element <bondArray> (global)

Namespace:	http://www.xml-cml.org/schema/cml2/react
Type:	anonymous complexType
Content:	complex, 8 attributes, 2 elements
Defined:	globally in cmlreact.xsd; see XML source
Includes:	definitions of 2 elements
Used:	at 1 location

XML Representation Summary

<bondArray

atomRef1	=	list of xsd:string
atomRef2	=	list of xsd:string
bondID	=	list of xsd:string
convention	=	xsd:string
dictRef	=	xsd:string
id	=	xsd:string
order	=	list of (("hbond" \| "partial01" \| "S" \| "1" \| "partial12" \| "D" \| "2" \| "partial23" \| "T" \| "3" \| "A") \| xsd:string)
title	=	xsd:string

Content:

bond+ | array*

</bondArray>

Content model elements (2):

array, bond

Included in content model of elements (1):

molecule

Known Usage Locations

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

Annotation

<h:div class="summary">A container for a number of bonds.</h:div> <h:div class="description">_bondArray_ is a child of _molecule_ and contains _bond_ information. There are two strategies: <h:ul> <h:li>Create individual <h:tt>bond</h:tt> elements under <h:tt>bondArray</h:tt> (in any order). This gives the greatest flexibility but is the most verbose.</h:li> <h:li>Create <h:tt>*Array</h:tt> attributes (e.g. of <h:tt>orderArrayType</h:tt> under <h:tt>bondArray</h:tt>. This requires all arrays to be of identical lengths with explicit values for all bonds in every array. This is NOT suitable for complexType bond children such as _bondStereo_ nor can IDs be added to bonds.. It also cannot be checked as easily by schema- and schematron validation. The _atomRef1Array_ and _atomRef2Array_ attributes are then mandatory. It is allowed (though not yet recommended) to add _*Array_ children such as _floatArray_ </h:li> </h:ul> <h:p>The attributes are directly related to the scalar attributes under _atom_ which should be consulted for more info.</h:p> </h:div> <h:div class="example" href="bondArray1.xml"> <h:p>Example - these are exactly equivalent representations</h:p> </h:div>

XML Source (see within schema source)

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

<xsd:annotation>

<xsd:documentation>

<h:div class="summary">A container for a number of bonds.</h:div>

<h:div class="description">

_bondArray_ is a child of _molecule_ and contains _bond_ information. There are two strategies:

<h:ul>

<h:li>

Create individual

<h:tt>bond</h:tt>

elements under

<h:tt>bondArray</h:tt>

(in any order). This gives the greatest flexibility but is the most verbose.

</h:li>

<h:li>

Create

<h:tt>*Array</h:tt>

attributes (e.g. of

<h:tt>orderArrayType</h:tt>

under

<h:tt>bondArray</h:tt>

. This requires all arrays to be of identical lengths with explicit values for all bonds in every array. This is NOT suitable for complexType bond children such as _bondStereo_ nor can IDs be added to bonds.. It also cannot be checked as easily by schema- and schematron validation. The _atomRef1Array_ and _atomRef2Array_ attributes are then mandatory. It is allowed (though not yet recommended) to add _*Array_ children such as _floatArray_

</h:li>

</h:ul>

<h:p>

The attributes are directly related to the scalar attributes under _atom_ which should be consulted for more info.

</h:p>

</h:div>

<h:div class="example" href="bondArray1.xml">

<h:p>

Example - these are exactly equivalent representations

</h:p>

</h:div>

</xsd:documentation>

</xsd:annotation>

<xsd:complexType>

<xsd:choice>

<xsd:element maxOccurs="unbounded" ref="bond"/>

<xsd:element maxOccurs="unbounded" minOccurs="0" ref="array"/>

</xsd:choice>

<xsd:attributeGroup ref="title"/>

<xsd:attributeGroup ref="id"/>

<xsd:attributeGroup ref="convention"/>

<xsd:attributeGroup ref="dictRef"/>

<xsd:attributeGroup ref="bondIDArray"/>

<xsd:attributeGroup ref="atomRef1Array"/>

<xsd:attributeGroup ref="atomRef2Array"/>

<xsd:attributeGroup ref="orderArray"/>

</xsd:complexType>

</xsd:element>

Attribute Detail (all declarations; 8/8)

atomRef1

Type:	atomRefArrayType
Use:	optional
Defined:	locally within atomRef1Array attributeGroup

<h:div class="summary">The first atoms in each bond.</h:div> <h:div class="description">Currently only used in bondArray in CML2 array mode.</h:div>

XML Source (see within schema source)

<xsd:attribute id="att.atomRef1Array" name="atomRef1" type="atomRefArrayType">

<xsd:annotation>

<xsd:documentation>

<h:div class="summary">The first atoms in each bond.</h:div>

<h:div class="description">

Currently only used in bondArray in CML2 array mode.

</h:div>

</xsd:documentation>

</xsd:annotation>

</xsd:attribute>

atomRef2

Type:	atomRefArrayType
Use:	optional
Defined:	locally within atomRef2Array attributeGroup

<h:div class="summary">The second atoms in each bond.</h:div> <h:div class="general">Only used in bondArray in CML2 array mode.</h:div>

XML Source (see within schema source)

<xsd:attribute id="att.atomRef2Array" name="atomRef2" type="atomRefArrayType">

<xsd:annotation>

<xsd:documentation>

<h:div class="summary">The second atoms in each bond.</h:div>

<h:div class="general">Only used in bondArray in CML2 array mode.</h:div>

</xsd:documentation>

</xsd:annotation>

</xsd:attribute>

bondID

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

<h:div class="summary">The IDs for an array of bond.</h:div> <h:div class="general">Required in CML2 array mode.</h:div>

XML Source (see within schema source)

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

<xsd:annotation>

<xsd:documentation>

<h:div class="summary">The IDs for an array of bond.</h:div>

<h:div class="general">Required in CML2 array mode.</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:	orderArrayType
Use:	optional
Defined:	locally within orderArray 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.orderArray" name="order" type="orderArrayType">

<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>

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; 2/2)

array

Type:	anonymous complexType (extension of xsd:string), simple content
Defined:	by reference within (this) bondArray element

XML Source (see within schema source)

<xsd:element maxOccurs="unbounded" minOccurs="0" ref="array"/>

bond

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

XML Source (see within schema source)

<xsd:element maxOccurs="unbounded" ref="bond"/>

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