href="potential1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="potential"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.product" name="product">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A product within a productList.</h:div>
<h:div class="description">
<h:tt>product</h:tt>
describes a product species which is produced in a reaction. See
<h:tt>reactant</h:tt>
for discussion of catalysis and solvents.
</h:div>
<h:div class="example" href="product1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:annotation>
<xsd:documentation>
<h:div class="description">
<h:p>
A product will normally be identified by name(s), formula, or molecule and at least one of these should normally be given. Amount(s) of product can be given after this identification and can describe mass, volume, percent yield, etc. but not stoichiometry
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="metadataList"/>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element minOccurs="0" ref="identifier"/>
<xsd:element minOccurs="0" ref="label"/>
<xsd:element minOccurs="0" ref="name"/>
</xsd:choice>
<xsd:element minOccurs="0" ref="molecule"/>
<xsd:element minOccurs="0" ref="electron"/>
<xsd:element minOccurs="0" ref="substance"/>
<xsd:element minOccurs="0" ref="substanceList"/>
<xsd:element minOccurs="0" ref="formula"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="amount"/>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="role"/>
<xsd:attributeGroup ref="count"/>
<xsd:attributeGroup ref="state"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.productList" name="productList">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A container for one or more products.</h:div>
<h:div class="description">
<h:p>
<h:tt>productList</h:tt>
can contain several products. These may be related in several ways, including
<h:ul>
<h:li>single list of products</h:li>
<h:li>grouping of products of parallel reactions</h:li>
</h:ul>
.
A productList can contain nested productLists. The semantics of this are currently undefined.
</h:p>
</h:div>
<h:div class="example" href="productList1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="metadataList"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="name"/>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="productList"/>
<xsd:element ref="product"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="role"/>
<xsd:attributeGroup ref="count">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">
The number of copies of the productList involved in the stoichiometric reaction. Probably not useful for simple reactions but could be used for parallel reactions.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.property" name="property">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A container for a property.</h:div>
<h:div class="description">
<h:tt>property</h:tt>
can contain one or more children, usually
<h:tt>scalar</h:tt>
,
<h:tt>array</h:tt>
or
<h:tt>matrix</h:tt>
. The
<h:tt>dictRef</h:tt>
attribute is required, even if there is a single scalar child with the same dictRef. The property may have a different dictRef from the child, thus providing an extension mechanism.
<h:p>
Properties may have a
<h:tt>state</h:tt>
attribute to distinguish the state of matter
</h:p>
</h:div>
<h:div class="example" href="property1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="metadataList"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="name"/>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="scalar"/>
<xsd:element ref="array"/>
<xsd:element ref="matrix"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="role">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">
Semantics are not yet controlled but could include thermochemistry, kinetics or other common properties.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
<xsd:attributeGroup ref="state"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.propertyList" name="propertyList">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A container for one or more properties.</h:div>
<h:div class="description">
<h:tt>propertyList</h:tt>
can contain several properties. These include (but are not limited to observations, or numeric quantities.
</h:div>
<h:div class="example" href="propertyList1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="metadataList"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="name"/>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="property"/>
<xsd:element ref="observation"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="role"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.reactant" name="reactant">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A reactant within a reactantList.</h:div>
<h:div class="description">
<h:tt>reactant</h:tt>
describes a reactant species which takes part in a reaction. Catalysts and supports are not normally classified as reactants, but this is subjective. Enzymes (or parts of enzymes) may well be reactants, as could be substances which underwent chemical change but were restored to their original state.
<h:tt>reactant</h:tt>
is a powerful concept as it can support stoichiometry (atom and molecule counting), mapping (for mechanisms), etc. Solvents are best contained within substanceList.
</h:div>
<h:div class="example" href="reactant1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:annotation>
<xsd:documentation>
<h:div>
A reactant will normally be identified by name(s), formula, or molecule and at least one of these should normally be given. Amount(s) of reactant can be given after this identification and can describe mass, volume, etc. but not stoichiometr.
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="metadataList"/>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="identifier"/>
<xsd:element ref="label"/>
<xsd:element ref="name"/>
</xsd:choice>
<xsd:element minOccurs="0" ref="molecule"/>
<xsd:element minOccurs="0" ref="electron"/>
<xsd:element minOccurs="0" ref="substance"/>
<xsd:element minOccurs="0" ref="substanceList"/>
<xsd:element minOccurs="0" ref="formula"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="amount"/>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="role">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">
The role of the reactant within a reactantList. Semantics are not yet controlled but could be limiting, oxidant, etc. TODO: a reactant might have multiple roles so this may have to become an element.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
<xsd:attributeGroup ref="count">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">
The number of copies of the reactant involved in the stoichiometric reaction. Could be non-integer but should not be used for actual ratios of materials added (for which amount should be used).
