element <bond> (global)

Namespace:	http://www.xml-cml.org/schema/cml2/react
Type:	anonymous complexType
Content:	complex, 9 attributes, 3 elements
Defined:	globally in cmlreact.xsd; see XML source
Includes:	definitions of 3 elements
Used:	at 4 locations

XML Representation Summary

<bond

atomRefs	=	list of xsd:string
atomRefs2	=	list of xsd:string
bondRefs	=	list of xsd:string
convention	=	xsd:string
dictRef	=	xsd:string
id	=	xsd:string
order	=	(("hbond" \| "partial01" \| "S" \| "1" \| "partial12" \| "D" \| "2" \| "partial23" \| "T" \| "3" \| "A") \| xsd:string)
ref	=	xsd:string
title	=	xsd:string

Content:

(bondType | electron | bondStereo)*

</bond>

Content model elements (3):

bondStereo, bondType, electron

Included in content model of elements (4):

bondArray, bondType, peak, peakGroup

Known Usage Locations

Within anonymous complexTypes of elements (4):
bondArray [ref], bondType [ref], peak [ref], peakGroup [ref]

Annotation

Annotation 1 [src]:

<h:div class="summary">A bond between atoms, or between atoms and bonds.</h:div> <h:div class="description">_bond_ is a child of _bondArray_ and contains bond information. Bond must refer to at least two atoms (normally using _atomRefs2_) but may also refer to more for multicentre bonds. Bond is often EMPTY but may contain _electron_, _length_ or _bondStereo_ elements.</h:div> <h:div class="example" href="bond1.xml"/>

Annotation 2 [src]:

<h:div class="validation" href="cmlCore.val.bond.xml"/>

XML Source (see within schema source)

<xsd:element id="el.bond" name="bond">

<xsd:annotation>

<xsd:documentation>

<h:div class="summary">A bond between atoms, or between atoms and bonds.</h:div>

<h:div class="description">

_bond_ is a child of _bondArray_ and contains bond information. Bond must refer to at least two atoms (normally using _atomRefs2_) but may also refer to more for multicentre bonds. Bond is often EMPTY but may contain _electron_, _length_ or _bondStereo_ elements.

</h:div>

<h:div class="example" href="bond1.xml"/>

</xsd:documentation>

<xsd:documentation>

<h:div class="validation" href="cmlCore.val.bond.xml"/>

</xsd:documentation>

<xsd:appinfo>

Validate Bonds

</comment>

<comment>Are atoms distinct?</comment>

<call-template name="error">

<with-param name="error">

BOND (

<value-of select="@id"/>

): ATOMS not distinct:

<value-of select="$at1"/>

</with-param>

</call-template>

</if>

<comment>Do both atoms exist in current molecule context?</comment>

<call-template name="error">

<with-param name="error">

BOND (

<value-of select="@id"/>

): ATOMREF not found:

<value-of select="$at1"/>

</with-param>

</call-template>

</if>

<call-template name="error">

<with-param name="error">

BOND (

<value-of select="@id"/>

): ATOMREF not found:

<value-of select="$at2"/>

</with-param>

</call-template>

</if>

</template>

</xsd:appinfo>

</xsd:annotation>

<xsd:complexType id="bond.content.id">

<xsd:choice>

<xsd:choice maxOccurs="unbounded" minOccurs="0">

<xsd:element ref="bondType"/>

<xsd:element ref="electron">

<xsd:annotation>

<xsd:documentation>

<h:div class="summary">One or more electrons associated with the bond.</h:div>

<h:div class="description">

The _bondRef_ on the _electron_ should point to the id on the bond. We may relax this later and allow reference by context.

</h:div>

</xsd:documentation>

</xsd:annotation>

</xsd:element>

<xsd:element ref="bondStereo">

<xsd:annotation>

<xsd:documentation>

<h:div class="summary">The stereo convention for the bond.</h:div>

<h:div class="general">only one convention allowed.</h:div>

</xsd:documentation>

</xsd:annotation>

</xsd:element>

</xsd:choice>

<xsd:attributeGroup ref="title"/>

<xsd:attributeGroup ref="id"/>

<xsd:attributeGroup ref="convention"/>

<xsd:attributeGroup ref="dictRef"/>

<xsd:attributeGroup ref="ref"/>

<xsd:attributeGroup ref="atomRefs2"/>

<xsd:attributeGroup ref="atomRefs">

<xsd:annotation>

<xsd:documentation>

<h:div class="specific">

This is designed for multicentre bonds (as in delocalised systems or electron-deficient centres. The semantics are experimental at this stage. As an example, a B-H-B bond might be described as
<bond atomRefs="b1 h2 b2"/.

