element <matrix> (global)
Namespace:
Type:
anonymous complexType (extension of xsd:string)
Content:
simple, 14 attributes
Defined:
globally in cmlreact.xsd; see XML source
Used:
at 11 locations
XML Representation Summary
<matrix
   
 = 
xsd:nonNegativeInteger
 = 
xsd:string
 = 
(("xsd:string" | "xsd:boolean" | "xsd:float" | "xsd:double" | "xsd:decimal" | "xsd:duration" | "xsd:dateTime" | "xsd:time" | "xsd:date" | "xsd:gYearMonth" | "xsd:gYear" | "xsd:gMonthDay" | "xsd:gDay" | "xsd:gMonth" | "xsd:hexBinary" | "xsd:base64Binary" | "xsd:anyURI" | "xsd:QName" | "xsd:NOTATION" | "xsd:normalizedString" | "xsd:token" | "xsd:language" | "xsd:IDREFS" | "xsd:ENTITIES" | "xsd:NMTOKEN" | "xsd:NMTOKENS" | "xsd:Name" | "xsd:NCName" | "xsd:ID" | "xsd:IDREF" | "xsd:ENTITY" | "xsd:integer" | "xsd:nonPositiveInteger" | "xsd:negativeInteger" | "xsd:long" | "xsd:int" | "xsd:short" | "xsd:byte" | "xsd:nonNegativeInteger" | "xsd:unsignedLong" | "xsd:unsignedInt" | "xsd:unsignedShort" | "xsd:unsignedByte" | "xsd:positiveInteger") | xsd:string)
 = 
xsd:string
 = 
xsd:string
 = 
(("observedRange" | "observedStandardDeviation" | "observedStandardError" | "estimatedStandardDeviation" | "estimatedStandardError") | xsd:string)
 = 
list of xsd:float
 = 
xsd:string
 = 
(("rectangular" | "square" | "squareSymmetric" | "squareSymmetricLT" | "squareSymmetricUT" | "squareAntisymmetric" | "squareAntisymmetricLT" | "squareAntisymmetricUT" | "diagonal" | "upperTriangular" | "upperTriangularUT" | "lowerTriangular" | "lowerTriangularLT" | "unit" | "unitary" | "rowEigenvectors" | "rotation22" | "rotationTranslation32" | "homogeneous33" | "rotation33" | "rotationTranslation43" | "homogeneous44") | xsd:string)
 = 
list of xsd:float
 = 
list of xsd:float
 = 
xsd:nonNegativeInteger
 = 
xsd:string
 = 
xsd:string
    >
   
Content: 
{ xsd:string }
</matrix>
Included in content model of elements (11):
arg, atom, atomType, bondType, eigen, gradient, lattice, molecule, parameter, property, symmetry
Known Usage Locations
Annotation
<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"/>
Anonymous Type Detail
Type Derivation Tree
xsd:string (extension)
  complexType
Derivation:
extension of xsd:string
XML Source (see within schema source)
<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>
Attribute Detail (all declarations; 14/14)
columns
Type:
Use:
optional
Defined:
locally within columns attributeGroup
<h:div class="summary">Number of columns.</h:div>
XML Source (see within schema source)
<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>

convention
Type:
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>

dataType
Type:
Use:
optional
Defined:
locally within dataType attributeGroup
<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>
XML Source (see within schema source)
<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>

delimiter
Type:
Use:
optional
Defined:
locally within delimiter attributeGroup
<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: <array delimiter="/" dictRef="pdb:atomTypes">/ N/ CA/CA/ N/</array> </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>
XML Source (see within schema source)
<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>

dictRef
Type:
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>

errorBasis
Type:
Use:
optional
Defined:
locally within errorBasis attributeGroup
<h:div class="summary">Basis of the error estimate.</h:div> <h:div class="description"/>
XML Source (see within schema source)
<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>

errorValueArray
Type:
Use:
optional
Defined:
locally within errorValueArray attributeGroup
<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>
XML Source (see within schema source)
<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>

id
Type:
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>

matrixType
Type:
Use:
optional
Defined:
locally within matrixType attributeGroup
<h:div class="summary">Type of matrix.</h:div> <h:div class="description">Mainly square, but extensible through the _xsd:union_ mechanis.</h:div>
XML Source (see within schema source)
<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>

maxValueArray
Type:
Use:
optional
Defined:
locally within maxValueArray attributeGroup
<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>
XML Source (see within schema source)
<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>

minValueArray
Type:
Use:
optional
Defined:
locally within minValueArray attributeGroup
<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>
XML Source (see within schema source)
<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>

rows
Type:
Use:
optional
Defined:
locally within rows attributeGroup
<h:div class="summary">Number of rows.</h:div>
XML Source (see within schema source)
<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>

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>

units
Type:
Use:
optional
Defined:
locally within units attributeGroup
<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>
XML Source (see within schema source)
<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>

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