cmlcore.xsd

化学图形处理软件

  </xsd:annotation>
  <xsd:restriction base="xsd:decimal">
    <xsd:minInclusive value="0.0"/>
    <xsd:maxInclusive value="180.0"/>
  </xsd:restriction>
</xsd:simpleType>

   <xsd:simpleType name="positiveAngleType" id="st.positiveAngleType">  
  <xsd:annotation>
    <xsd:documentation>
      <div class="summary">A non-signed angle, such as a cell angle. 
      Note that we also provide nonNegativeAngleType (e.g. for bond angles)</div>
      <div class="description">
        <p>Re-used by <a href="el.crystal">crystal</a></p>
      </div>
      <div class="example">
       <pre>  &lt;crystal z="4"&gt;
    &lt;stm:scalar title="alpha" units="degrees"&gt;70.123&lt;/stm:scalar&gt;
    &lt;stm:scalar title="beta" units="degrees"&gt;80.456&lt;/stm:scalar&gt;
    &lt;stm:scalar title="gamma" units="degrees"&gt;90.789&lt;/stm:scalar&gt;
  &lt;/crystal&gt;
</pre>
      </div>
    </xsd:documentation>
  </xsd:annotation>
  <xsd:restriction base="xsd:decimal">
    <xsd:minExclusive value="0.0"/>
    <xsd:maxInclusive value="180.0"/>
  </xsd:restriction>
</xsd:simpleType>



   <xsd:element name="amount" id="el.amount">  
  <xsd:annotation>
    <xsd:documentation>
      <div class="summary">The amount of a <a href="el.substance">substance</a></div>
      <div class="description">
        <p>
        The <tt>units</tt> attribute is mandatory and can be customised to support
        mass, volumes, moles, percentages, or rations (e.g. ppm). </p>
      </div>
      <div class="example">
        <pre>&lt;substanceList id="s1"&gt;
  &lt;amount units="units:ml"&gt;100&lt;/amount&gt;
  &lt;substance id="s1"&gt;
    &lt;amount units="units:l"&gt;1&lt;/amount&gt;
    &lt;molecule id="h2o" ref="mols:water"/&gt;
  &lt;/substance&gt;
  &lt;substance id="s2"&gt;
    &lt;amount units="units:mole"&gt;0.1&lt;/amount&gt;
    &lt;molecule id="nacl" formula="Na 1 O 1 H 1"/&gt;
  &lt;/substance&gt;
&lt;/substanceList&gt;
</pre>
      </div>
    </xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:simpleContent>
      <xsd:extension base="xsd:decimal">
        <xsd:attributeGroup ref="tit_id_conv_dictGroup"/>
        <xsd:attributeGroup ref="units" id="att.amount.units"/>
      </xsd:extension>
    </xsd:simpleContent>
  </xsd:complexType>
</xsd:element>

   <xsd:element name="angle" id="el.angle">  
  <xsd:annotation>
    <xsd:documentation>
      <div class="summary">A "bond" angle between three atoms</div>
      <div class="description">
        <p>It can be used for:</p>
        <ul>
           <li>Recording experimentally determined bond angles (e.g. in
        a crystallographic paper).</li>
           <li>Providing the angle component for internal coordinates (e.g.
        z-matrix).</li>
        </ul>
      </div>
      <div class="example"><pre>&lt;molecule id="m1"&gt;
  &lt;atomArray&gt;
    &lt;atom id="a1"/&gt;
    &lt;atom id="a2"/&gt;
    &lt;atom id="a3"/&gt;
  &lt;/atomArray&gt;
  &lt;angle units="degrees" atomRefs3="a1 a2 a3"&gt;123.4&lt;/angle&gt;
&lt;/molecule&gt;
</pre></div>
    </xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:simpleContent>
      <xsd:extension base="nonNegativeAngleType">
        <xsd:attributeGroup ref="tit_id_conv_dictGroup"/>
        <xsd:attributeGroup ref="atomRefs3"/>
        <xsd:attributeGroup ref="angleUnits"/>
        <xsd:attributeGroup ref="errorValue"/>
        <xsd:attributeGroup ref="errorBasis"/>
        <xsd:attributeGroup ref="min"/>
        <xsd:attributeGroup ref="max"/>
        <xsd:attributeGroup ref="ref"/>
      </xsd:extension>
    </xsd:simpleContent>
  </xsd:complexType>
</xsd:element>

