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Files changed (795)

+2005-10-16: Updated formula.xsd and added inline.xsd attributeGroup.
+
+2005-10-16: changed countType.xsd to use positiveNumberType.

File attributeGroups/abbreviation.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup 
+    xmlns:h="http://www.w3.org/1999/xhtml" 
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema" 
+    id="attGp.abbreviation" name="abbreviation">
+    <xsd:attribute id="att.abbreviation"
+        name="abbreviation" type="xsd:string">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">Abbreviation.</h:div>
+                <h:div class="description">Abbreviation for units, terms, etc.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/actionOrder.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.actionOrder" name="actionOrder">
+	<xsd:attribute name="order"
+    id="att.actionOrder" type="actionOrderType">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">Describes whether child elements are sequential or parallel.</h:div>
+                <h:div class="description">There is no default.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/alternativeType.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.alternativeType" name="alternativeType">
+<!-- Note: name differs from attributeGroup name -->    
+	<xsd:attribute name="type"
+    id="att.alternativeType" type="alternativeTypeType">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">The type of an alternative.</h:div>
+                <h:div class="general">This adds semantics to an _alternative_ and might be used by an RDF or related engine.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/angleUnits.xsd

+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.angleUnits" name="angleUnits">
+<!-- Note: name differs from attributeGroup name -->  
+<xsd:attribute id="att.angleUnits" name="units" type="angleUnitsType">
+    <xsd:annotation>
+      <xsd:documentation>
+        <h:div class="summary">Restricts units to radians or degrees.</h:div> 
+        <h:div class="description"></h:div> 
+      </xsd:documentation>
+    </xsd:annotation>
+  </xsd:attribute>
+</xsd:attributeGroup>
+   

File attributeGroups/atomIDArray.xsd

+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.atomIDArray" name="atomIDArray">
+  <!-- Note: name differs from attributeGroup name -->  
+	<xsd:attribute name="atomID"
+    id="att.atomIDArray" type="atomRefArrayType">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">An array of atom IDs.</h:div>
+                <h:div class="description">Normally an attribute of an array-based element.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/atomMap.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.atomMap" name="atomMap">
+    <xsd:attribute id="att.atomMap" name="atomMap" type="idType">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">A reference to a map providing mappings between atoms</h:div>
+                <h:div class="description">The map will normally be contained within the same document and referenced by its ID. It will contain a list of links with from and to attributes linking atoms. The topology of the linking is defined by the application - it could be overlay of molecular fragments, reactant/product mapping, etc. The reserved phrase "USE_IDS" assume that the sets of atoms are of equal size and have 1:1 mapping between each id. This is another way of saying that the atoms mapped by a given ID are "the same atom". </h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/atomRef.xsd

+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.atomRef" name="atomRef">
+  <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>
+</xsd:attributeGroup>
+   

File attributeGroups/atomRef1Array.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.atomRef1Array" name="atomRef1Array">
+  <!-- Note: name differs from attributeGroup name -->  
+	<xsd:attribute name="atomRef1"
+    id="att.atomRef1Array"  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>
+</xsd:attributeGroup>

File attributeGroups/atomRef2Array.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.atomRef2Array" name="atomRef2Array">
+<!-- Note: name differs from attributeGroup name -->
+<xsd:attribute name="atomRef2"
+    id="att.atomRef2Array" 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>
+</xsd:attributeGroup>

File attributeGroups/atomRefArray.xsd

+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.atomRefArray" name="atomRefArray">
+  <xsd:attribute id="att.atomRefArray" name="atomRefArray" type="atomRefArrayType">
+    <xsd:annotation>
+      <xsd:documentation>
+        <h:div class="summary">An array of references to atoms.</h:div> 
+        <h:div class="description">Typical use would be to atoms defining a plane.</h:div> 
+      </xsd:documentation>
+    </xsd:annotation>
+  </xsd:attribute>
+</xsd:attributeGroup>
+   

File attributeGroups/atomRefGroup.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.atomRefGroup" name="atomRefGroup">
+	<xsd:attribute id="att.atomRefGroup" name="atomRefGroup" type="atomIDType"/>
+</xsd:attributeGroup>

