Documentation for Chemical Markup Language (CML)
Definition Type: Element
Name: atomArray
Namespace: http://www.xml-cml.org/schema
Containing Schema: schema.xsd
Abstract
Documentation:
A container for a list of atoms. A child of _molecule_ and contains _atom_ information. There are two strategies: Create individual _atom_ elements under _atomArray_ (in any order). This gives the greatest flexibility but is the most verbose. Create *Array attributes (e.g. of _elementTypeArrayType_ under _atomArray_. This requires all arrays to be of identical lengths with explicit values for all atoms in every array. This is NOT suitable for complexType atom children such as _atomParity_. It also cannot be checked as easily by schema- and schematron validation. The _atomIDArray_ attribute is mandatory. It is allowed (though not yet recommended) to add _*Array_ children such as _floatArray_ The attributes are directly related to the scalar attributes under _atom_ which should be consulted for more info. Example - these are exactly equivalent representations
Collapse XSD Schema Diagram:
Drilldown into array in schema schema_xsd Drilldown into atom in schema schema_xsd Drilldown into atomID in schema schema_xsd Drilldown into atomIDArray in schema schema_xsd Drilldown into zFract in schema schema_xsd Drilldown into zFractArray in schema schema_xsd Drilldown into yFract in schema schema_xsd Drilldown into yFractArray in schema schema_xsd Drilldown into xFract in schema schema_xsd Drilldown into xFractArray in schema schema_xsd Drilldown into z3 in schema schema_xsd Drilldown into z3Array in schema schema_xsd Drilldown into y3 in schema schema_xsd Drilldown into y3Array in schema schema_xsd Drilldown into x3 in schema schema_xsd Drilldown into x3Array in schema schema_xsd Drilldown into y2 in schema schema_xsd Drilldown into y2Array in schema schema_xsd Drilldown into x2 in schema schema_xsd Drilldown into x2Array in schema schema_xsd Drilldown into occupancy in schema schema_xsd Drilldown into occupancyArray in schema schema_xsd Drilldown into hydrogenCount in schema schema_xsd Drilldown into hydrogenCountArray in schema schema_xsd Drilldown into formalCharge in schema schema_xsd Drilldown into formalChargeArray in schema schema_xsd Drilldown into count in schema schema_xsd Drilldown into countArray in schema schema_xsd Drilldown into elementType in schema schema_xsd Drilldown into elementTypeArray in schema schema_xsd Drilldown into ref in schema schema_xsd Drilldown into ref in schema schema_xsd Drilldown into dictRef in schema schema_xsd Drilldown into dictRef in schema schema_xsd Drilldown into convention in schema schema_xsd Drilldown into convention in schema schema_xsd Drilldown into id in schema schema_xsd Drilldown into id in schema schema_xsd Drilldown into title in schema schema_xsd Drilldown into title in schema schema_xsdXSD Diagram of atomArray in schema schema_xsd (Chemical Markup Language (CML))
Collapse XSD Schema Code: 
<xsd:element name="atomArray" id="el.atomArray">
    <xsd:annotation>
        <xsd:documentation>
            <h:div class="summary" xmlns:h="http://www.w3.org/1999/xhtml">A container for a list of atoms.</h:div>
            <h:div class="description" xmlns:h="http://www.w3.org/1999/xhtml">A child of _molecule_ and contains _atom_ information. There are two strategies:
        <h:ul><h:li>Create individual _atom_ elements under _atomArray_ (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 _elementTypeArrayType_ under _atomArray_. This requires all arrays to be of identical lengths with explicit values for all atoms in every array. This is NOT suitable for complexType atom children such as _atomParity_. It also cannot be checked as easily by schema- and schematron validation. The _atomIDArray_ attribute is mandatory. It is allowed (though not yet recommended) to add _*Array_ children such as _floatArray_
                    </h:li>
                </h:ul>
                The attributes are directly related to the scalar attributes under _atom_ which should be consulted for more info.</h:div>
            <h:div class="example" href="atomArray1.xml" xmlns:h="http://www.w3.org/1999/xhtml">
                <h:p>Example - these are exactly equivalent representations</h:p>
            </h:div>
        </xsd:documentation>
    </xsd:annotation>
    <xsd:complexType>
        <xsd:sequence>
            <xsd:element ref="atom" minOccurs="0" maxOccurs="unbounded" />
            <xsd:element ref="array" minOccurs="0" maxOccurs="unbounded" />
        </xsd:sequence>
        <xsd:attributeGroup ref="title" />
        <xsd:attributeGroup ref="id" />
        <xsd:attributeGroup ref="convention" />
        <xsd:attributeGroup ref="dictRef" />
        <xsd:attributeGroup ref="ref" />
        <xsd:attributeGroup ref="elementTypeArray" />
        <xsd:attributeGroup ref="countArray" />
        <xsd:attributeGroup ref="formalChargeArray" />
        <xsd:attributeGroup ref="hydrogenCountArray" />
        <xsd:attributeGroup ref="occupancyArray" />
        <xsd:attributeGroup ref="x2Array" />
        <xsd:attributeGroup ref="y2Array" />
        <xsd:attributeGroup ref="x3Array" />
        <xsd:attributeGroup ref="y3Array" />
        <xsd:attributeGroup ref="z3Array" />
        <xsd:attributeGroup ref="xFractArray" />
        <xsd:attributeGroup ref="yFractArray" />
        <xsd:attributeGroup ref="zFractArray" />
        <xsd:attributeGroup ref="atomIDArray" />
    </xsd:complexType>
</xsd:element>
Collapse Child Elements:
Name Type Min Occurs Max Occurs
atom nsA:atom 0 unbounded
array nsA:array 0 unbounded
Collapse Child Attributes:
Name Type Default Value Use
title nsA:title (Optional)
id nsA:id (Optional)
convention nsA:convention (Optional)
dictRef nsA:dictRef (Optional)
ref nsA:ref (Optional)
elementType nsA:elementType (Optional)
count nsA:count (Optional)
formalCharge nsA:formalCharge (Optional)
hydrogenCount nsA:hydrogenCount (Optional)
occupancy nsA:occupancy (Optional)
x2 nsA:x2 (Optional)
y2 nsA:y2 (Optional)
x3 nsA:x3 (Optional)
y3 nsA:y3 (Optional)
z3 nsA:z3 (Optional)
xFract nsA:xFract (Optional)
yFract nsA:yFract (Optional)
zFract nsA:zFract (Optional)
atomID nsA:atomID (Optional)
Documentation for Chemical Markup Language (CML)

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