element <atomParity> (global)

Namespace:	http://www.xml-cml.org/schema/cml2/react
Type:	anonymous complexType (extension of xsd:float)
Content:	simple, 5 attributes
Defined:	globally in cmlreact.xsd; see XML source
Used:	at 1 location

XML Representation Summary

<atomParity

atomRefs4	=	list of xsd:string
convention	=	xsd:string
dictRef	=	xsd:string
id	=	xsd:string
title	=	xsd:string

Content:

{ xsd:float }

</atomParity>

Included in content model of elements (1):

atom

Known Usage Locations

Within anonymous complexTypes of elements (1):
atom [ref]

Annotation

<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"/>

Anonymous Type Detail

Type Derivation Tree

xsd:float (extension)

complexType

Derivation:

extension of xsd:float

XML Source (see within schema source)

<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>

</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>

Attribute Detail (all declarations; 5/5)

atomRefs4

Type:	atomRefs4Type
Use:	optional
Defined:	locally within atomRefs4 attributeGroup

<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>

XML Source (see within schema source)

<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>

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>

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>

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>

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>

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