CML element bondStereo

Type Heirarchy
{http://www.w3.org/2001/XMLSchema}string (by restriction) {http://www.xml-cml.org/schema/cml2/core}stereoType (by extension) {http://www.xml-cml.org/schema/cml2/core}bondStereo

Abstract	false (This can be used in an instance)
Nillable	false (Instance values cannot use xsi:nil)
Target Namespace	http://www.xml-cml.org/schema/cml2/core
Declared Namespaces	xmlns:val=http://www.w3.org/1999/XSL/TransformX xmlns:stm=http://www.xml-cml.org/schema/stmml xmlns:xsd=http://www.w3.org/2001/XMLSchema xmlns:xlink=http://www.w3.org/1999/xlink xmlns:cml=http://www.xml-cml.org/schema/cml2/core xmlns=http://www.xml-cml.org/schema/cml2/core

<xsd:element name="bondStereo" id="el.bondStereo">
    <xsd:annotation>
        <xsd:documentation>
            <div class="summary">
A container supporting "cis/trans", "wedge hatch"
and other stereochemistry.
            </div>
            <div class="description">
                <p>
An explict
list of atomRefs must be given, or it must be a child of
                    <tt>bond</tt>
.
There are no implicit conventions
such as E/Z. This will be extended to other types
of stereochemistry.
                </p>
                <p>At present the following are supported:</p>
                <ul>
                    <li>No atomRefs attribute.
                        <b>Deprecated, but probably unavoidable</b>
.
This must be a child of
                        <tt>bond</tt>
where it picks up the two atomRefs
in the
                        <tt>atomRefs2</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
                        <tt>atomParity</tt>
wherever possible. Note that W/H makes
no sense without 2D atom coordinates.
                    </li>
                    <li>
                        <b>atomRefs4 attribute</b>
. The 4 atoms represent a cis or trans configuration.
This may or may not be a child of
                        <tt>bond</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
                        <tt>bondStereo</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
                        <tt>bondStereo</tt>
referring to the same ordered
4-atom list
                    </li>
                    <li>
                        <b>atomRefs attribute</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
                        <i>cis-</i>
,
                        <i>mer-</i>
, etc.
</li>
                </ul>
                <p>the
                    <tt>atomRefs</tt>
and
                    <tt>atomRefs4</tt>
attributes cannot be used
simultaneously.
                </p>
            </div>
            <div class="example">
                <pre>
<cml title="bondArray example">
<bondArray>
<bond id="b1" atomRefs2="a3 a8" order="D">
<electron bondRef="b1"/>
<bondStereo>C</bondStereo>
</bond>
<bond id="b2" atomRefs2="a3 a8" order="S">
<bondStereo convention="MDL" conventionValue="6"/>
</bond>
</bondArray>
</cml>
                </pre>
            </div>
        </xsd:documentation>
    </xsd:annotation>
    <xsd:complexType>
        <xsd:simpleContent>
            <xsd:extension base="stereoType">
                <xsd:attributeGroup ref="atomRefs4"/>
                <xsd:attributeGroup ref="atomRefArray"/>
                <xsd:attributeGroup ref="tit_id_conv_dictGroup"/>
                <xsd:attribute name="conventionValue" type="xsd:string">
                    <xsd:annotation>
                        <xsd:documentation>
                            <div class="summary">The stereo value when the
                                <tt>convention</tt>
attribute is used.
</div>
                            <div class="description">
When convention is used this attribute must be present
and element content must be empty.
                            </div>
                        </xsd:documentation>
                    </xsd:annotation>
                </xsd:attribute>
            </xsd:extension>
        </xsd:simpleContent>
    </xsd:complexType>
</xsd:element>

An explict list of atomRefs must be given, or it must be a child of bond. There are no implicit conventions such as E/Z. This will be extended to other types of stereochemistry.

At present the following are supported:

No atomRefs attribute. Deprecated, but probably unavoidable. This must be a child of bond where it picks up the two atomRefs in the atomRefs2 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 atomParity wherever possible. Note that W/H makes no sense without 2D atom coordinates.
atomRefs4 attribute. The 4 atoms represent a cis or trans configuration. This may or may not be a child of bond; 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 bondStereo not related to bonds is less clear (e.g. cumulenes, substituted ring nuclei) etc.It is currently an error to have more than one bondStereo referring to the same ordered 4-atom list
atomRefs attribute. 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 cis-, mer-, etc.

the atomRefs and atomRefs4 attributes cannot be used simultaneously.

element {http://www.xml-cml.org/schema/cml2/core}bondStereo

Source

Documentation