element <bondStereo> (global)

Namespace:	http://www.xml-cml.org/schema/cml2/react
Type:	anonymous complexType (extension of stereoType)
Content:	simple, 7 attributes
Defined:	globally in cmlreact.xsd; see XML source
Used:	at 1 location

XML Representation Summary

<bondStereo

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

Content:

{ "C" | "T" | "W" | "H" | "" }

</bondStereo>

Included in content model of elements (1):

bond

Known Usage Locations

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

Annotation

<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"/>

Anonymous Type Detail

Type Derivation Tree

xsd:string (restriction)

stereoType (extension)

complexType

Derivation:

extension of stereoType

XML Source (see within schema source)

<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>

Attribute Detail (all declarations; 7/7)

atomRefArray

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

<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>

XML Source (see within schema source)

<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>

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>

conventionValue

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

<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>

XML Source (see within schema source)

<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>

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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