File attributeGroups/atomRefs.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.atomRefs" name="atomRefs">
+    <xsd:attribute name="atomRefs"
+    id="att.atomRefs" type="atomRefArrayType">
+    <xsd:annotation>
+      <xsd:documentation>
+        <h:div class="summary">A reference to a list of atoms.</h:div> 
+        <h:div class="description">Used by bonds, electrons, atomSets, etc.</h:div> 
+      </xsd:documentation>
+    </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/atomRefs2.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.atomRefs2" name="atomRefs2">
+    <xsd:attribute name="atomRefs2"
+    id="att.atomRefs2" type="atomRefs2Type">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">References to two different atoms.</h:div>
+                <h:div class="description">Available for any reference to atoms but normally will be the normal reference attribute on the bond element. The order of atoms is preserved and may matter for some conventions (e.g. wedge/hatch or donor bonds.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/atomRefs3.xsd

+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.atomRefs3" name="atomRefs3">
+  <xsd:attribute id="att.atomRefs3" name="atomRefs3" type="atomRefs3Type">
+    <xsd:annotation>
+      <xsd:documentation>
+        <h:div class="summary">A list of three references to atoms.</h:div> 
+        <h:div class="description">Typically used for defining angles, 
+        but could also be used to define a three-centre bond.</h:div> 
+      </xsd:documentation>
+    </xsd:annotation>
+  </xsd:attribute>
+</xsd:attributeGroup>
+   

File attributeGroups/atomRefs4.xsd

+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.atomRefs4" name="atomRefs4">
+  <xsd:attribute id="att.atomRefs4" name="atomRefs4" type="atomRefs4Type">
+    <xsd:annotation>
+      <xsd:documentation>
+        <h:div class="summary">A list of 4 references to atoms.</h:div> 
+        <h:div class="description">Typically used for defining torsions and atomParities, 
+        but could also be used to define a four-centre bond.</h:div> 
+      </xsd:documentation>
+    </xsd:annotation>
+  </xsd:attribute>
+</xsd:attributeGroup>
+   

File attributeGroups/atomSetRef.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup 
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.atomSetRef" name="atomSetRef">
+<xsd:attribute name="atomSetRef" type="refType"
+    id="att.atomSetRef">
+    <xsd:annotation>
+        <xsd:documentation>
+            <h:div class="summary">An atomSet describing the region.</h:div>
+            <h:div class="description">Any point falling within atomOffset of any atom in the set lies within the region. This means the region could consist of disjoint fragments.</h:div>
+        </xsd:documentation>
+    </xsd:annotation>
+</xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/bondIDArray.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.bondIDArray" name="bondIDArray">
+  <!-- Note: name differs from attributeGroup name -->  
+	<xsd:attribute name="bondID"
+    id="att.bondIDArray" 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>
+</xsd:attributeGroup>