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
<xsd:attributeGroup ref="state"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.reactantList" name="reactantList">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A container for one or more reactants.</h:div>
<h:div class="description">
<h:p>
<h:tt>reactantList</h:tt>
can contain several reactants. These may be related in several ways, including
<h:ul>
<h:li>lists of related reactants</h:li>
<h:li>reactant schemes</h:li>
<h:li>multi-step reactants</h:li>
<h:li>parallel and/or coupled reactants</h:li>
</h:ul>
.
A reactantList can contain nested reactantLists. The semantics of this are currently undefined.
</h:p>
</h:div>
<h:div class="example" href="reactantList1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="metadataList"/>
<xsd:element minOccurs="0" ref="name"/>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="reactantList"/>
<xsd:element ref="reactant"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="role"/>
<xsd:attributeGroup ref="count"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.reaction" name="reaction">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A chemical reaction or reaction step.</h:div>
<h:div class="description">
<h:p>
<h:tt>reaction</h:tt>
is a container for reactants, products, conditions, properties and possibly other information relating to the reaction, often within a reactionList. Partial semantics exist:
<h:ul>
<h:li>
<h:b>name</h:b>
the name(s) of the reaction
</h:li>
<h:li>
<h:b>reactantList</h:b>
(normally only one) the grouped reactants
</h:li>
<h:li>
<h:b>substance</h:b>
or
<h:b>substanceList</h:b>
substances present in the reaction but not classified as reactants. Examples might be enzymes, catalysts, solvents, supports, workup, etc.
</h:li>
<h:li>
<h:b>condition</h:b>
conditions of the reaction. These may be text strings, but ideally will have clearer semantics such as scalars for temperature, etc.
</h:li>
<h:li>
<h:b>productList</h:b>
the grouped products. This allows for parallel reactions or other semantics.
</h:li>
<h:li>
<h:b>property</h:b>
properties (often physical) associated with the reaction. Examples might be heat of formation, kinetics or equilibrium constant.
</h:li>
</h:ul>
</h:p>
</h:div>
<h:div>
<h:p>
Reaction normally refers to an overall reaction or a step within a reactionList. For a complex "reaction", such as in enzymes or chain reactions, it may be best to use
<h:tt>reactionScheme</h:tt>
to hold the overall
<h:tt>reaction</h:tt>
and a
<h:tt>reactionList</h:tt>
of the individual
<h:tt>reaction</h:tt>
steps.
</h:p>
</h:div>
<h:div class="example" href="reaction1.xml"/>
<h:div class="example" href="reaction9a.xml"/>
<h:div class="example" href="reaction9b.xml"/>
<h:div class="example" href="reaction10a.xml"/>
<h:div class="example" href="reaction10b.xml"/>
<h:div class="example" href="reaction11.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:annotation>
<xsd:documentation>
<h:div>
<h:p>The semantics of the content model are</h:p>
<h:ul>
<h:li>metadataList for general metadata</h:li>
<h:li>
label for classifying or describing the reaction (e.g. "hydrolysis")
</h:li>
<h:li>
identifier for unique identification. This could be a classification such as EC (enzyme commission) or an IChI-like string generated from the components.
</h:li>
<h:li>
these are followed by the possible components of the reaction and/or a reactionList of further details.
</h:li>
</h:ul>
.
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="metadataList"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="label"/>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="name"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="identifier"/>
</xsd:choice>
<xsd:sequence maxOccurs="unbounded" minOccurs="0">
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="reactiveCentre"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="mechanism"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="reactantList"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="spectatorList"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="substanceList"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="conditionList"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="transitionState"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="productList"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="propertyList"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="map"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="object">
<xsd:annotation>
<xsd:documentation>
<h:div>
This allows any objects to be attached to the reaction, but particularly graphical primitives such as lines, arrows, etc. These should be provided as elements where possible (e.g. SVG) and should have references to the chemical objects they interact with (i.e. not simply relying on geometry). Markers with IDs can be included as part of the graphics object and their ids linked to the chemical elements using
<h:tt>link</h:tt>
.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:element>
</xsd:sequence>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="reactionFormat"/>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="reactionRole"/>
<xsd:attributeGroup ref="reactionType"/>
<xsd:attributeGroup ref="state"/>
<xsd:attributeGroup ref="atomMap"/>
<xsd:attributeGroup ref="electronMap"/>
<xsd:attributeGroup ref="bondMap"/>
<xsd:attributeGroup ref="yield">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">
<h:p>
The yield of the reaction. Note that this lies in the range 0-1.
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.reactionList" name="reactionList">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
A container for one or more reactions or reactionSchemes with no interrelations.
</h:div>
<h:div class="description">
A reactionList aggregates reactions and reactionSchemes but implies no semantics. The most common uses are to create small collections of reactions (e.g. databases or publications).
