element <atomType> (global)

Namespace:	http://www.xml-cml.org/schema/cml2/react
Type:	anonymous complexType
Content:	complex, 7 attributes, 7 elements
Defined:	globally in cmlreact.xsd; see XML source
Includes:	definitions of 7 elements
Used:	at 2 locations

XML Representation Summary

<atomType

atomRef	=	xsd:string
convention	=	xsd:string
dictRef	=	xsd:string
id	=	xsd:string
name	=	xsd:string
ref	=	xsd:string
title	=	xsd:string

Content:

</atomType>

Content model elements (7):

array, atom, label, matrix, molecule, property, scalar

Included in content model of elements (2):

atom, atomTypeList

Known Usage Locations

Within anonymous complexTypes of elements (2):
atom [ref], atomTypeList [ref]

Annotation

<h:div class="summary">An atomType.</h:div> <h:div class="description"> <h:p>atomTypes are used in a wide variety of ways in computational chemistry. They are normally labels added to existing atoms (or dummy atoms) in the molecule and have a number of defined properties. These properties are usually in addition to those deducible from the elementType of the atom. AtomTypes usually depend on the chemical or geometrical environment of the atom and are frequently assigned by algorithms with chemical perception. However they are often frequently set or "tweaked" by humans initiating a program run.</h:p> <h:p>AtomTypes on an atom have no formal relation to its <h:tt>elementType</h:tt>, which only describe the number of protons in the nucleus. It is not unknown (though potentially misleading) to use an "incompatible" atomType to alter the computational properties of an atom (e.g. pretend this K+ is a Ca++ to increase its effective charge). <h:tt>atomTypes</h:tt> will also be required to describe pseudoAtoms such as "halogen" (generic) or "methyl group" (unified atom). Atoms in computations can therefore have an <h:tt>atomTypeRef</h:tt> attribute.</h:p> <h:p>An atomType contains numeric or other quantities associated with it (charges, masses, use in force-fields, etc.) and also description of any perception algorithms (chemical and/or geometrical) which could be used to compute or constrain it. This is still experimental.</h:p> <h:p>atomTypes are referred to by their mandatory <h:tt>name</h:tt> attribute. An atom referes to one or more atomTypes through atomType/@ref children</h:p> </h:div> <h:div class="example" href="atomType1.xml"/> <h:div class="note">examples not yet teste.</h:div>

XML Source (see within schema source)

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

<xsd:annotation>

<xsd:documentation>

<h:div class="summary">An atomType.</h:div>

<h:div class="description">

<h:p>

atomTypes are used in a wide variety of ways in computational chemistry. They are normally labels added to existing atoms (or dummy atoms) in the molecule and have a number of defined properties. These properties are usually in addition to those deducible from the elementType of the atom. AtomTypes usually depend on the chemical or geometrical environment of the atom and are frequently assigned by algorithms with chemical perception. However they are often frequently set or "tweaked" by humans initiating a program run.

</h:p>

<h:p>

AtomTypes on an atom have no formal relation to its

<h:tt>elementType</h:tt>

, which only describe the number of protons in the nucleus. It is not unknown (though potentially misleading) to use an "incompatible" atomType to alter the computational properties of an atom (e.g. pretend this K+ is a Ca++ to increase its effective charge).

<h:tt>atomTypes</h:tt>

will also be required to describe pseudoAtoms such as "halogen" (generic) or "methyl group" (unified atom). Atoms in computations can therefore have an

<h:tt>atomTypeRef</h:tt>

attribute.

</h:p>

<h:p>

An atomType contains numeric or other quantities associated with it (charges, masses, use in force-fields, etc.) and also description of any perception algorithms (chemical and/or geometrical) which could be used to compute or constrain it. This is still experimental.

</h:p>

<h:p>

atomTypes are referred to by their mandatory

<h:tt>name</h:tt>

attribute. An atom referes to one or more atomTypes through atomType/@ref children

</h:p>

</h:div>

<h:div class="example" href="atomType1.xml"/>

<h:div class="note">examples not yet teste.</h:div>

</xsd:documentation>

</xsd:annotation>

<xsd:complexType>

<xsd:sequence>

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

<xsd:element ref="molecule"/>

<xsd:element ref="atom"/>

<xsd:element ref="label"/>

</xsd:choice>

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

<xsd:element ref="scalar"/>

<xsd:element ref="array"/>

<xsd:element ref="matrix"/>

<xsd:element ref="property"/>

</xsd:choice>

</xsd:sequence>

<xsd:attributeGroup ref="name">

<xsd:annotation>

<xsd:documentation>

<h:div class="specific">

The name will usually be namespaced as 'gulp:si', 'tripos:c.3', etc. It must occur except for atomType/@re.

</h:div>

</xsd:documentation>

</xsd:annotation>

</xsd:attributeGroup>

<xsd:attributeGroup ref="ref"/>

<xsd:attributeGroup ref="atomRef"/>

<xsd:attributeGroup ref="title"/>

<xsd:attributeGroup ref="id"/>

<xsd:attributeGroup ref="convention"/>

<xsd:attributeGroup ref="dictRef"/>

</xsd:complexType>

</xsd:element>

Attribute Detail (all declarations; 7/7)

atomRef

Type:	atomRefType
Use:	optional
Defined:	locally within atomRef attributeGroup

<h:div class="summary">A reference to an atom.</h:div> <h:div class="description">Used by bond, electron, etc.</h:div>

XML Source (see within schema source)

<xsd:attribute id="att.atomRef" name="atomRef" type="atomRefType">

<xsd:annotation>

<xsd:documentation>

<h:div class="summary">A reference to an atom.</h:div>

<h:div class="description">Used by bond, electron, 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>

name

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

<h:div class="summary">Name of the object.</h:div> <h:div class="description">A string by which the object is known. Often a required attribute. The may or may not be a semi-controlled vocabulary.</h:div>

XML Source (see within schema source)

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

<xsd:annotation>

<xsd:documentation>

<h:div class="summary">Name of the object.</h:div>

<h:div class="description">

A string by which the object is known. Often a required attribute. The may or may not be a semi-controlled vocabulary.

</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; 7/7)

array

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

XML Source (see within schema source)

<xsd:element ref="array"/>

atom

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

XML Source (see within schema source)

<xsd:element ref="atom"/>

label

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

XML Source (see within schema source)

<xsd:element ref="label"/>

matrix

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

XML Source (see within schema source)

<xsd:element ref="matrix"/>

molecule

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

XML Source (see within schema source)

<xsd:element ref="molecule"/>

property

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

XML Source (see within schema source)

<xsd:element ref="property"/>

scalar

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

XML Source (see within schema source)

<xsd:element ref="scalar"/>

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