File attributeGroups/bondMap.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.bondMap" name="bondMap">
+    <xsd:attribute id="att.bondMap" name="bondMap" type="xsd:QName">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">A reference to a map providing mappings between bonds</h:div>
+                <h:div class="description">The map will normally be contained within the same document and referenced by its ID. It will contain a list of links with from and to attributes linking bonds. The topology of the linking is defined by the application - it could be overlay of molecular fragments, reactant/product mapping, etc. The reserved phrase "USE_IDS" assume that the sets of bonds are of equal size and have 1:1 mapping between each id. This is another way of saying that the bonds mapped by a given ID are "the same bond". </h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/bondRef.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.bondRef" name="bondRef">
+    <xsd:attribute name="bondRef"
+    id="att.bondRef" type="bondRefType">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">A reference to a bond.</h:div>
+                <h:div class="description">used by electron, etc.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/bondRefs.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.bondRefs" name="bondRefs">
+    <xsd:attribute name="bondRefs"
+    id="att.bondRefs"  type="bondRefArrayType">
+    <xsd:annotation>
+      <xsd:documentation>
+        <h:div class="summary">A reference to a list of bonds.</h:div> 
+        <h:div class="description">Used by electrons, bondSets, etc.</h:div> 
+      </xsd:documentation>
+    </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/box3.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.box3" name="box3">
+    <xsd:attribute name="box3" type="box3Type"
+    id="att.box3">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">A parallelipiped box.</h:div>
+                <h:div class="description">By default the box uses isometric Cartesians axes but can also be linked to lattice Vector. Any point falling within the box or on a boundary is within the regio.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/builtin.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.builtin" name="builtin">
+    <xsd:attribute name="builtin"
+    id="att.builtin"  type="xsd:string">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">builtin children.</h:div>
+                <h:div class="description">CML1-only - now deprecated.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/cellParameterError.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup 
+  xmlns:h="http://www.w3.org/1999/xhtml" 
+  xmlns:xsd="http://www.w3.org/2001/XMLSchema" 
+	id="attGp.cellParameterError" name="cellParameterError">
+<!-- Note: name differs from attributeGroup name-->    
+    <xsd:attribute name="error" 
+		type="vector3Type"
+    id="att.cellParameterError">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">Error array for cellParameter</h:div>
+                <h:div class="description">3 numbers giving error limits on paremters.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/cellParameterType.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml" 
+  xmlns:xsd="http://www.w3.org/2001/XMLSchema" 
+  id="attGp.cellParameterType" name="cellParameterType">
+<!-- Note: name differs from attributeGroup name-->    
+    <xsd:attribute id="att.cellParameterType" name="type" type="xsd:string">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">The type of a cellParameter.</h:div>
+                <h:div class="description">length or angle</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/chirality.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.chirality" name="chirality">
+    <xsd:attribute name="chirality"
+    id="att.chirality"  type="chiralityType">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">The chirality of a system or molecule.</h:div>
+                <h:div class="description">This is being actively investigated by a IUPAC committee (2002) so the convention is likely to change. No formal default.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/columns.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.columns" name="columns">
+    <xsd:attribute name="columns"
+    id="att.columns" type="sizeType">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">Number of columns.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/concise.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.concise" name="concise">
+    <xsd:attribute name="concise"
+    id="att.concise" type="formulaType">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">A concise formula.</h:div>
+                <h:div class="general">The string represents an (unstructured) formula i.e. no submolecules.
+                 Recommended to use the format "H 2 O 1", etc.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/constantToData.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup 
+  xmlns:h="http://www.w3.org/1999/xhtml" 
+  xmlns:xsd="http://www.w3.org/2001/XMLSchema" 
+    id="attGp.constantToData" name="constantToData">
+    <xsd:attribute id="att.constantToData" name="constantToData" 
+    type="xsd:double" default="0.0">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">The constant to add to the raw data.</h:div>
+                <h:div class="description"> add *after* applying any multiplier.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/constantToSI.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup 
+  xmlns:h="http://www.w3.org/1999/xhtml" 
+  xmlns:xsd="http://www.w3.org/2001/XMLSchema" 
+  id="attGp.constantToSI" name="constantToSI">
+    <xsd:attribute id="att.constantToSI" name="constantToSI" type="xsd:double">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">Additive constant to generate SI equivalent.</h:div>
+                <h:div class="description">The amount to add to a quantity in non-SI units to convert its representation to SI Units. This is applied *after* multiplierToSI. It is necessarily zero for SI units.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/constraint.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml" 
+xmlns:xsd="http://www.w3.org/2001/XMLSchema" 
+id="attGp.constraint" name="constraint">
+    <xsd:attribute name="constraint"
+    id="att.constraint" type="xsd:string">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">Constraint on a parameter.</h:div>
+                <h:div class="description">Semantics not yet finalised. We anticipate "fixed", 
+                "none" and symbolic relationships to other parameters.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/content.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml" 
+  xmlns:xsd="http://www.w3.org/2001/XMLSchema" 
+  id="attGp.content" name="content">
+    <xsd:attribute name="content" type="xsd:string"
+    id="att.content">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">content of metadata.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/convention.xsd

+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema" name="convention"
+    id="attGp.convention">
+    <xsd:attribute id="att.convention" name="convention" type="refType">
+        <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"
+    id="ex" href="convGroup1.xml"></h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>   