</h:div>
<h:div class="example" href="reactionList1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:annotation>
<xsd:documentation>
<h:div/>
</xsd:documentation>
</xsd:annotation>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="metadataList"/>
<xsd:choice>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="reactionScheme"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="reaction"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="name"/>
<xsd:attributeGroup ref="ref"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.reactionScheme" name="reactionScheme">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
A container for two or more related reactions and their relationships.
</h:div>
<h:div class="description">
Where reactions are closely related (and often formally dependent on each other) they should be contained within the reactionStepList of a reactionScheme. The semantics which have informed this design include:
<h:ul>
<h:li>Steps within an organic synthesis.</h:li>
<h:li>
Two or more individual (primitive) steps provding the detailed mechanism for an overall reaction.
</h:li>
<h:li>
Coupled or sequential reactions within biochemical pathways.
</h:li>
</h:ul>
<h:p>
This design is general because "reaction" is used in several ways. A biochemical pathway (e.g. oxidation of glucose to CO2 and water) involves many coupled enzyme reactions proceeding both in parallel and in sequence. Each of these steps ("reactions" in their own right) is itself complex and can include several mechanistics steps which are themselves reactions with products, reactants, etc.
<h:tt>reactionScheme</h:tt>
can therefore include reactionStepLists (with more reactionScheme children) which provide a more detailed view of the individual components.
</h:p>
<h:p>Where a set of reactions are primitives...</h:p>
</h:div>
<h:div class="example" href="reactionScheme1.xml"/>
<h:div class="example" href="reactionScheme3.xml"/>
<h:div class="example" href="reactionScheme4a.xml"/>
<h:div class="example" href="reactionScheme4b.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:annotation>
<xsd:documentation>
<h:div class="description">
<h:p>The semantics of the content model are</h:p>
<h:ul>
<h:li>metadataList for general metadata</h:li>
<h:li>
label for classifying or describing the reaction (e.g. "hydrolysis")
</h:li>
<h:li>
identifier for unique identification. This could be a classification such as EC (enzyme commission) or an IChI-like string generated from the components.
</h:li>
<h:li>
these are followed by the possible components of the reaction and/or a reactionList of further details.
</h:li>
</h:ul>
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="metadataList"/>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="label"/>
<xsd:element ref="name"/>
<xsd:element ref="identifier"/>
</xsd:choice>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="reaction"/>
<xsd:element ref="reactionStepList"/>
<xsd:element ref="reactionScheme"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="reactionRole"/>
<xsd:attributeGroup ref="reactionType"/>
<xsd:attributeGroup ref="state"/>
<xsd:attributeGroup ref="reactionFormat"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.reactionStep" name="reactionStep">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
A child of reactionStepList and a container for reaction or reactionScheme.
</h:div>
<h:div class="description">
<h:p>
<h:tt>reactionStep</h:tt>
is always contained within reactionStepList and is designed to manage "sub-reactions" which have close relationships. These will often involve reactions which, taken together, describe a higher level reaction or reaction type. Examples are:
<h:ul>
<h:li>biochemical pathways</h:li>
<h:li>synthetic reaction schemes</h:li>
<h:li>multi-step reactions</h:li>
<h:li>parallel and/or coupled reactions</h:li>
</h:ul>
.
A reactionStep normally contains a single reaction or reactionScheme. It can have attributes such as yield and ratio which can be used by the parent reactionStepList.
</h:p>
</h:div>
<h:div class="example" href="reactionStepList4.xml"/>
<h:div class="example" href="reactionStepList5a.xml"/>
<h:div class="example" href="reactionStepList5b.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:annotation>
<xsd:documentation>
<h:div>
<h:p>
The
<h:tt>name</h:tt>
applies to the overall schema of reactions.
<h:tt>label</h:tt>
is for additional textual information and classification.
<h:tt>reactionStepList</h:tt>
normally contains
<h:tt>reaction</h:tt>
s but we make provision for nested reactionSchemes if required.
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="metadataList"/>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="name"/>
<xsd:element ref="label"/>
</xsd:choice>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="reactionScheme"/>
<xsd:element ref="reaction"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="yield">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">
<h:p>
The yield of the reactionStep. Note that this lies in the range 0-1.
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
<xsd:attributeGroup ref="ratio">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">
<h:p>
The ratio of this step to one or more sibling steps. Note that this lies in the range 0-1. It is meaningless to use this unless there are siblings, in which case it refers to the relative molar fluxes through each. The "percentage yields" will need to be transformed to this range. There is no requirement that the sum of fluxes through a group of siblings sum to 1.0, though they should not sum to more.
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.reactionStepList" name="reactionStepList">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
A container for one or more related reactionSteps.
</h:div>
<h:div class="description">
<h:p>
<h:tt>reactionStepList</h:tt>
is always contained within reactionScheme and is designed to manage "sub-reactions" which have close relationships. These will often involve reactions which, taken together, describe a higher level reaction or reaction type. Examples are:
<h:ul>
<h:li>biochemical pathways</h:li>
<h:li>synthetic reaction schemes</h:li>
<h:li>multi-step reactions</h:li>
<h:li>parallel and/or coupled reactions</h:li>
</h:ul>
.
