Docs for schema item atomType in Chemical Markup Language (CML)

An atomType. 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. AtomTypes on an atom have no formal relation to its elementType, 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). atomTypes will also be required to describe pseudoAtoms such as "halogen" (generic) or "methyl group" (unified atom). Atoms in computations can therefore have an atomType child with a "ref" attribute. 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. atomTypes are referred to by their mandatory name attribute. An atom refers to one or more atomTypes through atomType/@ref children examples not yet teste.

<xsd:element name="atomType" id="el.atomType"> <xsd:annotation> <xsd:documentation> <h:div class="summary" xmlns:h="http://www.w3.org/1999/xhtml">An atomType.</h:div> <h:div class="description" xmlns:h="http://www.w3.org/1999/xhtml"> <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" xmlns:h="http://www.w3.org/1999/xhtml" /> <h:div class="note" xmlns:h="http://www.w3.org/1999/xhtml">examples not yet teste.</h:div> </xsd:documentation> </xsd:annotation> <xsd:complexType> <xsd:sequence> <xsd:choice minOccurs="0" maxOccurs="unbounded"> <xsd:element ref="molecule" /> <xsd:element ref="atom" /> <xsd:element ref="label" /> </xsd:choice> <xsd:choice minOccurs="0" maxOccurs="unbounded"> <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" xmlns:h="http://www.w3.org/1999/xhtml">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>

Definition Type:	Element
Name:	atomType
Namespace:	http://www.xml-cml.org/schema
Containing Schema:	schema.xsd
Abstract
Documentation:	An atomType. 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. AtomTypes on an atom have no formal relation to its elementType, 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). atomTypes will also be required to describe pseudoAtoms such as "halogen" (generic) or "methyl group" (unified atom). Atoms in computations can therefore have an atomType child with a "ref" attribute. 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. atomTypes are referred to by their mandatory name attribute. An atom refers to one or more atomTypes through atomType/@ref children examples not yet teste.