File attributeGroups/conventionValue.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.conventionValue" name="conventionValue">
+    <xsd:attribute name="conventionValue"
+    id="att.conventionValue" type="xsd:string">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">The value of an element with a _convention_.</h:div>
+                <h:div class="description">When convention is used this attribute must be present and element content must be empty.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/count.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml" 
+  xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.count" name="count">
+    <xsd:attribute id="att.count" name="count" type="positiveNumberType">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">The count of the object.</h:div>
+                <h:div class="description">No fixed semantics or default, normally integers. 
+                It is presumed that the element can be multiplied by the count value.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/countArray.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.countArray" name="countArray">
+    <xsd:attribute id="att.countArray" name="count" type="countArrayType">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">Array of object counts.</h:div>
+                <h:div class="description">No fixed semantics or default, normally integral. It is presumed that the element can be multiplied by the count value.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/countExpression.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml" 
+  xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.countExpression" name="countExpression">
+    <xsd:attribute id="att.countExpression" 
+    name="countExpression" type="xsd:string">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">General formula for the repeat count of the element.</h:div>
+                <h:div class="description">Experimental.
+                No fixed semantics or default. </h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/dataType.xsd

+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml" 
+xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.dataType" name="dataType">
+    <xsd:attribute id="att.dataType" name="dataType" type="dataTypeType">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">The data type of the object.</h:div>
+                <h:div class="description">Normally applied to scalar/array 
+                objects but may extend to more complex one.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/default.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.default" name="default">
+    <xsd:attribute name="default" type="xsd:string"
+    id="att.default">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">default value in an enumeration.</h:div>
+                <h:div class="description">A non-whitespace string (value is irrelevant) indicates that the content of this enumeration is the default value (usually of a scalar). It is an error to have more than one default. If the scalar in an instance document has no value (i.e. is empty or contains only whitespace) its value is given by the default. If the scalar in the instance is empty and no enumerations have a default attribute, an application may throw an error.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/delete.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.delete" name="delete">
+    <xsd:attribute name="delete"
+    id="att.delete" type="xsd:string">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">A flag indicated that the element can detach/delete itself.</h:div>
+                <h:div class="description">An element containg this attribute may only have a transient existence
+                (e.g. a template to create other elements) and this attribute shows that 
+                the element can be deleted at the appropriate stage. The time at which this
+                is called is application dependent. At present the presence of the attribute
+                is sufficient to trigger this; later a controlled vocabulary will be developed.</h:div>
+                <h:div class="summary">2006-05-21: PMR added attribute.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/delimiter.xsd

+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.delimiter" name="delimiter">
+    <xsd:attribute id="att.delimiter" name="delimiter" type="delimiterType">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">A delimiter character for arrays and matrices.</h:div>
+                <h:div class="description">By default array components ('elements' in the non-XML sense) are whitespace-separated. This fails for components with embedded whitespace or missing completely:
+        <h:pre>
+        Example:
+        In the protein database ' CA' and 'CA' are different atom types, and and array could be:
+        &lt;array delimiter="/" dictRef="pdb:atomTypes">/ N/ CA/CA/ N/&lt;/array> 
+        </h:pre>
+        Note that the array starts and ends with the delimiter, which must be chosen to avoid accidental use. There is currently no syntax for escaping delimiters.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>
+

File attributeGroups/dictRef.xsd

+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema" name="dictRef"
+    id="attGp.dictRef">
+    <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"></h:div>
+<!--                
+                <h:div class="example" href="dictRefGroup2.xml"></h:div>
+-->
+                </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/dictionaryPrefix.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml" 
+ xmlns:xsd="http://www.w3.org/2001/XMLSchema" 
+ id="attGp.dictionaryPrefix" name="dictionaryPrefix">
+    <xsd:attribute id="att.dictionaryPrefix" name="dictionaryPrefix" 
+      type="dictionaryPrefixType">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">The namespacePrefix for a data item.</h:div>
+                <h:div class="description">The dictionaryPrefix is associated with elements 
+                such as dictionaries and units and allows them to be referenced namespaces.
+                The dictionaryPrefix is normally unbound but it may be necessary to hardcode them
+                occasionally. Thus if a value is fixed (e.g. "xsd:double") the prefix must
+                be identified and fixed.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/dimensionBasis.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.dimensionBasis" name="dimensionBasis">
+        <xsd:attribute name="dimensionBasis" type="dimensionType"
+    id="att.dimensionBasis">
+            <xsd:annotation>
+                <xsd:documentation>
+                    <h:div class="summary">The basis of the dimension.</h:div>
+                    <h:div class="description">Normally taken from the seven SI types but possibly expandable.</h:div>
+                </xsd:documentation>
+            </xsd:annotation>
+        </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/dimensionality.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml" 
+xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.dimensionality" name="dimensionality">
+    <xsd:attribute name="dimensionality"
+    id="att.dimensionality" type="xsd:positiveInteger">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">Dimensionality of a coordinate system.</h:div>
+                <h:div class="description">Note that this means that coordinates of higher dimensionality 
+                are ignored or an error is flagged. Thus z3 and dimensionality='2' are incompatible. 
+                At present higher dimensionalities than 3 (cf. Wondratschek) are not supported. 
+                The labelling of the axes id not controlled. ?? should we have an explicit 
+                attribute for labelling convention?.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/duration.xsd