A reactionStepList contains reactionSteps (each of which contains reactions and/or reactionSchemes (e.g. where part of the process is known in greater detail)). It may not directly contain child reactionStepLists.
</h:p>
<h:p>
The child reactionSteps can have attributes such as yield and ratio which describe the relationship of the component steps.
</h:p>
<h:p>
Guidance on use:
<h:ul>
<h:li>
reactionScheme describes a complex of reactions with metadata, one (or more) overall reactions and a reactionStepList with the overall component reactions.
</h:li>
<h:li>
reactionStepList aggregates and structures the individual subreactions.
</h:li>
<h:li>
reactionList is a container for reactions and reactionSchemes with no semantics (e.g. a book or database of selected reactions).
</h:li>
</h:ul>
</h:p>
</h:div>
<h:div class="example" href="reactionStepList2.xml"/>
<h:div class="example" href="reactionStepList3.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:annotation>
<xsd:documentation>
<h:div>
<h:p>
The
<h:tt>name</h:tt>
applies to the overall schema of reactions.
<h:tt>label</h:tt>
is for additional textual information and classification.
<h:tt>reactionStepList</h:tt>
normally contains
<h:tt>reactionStep</h:tt>
s.
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="metadataList"/>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="name"/>
<xsd:element ref="label"/>
</xsd:choice>
<xsd:sequence maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="reactionStep"/>
</xsd:sequence>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="type"/>
<xsd:attributeGroup ref="reactionFormat"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.reactiveCentre" name="reactiveCentre">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The reactiveCentre in a reaction.</h:div>
<h:div class="description">
This describes the set(s) of bonds and atoms involved in the reaction. The semantics are flexible, but a common usage would be to create atomSet(s) and bondSet(s) mapping to groups which undergo changes.
</h:div>
<h:div class="example" href="reactiveCentre1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element minOccurs="0" ref="description"/>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="atomTypeList"/>
<xsd:element ref="bondTypeList"/>
<xsd:element ref="atomSet"/>
<xsd:element ref="bondSet"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.region" name="region">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A region of the system.</h:div>
<h:div class="description">
Under development. A subdivision of the system to which special protocols or properties may be attached. Typical regions could be defined by the presence of atoms belonging to an atomSet or geometrical boundaries.
</h:div>
<h:div class="note">
A region element will not always contain other elements, but may have references from other elements. It may create a protocol, e.g. atoms within a region might be replaced by a continuum model or be subject ro a field. Semantics yet to be determined.
</h:div>
<h:div>
Regions can be created by the unions of two or more regions. This allows a region to be built from a series of (say) spheres or boxes filling space.
</h:div>
<h:div class="example" href="region1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence/>
<xsd:attributeGroup ref="sphere3"/>
<xsd:attributeGroup ref="box3"/>
<xsd:attributeGroup ref="atomSetRef"/>
<xsd:attributeGroup ref="regionRefs"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.relatedEntry" name="relatedEntry">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
An entry related in some way to a dictionary entry.
</h:div>
<h:div class="description">
The range of relationships is not restricted but should include parents, aggregation, seeAlso and so on. DataCategories from ISO12620 can be referenced through the namespaced mechanism.
</h:div>
<h:div class="example" href="relatedEntry1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType mixed="true">
<xsd:attributeGroup ref="relatedEntryType"/>
<xsd:attributeGroup ref="href">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">The related entry.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.sample" name="sample">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An analytical or spectral sample.</h:div>
<h:div class="description">
The
<h:tt>sample</h:tt>
should contain information on what things were in the sample and their roles. It can include
<h:tt>molecule</h:tt>
,
<h:tt>substance</h:tt>
and
<h:tt>substanceList</h:tt>
. Typical rolos include solvent, mulling agents, salt disks, molecular supports, etc. but should not cover apparatus or conditions.
</h:div>
<h:div class="example" href="sample1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="metadataList"/>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="molecule">
<xsd:annotation>
<xsd:documentation>
<h:div>A molecular description.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element ref="substance">
<xsd:annotation>
<xsd:documentation>
<h:div>A substance in the sample.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element ref="substanceList">
<xsd:annotation>
<xsd:documentation>
<h:div>A list of substances in the sample.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:element>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="state"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.scalar" name="scalar">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An element to hold scalar data.</h:div>
<h:div class="description">
<h:tt>scalar</h:tt>
holds scalar data under a single
generic container. The semantics are usually resolved by
linking to a dictionary.
<h:b>scalar</h:b>
defaults to a scalar string but
has attributes which affect the type.
<h:p>
<h:tt>scalar</h:tt>
does not necessarily reflect a physical object (for which
<h:a href="el.object">object</h:a>
should be used). It may reflect a property of an object
such as temperature, size, etc.