</h:div>

</xsd:documentation>

</xsd:annotation>

</xsd:attributeGroup>

<xsd:attributeGroup ref="bondRefs">

<xsd:annotation>

<xsd:documentation>

<h:div class="specific">

This is designed for pi-bonds and other systems where formal valence bonds are not drawn to atoms. The semantics are experimental at this stage. As an example, a Pt-|| bond (as the Pt-ethene bond in Zeise's salt) might be described as <bond atomRefs="pt1" bondRefs="b32"/.

</h:div>

</xsd:documentation>

</xsd:annotation>

</xsd:attributeGroup>

<xsd:attributeGroup ref="order"/>

</xsd:complexType>

</xsd:element>

Attribute Detail (all declarations; 9/9)

atomRefs

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

<h:div class="summary">A reference to a list of atoms.</h:div> <h:div class="description">Used by bonds, electrons, atomSets, etc.</h:div>

XML Source (see within schema source)

<xsd:attribute id="att.atomRefs" name="atomRefs" type="atomRefArrayType">

<xsd:annotation>

<xsd:documentation>

<h:div class="summary">A reference to a list of atoms.</h:div>

<h:div class="description">Used by bonds, electrons, atomSets, etc.</h:div>

</xsd:documentation>

</xsd:annotation>

</xsd:attribute>

atomRefs2

Type:	atomRefs2Type
Use:	optional
Defined:	locally within atomRefs2 attributeGroup

<h:div class="summary">References to two different atoms.</h:div> <h:div class="description">Available for any reference to atoms but normally will be the normal reference attribute on the bond element. The order of atoms is preserved and may matter for some conventions (e.g. wedge/hatch or donor bonds.</h:div>

XML Source (see within schema source)

<xsd:attribute id="att.atomRefs2" name="atomRefs2" type="atomRefs2Type">

<xsd:annotation>

<xsd:documentation>

<h:div class="summary">References to two different atoms.</h:div>

<h:div class="description">

Available for any reference to atoms but normally will be the normal reference attribute on the bond element. The order of atoms is preserved and may matter for some conventions (e.g. wedge/hatch or donor bonds.

</h:div>

</xsd:documentation>

</xsd:annotation>

</xsd:attribute>

bondRefs

Type:	bondRefArrayType
Use:	optional
Defined:	locally within bondRefs attributeGroup

<h:div class="summary">A reference to a list of bonds.</h:div> <h:div class="description">Used by electrons, bondSets, etc.</h:div>

XML Source (see within schema source)

<xsd:attribute id="att.bondRefs" name="bondRefs" type="bondRefArrayType">

<xsd:annotation>

<xsd:documentation>

<h:div class="summary">A reference to a list of bonds.</h:div>

<h:div class="description">Used by electrons, bondSets, etc.</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>

order

Type:	orderType
Use:	optional
Defined:	locally within order attributeGroup

<h:div class="summary">The order of the bond.</h:div> <h:div class="description">There is NO default. This order is for bookkeeping only and is not related to length, QM calculations or other experimental or theoretical calculations.</h:div>

XML Source (see within schema source)

<xsd:attribute id="att.order" name="order" type="orderType">

<xsd:annotation>

<xsd:documentation>

<h:div class="summary">The order of the bond.</h:div>

<h:div class="description">

There is NO default. This order is for bookkeeping only and is not related to length, QM calculations or other experimental or theoretical calculations.

</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>

Content Element Detail (all declarations; 3/3)

bondStereo

Type:	anonymous complexType (extension of stereoType), simple content
Defined:	by reference within (this) bond element

<h:div class="summary">The stereo convention for the bond.</h:div> <h:div class="general">only one convention allowed.</h:div>

XML Source (see within schema source)

<xsd:element ref="bondStereo">

<xsd:annotation>

<xsd:documentation>

<h:div class="summary">The stereo convention for the bond.</h:div>

<h:div class="general">only one convention allowed.</h:div>

</xsd:documentation>

</xsd:annotation>

</xsd:element>

bondType

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

XML Source (see within schema source)

<xsd:element ref="bondType"/>

electron

Type:	anonymous complexType, empty content
Defined:	by reference within (this) bond element

<h:div class="summary">One or more electrons associated with the bond.</h:div> <h:div class="description">The _bondRef_ on the _electron_ should point to the id on the bond. We may relax this later and allow reference by context.</h:div>

XML Source (see within schema source)

<xsd:element ref="electron">

<xsd:annotation>

<xsd:documentation>

<h:div class="summary">One or more electrons associated with the bond.</h:div>

<h:div class="description">

The _bondRef_ on the _electron_ should point to the id on the bond. We may relax this later and allow reference by context.

</h:div>

</xsd:documentation>

</xsd:annotation>

</xsd:element>

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