      <xsd:element name="atom" id="el.atom">  
      <xsd:annotation>
         <xsd:documentation>
          <div class="summary">An atom</div>
           <div documentation="general">
            <p>
               Usually within a <tt>molecule</tt>.
        It is almost always contained within <tt>atomArray</tt>.
        </p>
         </div>
          <div class="example"><pre>
&lt;atom id="a1" title="O3'" elementType="O" 
  formalCharge="1" hydrogenCount="1"
  isotope="17" occupancy="0.7" 
  x2="1.2" y2="2.3" 
  x3="3.4" y3="4.5" z3="5.6"
  convention="ABC" dictRef="chem:atom"
  xmlns:stm="http://www.xml-cml.org/schema/stmml"
&gt;
  &lt;stm:scalar title="dipole" dictRef="d:dip" 
    units="unit:debye"&gt;0.2&lt;/stm:scalar&gt;
  &lt;atomParity atomRefs4="a3 a7 a2 a4"&gt;1&lt;/atomParity&gt;
  &lt;electron id="e1" atomRef="a1" count="2"/&gt;
&lt;/atom&gt;
</pre></div>
         </xsd:documentation>
         <xsd:appinfo>
         </xsd:appinfo>
      </xsd:annotation>
      <xsd:complexType>

     <xsd:choice>
         <xsd:choice minOccurs="0" maxOccurs="unbounded">
            <xsd:element ref="name"/>
            <xsd:element ref="array"/>
            <xsd:element ref="matrix"/>
            <xsd:element ref="scalar"/>
            <xsd:element ref="atomParity"/>
            <xsd:element ref="electron">
               <xsd:annotation>
                  <xsd:documentation>
                     <div class="general"><p>
                     One or more electrons associated with the atom. The <a href="st.atomRefType">atomRef</a> on the <tt>electron</tt> should
                     point to the id on the atom. We may relax this later and allow
                     reference by context.</p>
                    </div>
                  </xsd:documentation>
               </xsd:annotation>
            </xsd:element>        
         </xsd:choice>
<!-- CML-1 (deprecated) -->
         <xsd:choice minOccurs="0" maxOccurs="unbounded">
	   <xsd:element ref="float" minOccurs="0" maxOccurs="unbounded"/>
	   <xsd:element ref="integer" minOccurs="0" maxOccurs="unbounded"/>
	   <xsd:element ref="string" minOccurs="0" maxOccurs="unbounded"/>
	 </xsd:choice>
     </xsd:choice>
    