</h:p>
<h:p>
Note that normal Schema validation tools cannot validate the data type
of
<h:b>scalar</h:b>
(it is defined as
<h:tt>string</h:tt>
), but that a temporary schema
can be constructed from the type and used for validation. Also the type
can be contained in a dictionary and software could decide to retrieve this
and use it for validation.
</h:p>
</h:div>
<h:div class="example" href="scalar1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:simpleContent>
<xsd:extension base="xsd:string">
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="dataType"/>
<xsd:attributeGroup ref="errorValue"/>
<xsd:attributeGroup ref="errorBasis"/>
<xsd:attributeGroup ref="min"/>
<xsd:attributeGroup ref="max"/>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="units"/>
</xsd:extension>
</xsd:simpleContent>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.spectator" name="spectator">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A spectator object in a reaction.</h:div>
<h:div class="description">
Objects are often present during a reaction which are not formally involved in bond breaking/formation and which are not modified during the reaction. They may be catalysts, but may also be objects which in some way constrain or help the reaction to take place (surfaces, micelles, groups in enzyme active sites, etc.). In some cases molecules present in a reaction mixture may act as spectators in steps in which they are not transformed.
</h:div>
<h:div class="example" href="spectator1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="metadataList"/>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="label"/>
<xsd:element ref="molecule"/>
<xsd:element ref="object"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="role">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">
No controlled vocabulary. Examples could be 'host', 'hydrophobic ligand', 'charge-stabilizer', etc..
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.spectatorList" name="spectatorList">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A container for spectators in a reaction.</h:div>
<h:div class="description"/>
<h:div class="example" href="spectatorList1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence maxOccurs="unbounded">
<xsd:element ref="spectator"/>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.spectrum" name="spectrum">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A spectrum and relevant data or metadata.</h:div>
<h:div class="description">
The
<h:tt>spectrum</h:tt>
construct can hold
<h:tt>metadataList</h:tt>
,
<h:tt>sample</h:tt>
(which can contain molecule),
<h:tt>conditionList</h:tt>
(mainly for physical/chemical conditions, not instrumental),
<h:tt>spectrumData</h:tt>
for the actual data and instrumental settings/procedure and
<h:tt>peakList</h:tt>
for the assigned peaks. This approach puts the spectrum as the primary object of interest. It could also be possible to make
<h:tt>spectrum</h:tt>
a child of
<h:tt>molecule</h:tt>
(although a reference using
<h:tt>ref</h:tt>
might be preferable).
</h:div>
<h:div class="example" href="spectrum1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="metadataList"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="sample">
<xsd:annotation>
<xsd:documentation>
<h:div>
A (complete) description of the thing to which the spectrum relates. May contain
<h:tt>molecule</h:tt>
or
<h:tt>substanceList</h:tt>
. Solvents, mulls, etc should be described here.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="conditionList">
<xsd:annotation>
<xsd:documentation>
<h:div>
The conditions relating to the spectrum (complementary to substanceList.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="spectrumData"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="peakList">
<xsd:annotation>
<xsd:documentation>
<h:div>
A list of peaks. This may occur independently of the xaxis/yaxis data.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:element>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="moleculeRef">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">The molecule to which the spectrum refers.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
<xsd:attributeGroup ref="spectrumType"/>
<xsd:attributeGroup ref="format"/>
<xsd:attributeGroup ref="measurement"/>
<xsd:attributeGroup ref="ft"/>
<xsd:attributeGroup ref="state">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">
Although this may also be contained in the
<h:tt>sample</h:tt>
element it is useful to state it here. No default.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.spectrumData" name="spectrumData">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Data for the spectrum.</h:div>
<h:div class="description">
This is primarily to record the data in interchangeable format and machine and manufacturers settings and can include other MLs in this area (AniML, SpectroML, etc.). We recommend ASCII representations of data and this is the only format that CMLSpect implementers have to support, but we also allow for the carriage of JCAMP and other data (in ML wrappers such as AniML). All numeric data should carry units and dictionary references if possible to allow for semantic interoperability.
</h:div>
<h:div class="example" href="spectrumData1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:sequence minOccurs="0">
<xsd:element ref="xaxis">
<xsd:annotation>
<xsd:documentation>
<h:div>
The x-axis/es, usually including the list of points at which data are recorded. Mandatory if y-axis data are given. Multiple x-axes are initially reserved for multiple scales rather than different measurements (for which an additional spectrum should be used).
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element maxOccurs="unbounded" ref="yaxis">
<xsd:annotation>
<xsd:documentation>
<h:div>
The y-axis/es, usually including the list of points at which data are recorded. Mandatory if x-axis data are given. Multiple y-axes are initially reserved for multiple scales rather than different measurements (for which an additional spectrum should be used).
