atomType 

<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>atomType</h:tt>child with a "ref" 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 refers 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>

Element Information

Model

anyCml | ANY element from ANY namespace OTHER than 'http://www.xml-cml.org/schema' | ANY element from LOCAL namespace 'No Namespace'
Children: anyCml

Attributes

QName Type Fixed Default Use Inheritable Annotation
atomRef atomRefType optional 
<h:div class="summary">A reference to an atom.</h:div>
<h:div class="description">Used by bond, electron, etc.</h:div>
convention namespaceRefType optional 
<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" id="ex" href="convGroup1.xml"/>
dictRef namespaceRefType optional 
<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 doc containing _entry_ elements and validated against STMML Schema.
  <h:p>Where there is concern about the dictionary becoming separated from the doc 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"/>
id idType optional 
<h:div class="summary">A unique ID for an element.</h:div>
<h:div class="description">Id is used for machine identification of elements and in general should not have application semantics. It is similar to the XML ID type as containing only alphanumerics, '_', ',' and '-' and and must start with an alphabetic character. Ids are case sensitive. Ids should be unique within local scope, thus all atoms within a molecule should have unique ids, but separated molecules within a doc (such as a published article) might have identical ids. Software should be able to search local scope (e.g. all atoms within a molecule). However this is under constant review.</h:div>
name xsd:string optional 
<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>
ref refType optional 
<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 doc. 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 xmlns=""/>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"/>
title xsd:string optional 
<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"/>
Wildcard: ANY attribute from ANY namespace OTHER than 'http://www.xml-cml.org/schema'

Source 

<xsd:element name="atomType" id="el.atomType" substitutionGroup="anyCml">
  <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>atomType</h:tt>child with a "ref" 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 refers 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:choice minOccurs="0" maxOccurs="unbounded">
      <xsd:element ref="anyCml"/>
      <xsd:any namespace="##other" processContents="lax"/>
      <xsd:any namespace="##local" processContents="lax"/>
    </xsd:choice>
    <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:anyAttribute namespace="##other" processContents="lax"/>
  </xsd:complexType>
</xsd:element>

Sample