element <atomArray> (global)

Namespace:	http://www.xml-cml.org/schema/cml2/react
Type:	anonymous complexType
Content:	complex, 19 attributes, 1 element
Defined:	globally in cmlreact.xsd; see XML source
Includes:	definition of 1 element
Used:	at 2 locations

XML Representation Summary

<atomArray

atomID	=	list of xsd:string
convention	=	xsd:string
countArray	=	list of xsd:nonNegativeInteger
dictRef	=	xsd:string
elementType	=	list of (("Ac" \| "Al" \| "Ag" \| "Am" \| "Ar" \| "As" \| "At" \| "Au" \| "B" \| "Ba" \| "Bh" \| "Bi" \| "Be" \| "Bk" \| "Br" \| "C" \| "Ca" \| "Cd" \| "Ce" \| "Cf" \| "Cl" \| "Cm" \| "Co" \| "Cr" \| "Cs" \| "Cu" \| "Db" \| "Dy" \| "Er" \| "Es" \| "Eu" \| "F" \| "Fe" \| "Fm" \| "Fr" \| "Ga" \| "Gd" \| "Ge" \| "H" \| "He" \| "Hf" \| "Hg" \| "Ho" \| "Hs" \| "I" \| "In" \| "Ir" \| "K" \| "Kr" \| "La" \| "Li" \| "Lr" \| "Lu" \| "Md" \| "Mg" \| "Mn" \| "Mo" \| "Mt" \| "N" \| "Na" \| "Nb" \| "Nd" \| "Ne" \| "Ni" \| "No" \| "Np" \| "O" \| "Os" \| "P" \| "Pa" \| "Pb" \| "Pd" \| "Pm" \| "Po" \| "Pr" \| "Pt" \| "Pu" \| "Ra" \| "Rb" \| "Re" \| "Rf" \| "Rh" \| "Rn" \| "Ru" \| "S" \| "Sb" \| "Sc" \| "Se" \| "Sg" \| "Si" \| "Sm" \| "Sn" \| "Sr" \| "Ta" \| "Tb" \| "Tc" \| "Te" \| "Th" \| "Ti" \| "Tl" \| "Tm" \| "U" \| "Uun" \| "Uuu" \| "Uub" \| "Uut" \| "Uuq" \| "Uup" \| "Uuh" \| "Uus" \| "Uuo" \| "V" \| "W" \| "Xe" \| "Y" \| "Yb" \| "Zn" \| "Zr" \| "Dummy" \| "Du" \| "R") \| xsd:string)
formalCharge	=	list of xsd:integer
hydrogenCount	=	list of xsd:nonNegativeInteger
id	=	xsd:string
occupancy	=	list of xsd:float
ref	=	xsd:string
title	=	xsd:string
x2	=	list of xsd:float
x3	=	list of xsd:float
xFract	=	list of xsd:float
y2	=	list of xsd:float
y3	=	list of xsd:float
yFract	=	list of xsd:float
z3	=	list of xsd:float
zFract	=	list of xsd:float

Content:

atom*

</atomArray>

Content model elements (1):

atom

Included in content model of elements (2):

formula, molecule

Known Usage Locations

Within anonymous complexTypes of elements (2):
formula [ref], molecule [ref]

Annotation

<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>

XML Source (see within schema source)

<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>

Attribute Detail (all declarations; 19/19)

atomID

Type:	atomRefArrayType
Use:	optional
Defined:	locally within atomIDArray attributeGroup

<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>

XML Source (see within schema source)

<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>

convention

Type:	namespaceRefType
Use:	optional
Defined:	locally within convention attributeGroup

<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"/>

XML Source (see within schema source)

<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>

countArray

Type:	countArrayType
Use:	optional
Defined:	locally within countArray attributeGroup

<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>

XML Source (see within schema source)

<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>

dictRef

Type:	namespaceRefType
Use:	optional
Defined:	locally within dictRef attributeGroup

<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"/>

XML Source (see within schema source)

<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>

elementType

Type:	elementTypeArrayType
Use:	optional
Defined:	locally within elementTypeArray attributeGroup

<h:div class="summary">The identity of a chemical element.</h:div> <h:div class="description">Normally mandatory on _atom_, _isotope_, etc.</h:div>

XML Source (see within schema source)

<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>

formalCharge

Type:	formalChargeArrayType
Use:	optional
Defined:	locally within formalChargeArray attributeGroup

<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>

XML Source (see within schema source)

<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>

hydrogenCount

Type:	hydrogenCountArrayType
Use:	optional
Defined:	locally within hydrogenCountArray attributeGroup

<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>

XML Source (see within schema source)

<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>

Type:	idType
Use:	optional
Defined:	locally within id attributeGroup

<h:div class="summary">An attribute providing a unique ID for an element.</h:div> <h:div class="description"/>

XML Source (see within schema source)

<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>

occupancy

Type:	occupancyArrayType
Use:	optional
Defined:	locally within occupancyArray attributeGroup

<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>

XML Source (see within schema source)

<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>

ref

Type:	refType
Use:	optional
Defined:	locally within ref attributeGroup

<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/> 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"/>

XML Source (see within schema source)

<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.

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>

title

Type:	xsd:string, predefined
Use:	optional
Defined:	locally within title attributeGroup

<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"/>

XML Source (see within schema source)

<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>

Type:	coordinateComponentArrayType
Use:	optional
Defined:	locally within x2Array attributeGroup

<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>

XML Source (see within schema source)

<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>

Type:	coordinateComponentArrayType
Use:	optional
Defined:	locally within x3Array attributeGroup

<h:div class="summary">An array of x3 coordinate.</h:div> <h:div class="summary">Normally used in CML2 array mode.</h:div>

XML Source (see within schema source)

<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>

xFract

Type:	coordinateComponentArrayType
Use:	optional
Defined:	locally within xFractArray attributeGroup

<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>

XML Source (see within schema source)

<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>

Type:	coordinateComponentArrayType
Use:	optional
Defined:	locally within y2Array attributeGroup

<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>

XML Source (see within schema source)

<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">

</h:div>

</xsd:documentation>

</xsd:annotation>

</xsd:attribute>

Type:	coordinateComponentArrayType
Use:	optional
Defined:	locally within y3Array attributeGroup

<h:div class="summary">An array of y3 coordinate.</h:div> <h:div class="summary">Normally used in CML2 array mode.</h:div>

XML Source (see within schema source)

<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>

yFract

Type:	coordinateComponentArrayType
Use:	optional
Defined:	locally within yFractArray attributeGroup

<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>

XML Source (see within schema source)

<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>

Type:	coordinateComponentArrayType
Use:	optional
Defined:	locally within z3Array attributeGroup

<h:div class="summary">An array of z3 coordinate.</h:div> <h:div class="summary">Normally used in CML2 array mode.</h:div>

XML Source (see within schema source)

<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>

zFract

Type:	coordinateComponentArrayType
Use:	optional
Defined:	locally within zFractArray attributeGroup

<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>

XML Source (see within schema source)

<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>

Content Element Detail (all declarations; 1/1)

atom

Type:	anonymous complexType, complex content
Defined:	by reference within (this) atomArray element

XML Source (see within schema source)

<xsd:element maxOccurs="unbounded" minOccurs="0" ref="atom"/>

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