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:element>
</xsd:sequence>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="ref"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.spectrumList" name="spectrumList">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A container for one or more spectra.</h:div>
<h:div class="description">
<h:p>
<h:tt>spectrumList</h:tt>
can contain several spectra. These may be related in several ways, including
<h:ul>
<h:li>lists of related spectra</h:li>
<h:li>
bundle of common analytical spectra (NMR, IR, UV...)
</h:li>
<h:li>repeat measurements</h:li>
</h:ul>
.
A spectrumList can contain nested spectrumLists.
</h:p>
</h:div>
<h:div class="example" href="spectrumList1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:annotation>
<xsd:documentation>
<h:div>
<h:tt>metadataList</h:tt>
contains
<h:tt>metadata</h:tt>
.
<h:tt>list</h:tt>
is for experimental and other data.
<h:tt>spectrumList</h:tt>
normally contains
<h:tt>spectrum</h:tt>
s but we make provision for nested spectrumLists if required. The
<h:tt>molecule</h:tt>
s can be a set of reference molecules which occur in the
<h:tt>spectrum</h:tt>
s and can be referenced. This makes the spectrums more readable and normalizes data when molecules are used more than once.
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="metadataList"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="list"/>
<xsd:choice>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="spectrumList"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="spectrum"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="moleculeRef"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.sphere3" name="sphere3">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A sphere in 3-space.</h:div>
<h:div class="description"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:simpleContent>
<xsd:extension base="sphere3Type">
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="units"/>
</xsd:extension>
</xsd:simpleContent>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.stmml" name="stmml">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An element to hold stmml data.</h:div>
<h:div class="description">
<h:tt>stmml</h:tt>
holds stmml data under a single
generic container. Other namespaces may be present as children.
No semantics implied.
</h:div>
<h:div class="example" href="stmml1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence maxOccurs="unbounded" minOccurs="0">
<xsd:any processContents="lax"/>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.substance" name="substance">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A chemical substance.</h:div>
<h:div class="description">
<h:tt>substance</h:tt>
represents a
<h:i>chemical substance</h:i>
which is deliberately very general. It can represent things that may or may not be molecules, can and cannot be stored in bottles and may or may not be microscopic. Solutions and mixtures can be described by _substanceList_s of substances. The
<h:tt>type</h:tt>
attribute can be used to give qualitative information characterising the substance ("granular", "90%", etc.) and _role_ to describe the role in process ("desiccant", "support", etc.). There is currently no controlled vocabulary. Note that
<h:tt>reaction</h:tt>
is likely to have more precise semantics. The amount of a substance is controlled by the optional _amount_ child.
</h:div>
<h:div class="example" href="substance1.xml"/>
</xsd:documentation>
<xsd:documentation>
<h:div class="curation">
<h:p>Added property as a child 2002-12-29</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="metadataList"/>
<xsd:element minOccurs="0" ref="amount"/>
<xsd:choice>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="molecule"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="name"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="property"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="type"/>
<xsd:attributeGroup ref="role">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">
<h:tt>role</h:tt>
depends on context, and indicates some purpose associated with the substance. It might indicate 'catalyst', 'solvent', 'antoxidant', etc. but is not limited to any vocabulary.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="count"/>
<xsd:attributeGroup ref="state"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.substanceList" name="substanceList">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A list of chemical substances.</h:div>
<h:div class="description">
Deliberately very general - see substance. substanceList is designed to manage solutions, mixtures, etc. and there is a small enumerated controlled vocabulary, but this can be extended through dictionaries.
<h:p>
substanceList can have an amount child. This can indicate the amount of a solution or mixture; this example describes 100 ml of 0.1M NaOH(aq). Although apparently longwinded it is precise and fully machine-interpretable
</h:p>
</h:div>
<h:div class="curation">Added role attribute, 2003-03-12.</h:div>
<h:div class="example" href="substanceList1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="metadataList"/>
<xsd:element minOccurs="0" ref="amount"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="substance"/>
<xsd:element minOccurs="0" ref="propertyList"/>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="substanceListType"/>
<xsd:attributeGroup ref="role"/>
<xsd:attributeGroup ref="ref"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.symmetry" name="symmetry">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Molecular, crystallographic or other symmetry.</h:div>
<h:div class="description">
<h:p>
<h:tt>symmetry</h:tt>
provides a label and/or symmetry operations for molecules
or crystals. Point and spacegroups can be specified by strings, though these are not
enumerated, because of variability in syntax (spaces, case-sensitivity, etc.),
potential high symmetries (e.g. TMV disk is D17) and
non-standard spacegroup settings. Provision is made for explicit symmetry operations
through &lt;matrix&gt; child elements.
</h:p>
<h:p>
By default the axes of symmetry are defined by the symbol - thus C2v requires
z to be the unique axis, while P21/c requires b/y. Spacegroups imply the semantics
defined in International Tables for Crystallography, (Int Union for Cryst., Munksgaard).