+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema" name="duration"
+    id="attGp.duration">
+    <xsd:attribute name="duration" type="xsd:string"
+    id="att.duration">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">The duration of the action.</h:div>
+                <h:div class="description">Semantics undefined.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>
+

File attributeGroups/eigenOrientation.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup 
+  xmlns:h="http://www.w3.org/1999/xhtml" 
+  xmlns:xsd="http://www.w3.org/2001/XMLSchema" 
+  id="attGp.eigenOrientation" 
+  name="eigenOrientation">
+<!-- Note: name differs from attributeGroup name-->    
+<xsd:attribute name="orientation" type="eigenOrientationType" 
+  id="att.eigenOrientation">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">The orientation of the eigenvector matrix.</h:div>
+				<h:div class="description">Describes whether the vectors are columns or 
+				rows. No default, so effectively mandatory unless you want to make implementers
+				guess and break applications.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/electronMap.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.electronMap" name="electronMap">
+    <xsd:attribute id="att.electronMap" name="electronMap" type="idType">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">A reference to a map providing mappings between electrons</h:div>
+                <h:div class="description">The map will normally be contained within the same document and referenced by its ID. It will contain a list of links with from and to attributes linking electrons. The topology of the linking is defined by the application - it could be reactant/product mapping, etc. The reserved phrase "USE_IDS" assume that the sets of electrons are of equal size and have 1:1 mapping between each id. This is another way of saying that the electrons mapped by a given ID are "the same electron". </h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/elementType.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.elementType" name="elementType">
+    <xsd:attribute id="att.elementType" name="elementType" type="elementTypeType">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">The identity of a chemical element.</h:div>
+                <h:div class="description">Normally mandatory on _atom_, _isotope_, etc.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/elementTypeArray.xsd

+<?xml version="1.0"?>
+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.elementTypeArray" name="elementTypeArray">
+<!-- Note: name differs from attributeGroup name -->    
+<xsd:attribute id="att.elementTypeArray" name="elementType" type="elementTypeArrayType">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">The identity of a chemical element.</h:div>
+                <h:div class="description">Normally mandatory on _atom_, _isotope_, etc.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>

File attributeGroups/end.xsd

+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema" name="end"
+    id="attGp.end">
+    <xsd:attribute name="end" type="xsd:string"
+    id="att.end">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">The end value.</h:div>
+                <h:div class="description">The end value in any allowable XSD representation 
+                of data.</h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>
+

File attributeGroups/endCondition.xsd

+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema" name="endCondition"
+    id="attGp.endCondition">
+    <xsd:attribute name="endCondition" type="xsd:string"
+    id="att.endCondition">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">The end condition.</h:div>
+                <h:div class="description">
+                    <h:p>At present a human-readable string describing some condition when the
+          ac tion should end. As XML develops it may be possible to add machine-processable
+          semantics in this field.</h:p></h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>
+

File attributeGroups/errorBasis.xsd

+<xsd:attributeGroup
+    xmlns:h="http://www.w3.org/1999/xhtml"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+    id="attGp.errorBasis" name="errorBasis">
+    <xsd:attribute id="att.errorBasis" name="errorBasis" type="errorBasisType">
+        <xsd:annotation>
+            <xsd:documentation>
+                <h:div class="summary">Basis of the error estimate.</h:div>
+                <h:div class="description"></h:div>
+            </xsd:documentation>
+        </xsd:annotation>
+    </xsd:attribute>
+</xsd:attributeGroup>
+