         <xsd:attributeGroup id="el.atom.id" ref="mandatoryId"/>
<!-- do not understand this; error in Xerces -->
         <xsd:attribute id="el.atom.count" name="count" type="countType">
<!--         <xsd:attribute id="el.atom.count" name="count" type="xsd:decimal" default="1">-->
            <xsd:annotation>
               <xsd:documentation>
                  <div class="summary">The occurrence count of the atom. 
               </div>
                  <div class="description">Most useful in <tt>formula</tt>
                  but possibly useful in <tt>atomArray</tt> where coordinates and
                  connectivity is not defined. No formal default, but assumed to be 1. 
               </div>
              </xsd:documentation>
            </xsd:annotation>
         </xsd:attribute>
         <xsd:attribute id="el.atom.elementType" name="elementType" type="elementTypeType">
            <xsd:annotation>
               <xsd:documentation>
               <div class="general"><p>The elementType. Almost mandatory</p> 
               </div>
              </xsd:documentation>
            </xsd:annotation>
         </xsd:attribute>
         <xsd:attribute id="el.atom.formalCharge" name="formalCharge" type="formalChargeType">
            <xsd:annotation>
               <xsd:documentation>
                 <div class="summary">The formalCharge on the atom</div>
               <div class="description">NOT the calculated charge or oxidation state. No formal default, but its absence implies 0. It may be good practice to include it explicitly.
               </div>
              </xsd:documentation>
            </xsd:annotation>
         </xsd:attribute>
         <xsd:attribute id="el.atom.hydrogenCount" name="hydrogenCount" type="hydrogenCountType">
            <xsd:annotation>
               <xsd:documentation>
               <div class="general"><p>The explicit hydrogen count</p> 
               </div>
              </xsd:documentation>
            </xsd:annotation>
         </xsd:attribute>
         <xsd:attribute id="el.atom.nonHydrogenCount" name="nonHydrogenCount" type="nonHydrogenCountType">
            <xsd:annotation>
               <xsd:documentation>
               <div class="general"><p>The non-hydrogen count (obsolete - moved to CML Query)</p> 
               </div>
              </xsd:documentation>
            </xsd:annotation>
         </xsd:attribute>
         <xsd:attribute id="el.atom.isotope" name="isotope" type="isotopeType">
            <xsd:annotation>
               <xsd:documentation>
                <div class="general"><p>The isotopic mass. Default implies "natural abundance"</p> 
               </div>
              </xsd:documentation>
            </xsd:annotation>
         </xsd:attribute>
         <xsd:attribute id="el.atom.occupancy" name="occupancy" type="occupancyType">
            <xsd:annotation>
               <xsd:documentation>
                <div class="general"><p>The occupancy (mainly from crystallography)</p> 
               </div>
              </xsd:documentation>
            </xsd:annotation>
         </xsd:attribute>
         <xsd:attribute id="el.atom.x2" name="x2" type="xsd:decimal">
            <xsd:annotation>
               <xsd:documentation>
              <div class="general"><p>The x coordinate of a 2-D representation (unrelated to 3-D structure).
             Note that x- and y- 2D coordinates are required for graphical stereochemistry
             such as wedge/hatch. x- and y- coordinates must be both present or both absent.</p> 
               </div>
              </xsd:documentation>
            </xsd:annotation>
         </xsd:attribute>
         <xsd:attribute id="el.atom.x3" name="x3" type="xsd:decimal">
            <xsd:annotation>
               <xsd:documentation>
              <div class="general"><p>The x coordinate of a 3-D cartesian representation.
              x3 y3 and z3 coordinates must be both present or both absent.</p> 
               </div>
              </xsd:documentation>
            </xsd:annotation>
         </xsd:attribute>
         <xsd:attribute id="el.atom.xFract" name="xFract" type="xsd:decimal">
            <xsd:annotation>
               <xsd:documentation>
              <div class="general"><p>The fractional x coordinate in a crystal structure.
              xFract, yFract and zFract coordinates must be all present or all absent.
              A <tt>crystal</tt> element is required</p> 
               </div>
              </xsd:documentation>
            </xsd:annotation>
         </xsd:attribute>
         <xsd:attribute id="el.atom.xy2" name="xy2" type="coordinate2Type">
            <xsd:annotation>
               <xsd:documentation>
               <div class="general"><p>The combined x and y coordinates of a 2-D representation (unrelated to 3-D structure).
             Note that x- and y- 2D coordinates are required for graphical stereochemistry
             such as wedge/hatch.</p> 
               </div>
              </xsd:documentation>
            </xsd:annotation>
         </xsd:attribute>
         <xsd:attribute id="el.atom.xyz3" name="xyz3" type="coordinate3Type">
            <xsd:annotation>
               <xsd:documentation>
               <div class="general"><p>The combined x, y, z coordinates of a 3-D cartesian representation.</p> 
               </div>
              </xsd:documentation>
            </xsd:annotation>
         </xsd:attribute>
         <xsd:attribute id="el.atom.xyzFract" name="xyzFract" type="coordinate3Type">
            <xsd:annotation>
               <xsd:documentation>
              <div class="general"><p>The combined x, y, z fractional coordinates in a crystal structure.
              A <tt>crystal</tt> element is required</p> 
               </div>
              </xsd:documentation>
            </xsd:annotation>
         </xsd:attribute>
         <xsd:attribute id="el.atom.y2" name="y2" type="xsd:decimal">
            <xsd:annotation>
               <xsd:documentation>
              <div class="general"><p>The y coordinate of a 2-D representation (unrelated to 3-D structure).
             Note that x2 and y2 coordinates are required for graphical stereochemistry
             such as wedge/hatch. x2 and y2 coordinates must be both present or both absent.</p> 
               </div>
              </xsd:documentation>
            </xsd:annotation>
         </xsd:attribute>
         <xsd:attribute id="el.atom.y3" name="y3" type="xsd:decimal">
            <xsd:annotation>
               <xsd:documentation>
              <div class="general"><p>The y coordinate of a 3-D cartesian representation.
              x3 y3 and z3 coordinates must be both present or both absent.</p> 
               </div>
              </xsd:documentation>
            </xsd:annotation>
         </xsd:attribute>
         <xsd:attribute id="el.atom.yFract" name="yFract" type="xsd:decimal">
            <xsd:annotation>
               <xsd:documentation>
              <div class="general"><p>The fractional x coordinate in a crystal structure.
              xFract, yFract and zFract coordinates must be all present or all absent.
              A <tt>crystal</tt> element is required</p> 
               </div>
              </xsd:documentation>
            </xsd:annotation>
         </xsd:attribute>
         <xsd:attribute id="el.atom.z3" name="z3" type="xsd:decimal">
            <xsd:annotation>
               <xsd:documentation>
              <div class="general"><p>The z coordinate of a 3-D cartesian representation.
              x3 y3 and z3 coordinates must be both present or both absent.</p> 
               </div>
              </xsd:documentation>
            </xsd:annotation>