Point groups are also defined therein.
</h:p>
<h:p>
The element may also be used to give a label for the symmetry species (irreducible
representation) such as "A1u" for a vibration or orbital.
</h:p>
<h:p>
The matrices should be 3x3 for point group operators and 3x4 for spacegroup operators.
The use of crystallographic notation ("x,1/2+y,-z") is not supported - this would
be &lt;matrix&gt;1 0 0 0.0 0 1 0 0.5 0 0 1 0.0&lt;matrix&gt;.
</h:p>
<h:p>
The default convention for point group symmetry is
<h:tt>Schoenflies</h:tt>
and for
spacegroups is "H-M". Other conventions (e.g. "Hall") must be specfied through
the
<h:tt>convention</h:tt>
attribute.
</h:p>
<h:p>
This element implies that the Cartesians or fractional coordinates in a molecule
are oriented appropriately. In some cases it may be useful to specify the symmetry of
an arbitarily oriented molecule and the &lt;molecule&gt; element has the attribute
<h:tt>symmetryOriented</h:tt>
for this purpose.
</h:p>
</h:div>
<h:div class="example" href="symmetry1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="matrix"/>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="pointGroup"/>
<xsd:attributeGroup ref="spaceGroup"/>
<xsd:attributeGroup ref="irreducibleRepresentation"/>
<xsd:attributeGroup ref="number">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">
The rotational symmetry number. Used for calculation of entropy, etc.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.system" name="system">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
The complete system of components in a calculation.
</h:div>
<h:div class="description">There is no controlled vocabulary.</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:any maxOccurs="unbounded" minOccurs="0" processContents="lax"/>
</xsd:sequence>
<xsd:attributeGroup ref="dimensionality"/>
<xsd:attributeGroup ref="periodicity"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.table" name="table">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A rectangular table of any quantities.</h:div>
<h:div class="description">
<h:p>
By default
<h:tt>table</h:tt>
represents a rectangular table of any quantities
representable as XSD or STMML dataTypes. The default layout is columnwise,
with
<h:tt>columns</h:tt>
columns,
where each column is a (homogeneous)
<h:a href="el.array">array</h:a>
of
size
<h:tt>rows</h:tt>
data. This is the "normal" orientation of data tables
but the table display could be transposed by XSLT transformation if required.
Access is to columns, and thence to the data within them. DataTyping, delimiters,
etc are delegated to the arrays, which must all be of the same size. For
verification it is recommended that tables carry
<h:tt>rows</h:tt>
and
<h:tt>columns</h:tt>
attributes.
</h:p>
<h:p>
An alternative is to use the standard HTML table layout (tr and td). The identities
of the columns (dictRef), their dataTypes and their units are given by leading
<h:tt>tr</h:tt>
elements with the
<h:tt>type</h:tt>
attribute. This is harder to process and the column-wise approach should be used where possible if dataTypes, etc. are important
</h:p>
</h:div>
<h:div class="example" href="table1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:choice>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="array"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="rows"/>
<xsd:attributeGroup ref="columns"/>
<xsd:attributeGroup ref="units"/>
<xsd:attributeGroup ref="dataType"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.torsion" name="torsion">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
A torsion angle ("dihedral") between 4 distinct atoms.
</h:div>
<h:div class="description">
<h:p>
The atoms need not be formally bonded. It can be used for:
</h:p>
<h:ul>
<h:li>
Recording experimentally determined torsion angles (e.g. in
a crystallographic paper).
</h:li>
<h:li>
Providing the torsion component for internal coordinates (e.g.
z-matrix).
</h:li>
</h:ul>
<h:p>Note that the order of atoms is important.</h:p>
</h:div>
<h:div class="example" href="torsion1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:simpleContent>
<xsd:extension base="torsionAngleType">
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="atomRefs4"/>
<xsd:attributeGroup ref="units"/>
<xsd:attributeGroup ref="errorValue"/>
<xsd:attributeGroup ref="errorBasis"/>
<xsd:attributeGroup ref="min"/>
<xsd:attributeGroup ref="max"/>
<xsd:attributeGroup ref="ref"/>
</xsd:extension>
</xsd:simpleContent>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.transform3" name="transform3">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A transform in 3-space.</h:div>
<h:div class="description">A 3-D transform. Conventionally a 4x4 matrix.</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:simpleContent>
<xsd:extension base="matrix44Type">
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="title"/>
</xsd:extension>
</xsd:simpleContent>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.transitionState" name="transitionState">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The transition state in a reaction.</h:div>
<h:div class="description">
<h:p>
This will normally contain a
<h:tt>molecule</h:tt>
which in its 2D representation will have partial bonds. These are yet to be formalized for the
<h:tt>molecule</h:tt>
element.
</h:p>
<h:p>
Although spectators may stabilise or otherwise interact with the transitionState they are not contained within it.
</h:p>
<h:p>
A
<h:tt>propertyList</h:tt>
is provided to capture transitionState properties.
</h:p>
<h:p>Still experimental.</h:p>
</h:div>
<h:div class="example" href="transitionState1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="molecule"/>
<xsd:element minOccurs="0" ref="propertyList"/>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.unit" name="unit">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A scientific unit.</h:div>
<h:div class="description">
<h:p>
A scientific unit. Units are of the following types:
</h:p>
<h:ul>
<h:li>
SI Units. These may be one of the seven fundamental types
(e.g. meter) or may be derived (e.g. joule). An SI unit is
identifiable because it has no parentSI attribute and will have
a unitType attribute.
</h:li>
<h:li>
nonSI Units. These will normally have a parent SI unit
(e.g. calorie has joule as an SI parent).
</h:li>
<h:li/>
</h:ul>
</h:div>
<h:div class="example" href="unit1.xml"/>
<h:div class="curation">
2003:04-09 Description or parentSI attribute enhance.
</h:div>
</xsd:documentation>
<xsd:appinfo/>
</xsd:annotation>
<xsd:complexType>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="description"/>
<xsd:element ref="annotation"/>
</xsd:choice>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="abbreviation"/>
<xsd:attributeGroup ref="name"/>
<xsd:attributeGroup ref="parentSI"/>
<xsd:attributeGroup ref="unitType"/>
<xsd:attributeGroup ref="multiplierToSI"/>
<xsd:attributeGroup ref="constantToSI"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.unitList" name="unitList">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A container for several unit entries.</h:div>
<h:div class="description">
Usually forms the complete units dictionary (along with metadata).
</h:div>
<h:div class="example" href="unitList1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="unitType"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="unit"/>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="href">
<xsd:annotation>
<xsd:documentation>
<h:div class="specific">
Maps dictRef prefix to the location of a dictionary. This requires the prefix and the physical URI address to be contained within the same file. We can anticipate that better mechanisms will arise - perhaps through XMLCatalogs. At least it works at present.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:attributeGroup>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.unitType" name="unitType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The type of a scientific unit.</h:div>
<h:div class="description">
<h:p>
Mandatory for SI Units, optional for nonSI units since they should be able to obtain this from their parent. For complex derived units without parents it may be useful.
</h:p>
<h:p>Used within a unitList</h:p>
<h:p>
Distinguish carefully from
<h:a href="st.unitsType">unitsType</h:a>
which is primarily used for attributes describing the units that elements
carry
</h:p>
</h:div>
<h:div class="example" href="unitType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="alternative"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="dimension"/>
</xsd:sequence>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="name"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.vector3" name="vector3">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A vector in 3-space.</h:div>
<h:div class="description">
The vector may have magnitude but is not rooted on any points (use line3).
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:simpleContent>
<xsd:extension base="vector3Type">
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="units"/>
</xsd:extension>
</xsd:simpleContent>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.xaxis" name="xaxis">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The x-axis.</h:div>
<h:div class="description">
A container for all information relating to the x-axis (including scales, offsets, etc.) and the data themselves (in an
<h:tt>array</h:tt>
). Note: AniML uses "xValues" so avoid confusion with this.
</h:div>
<h:div class="example" href="xaxis1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="array">
<xsd:annotation>
<xsd:documentation>
<h:div>
The x-data. These must match the y-data in number and order. There are tools to allow scaling and transformation (though unscaled data must be very carefully defined).
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:element>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="multiplierToData"/>
<xsd:attributeGroup ref="constantToData"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.yaxis" name="yaxis">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The y-axis.</h:div>
<h:div class="description">
A container for all information relating to the y-axis (including scales, offsets, etc.) and the data themselves (in an
<h:tt>array</h:tt>
).
</h:div>
<h:div class="example" href="yaxis1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="array">
<xsd:annotation>
<xsd:documentation>
<h:div>
The y-data. These must match the x-data in number and order. There are tools to allow scaling and transformation (though unscaled data must be very carefully defined).
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:element>
</xsd:sequence>
<xsd:attributeGroup ref="dictRef"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="ref"/>
<xsd:attributeGroup ref="multiplierToData"/>
<xsd:attributeGroup ref="constantToData"/>
</xsd:complexType>
</xsd:element>
<xsd:element id="el.zMatrix" name="zMatrix">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A zMatrix.</h:div>
<h:div class="description">
A container for
<h:tt>length</h:tt>
,
<h:tt>angle</h:tt>
and
<h:tt>torsion</h:tt>
, which must be arranged in the conventional zMatrix format.
</h:div>
<h:div class="example" href="zMatrix1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:choice maxOccurs="unbounded" minOccurs="0">
<xsd:element ref="length"/>
<xsd:element ref="angle"/>
<xsd:element ref="torsion"/>
</xsd:choice>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
</xsd:complexType>
</xsd:element>
</xsd:schema>
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