reactionStep

<h:div class="summary">A child of reactionStepList and a container for reaction or reactionScheme.</h:div>
<h:div class="description">
  <h:p>
    <h:tt>reactionStep</h:tt>is always contained within reactionStepList and is designed to manage "sub-reactions" which have close relationships. These will often involve reactions which, taken together, describe a higher level reaction or reaction type. Examples are:
    <h:ul>
      <h:li>biochemical pathways</h:li>
      <h:li>synthetic reaction schemes</h:li>
      <h:li>multi-step reactions</h:li>
      <h:li>parallel and/or coupled reactions</h:li>
    </h:ul>. A reactionStep normally contains a single reaction or reactionScheme. It can have attributes such as yield and ratio which can be used by the parent reactionStepList.</h:p>
</h:div>
<h:div class="example" href="reactionStepList4.xml"/>
<h:div class="example" href="reactionStepList5a.xml"/>
<h:div class="example" href="reactionStepList5b.xml"/>

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
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>
ratio occupancyType optional
<h:div class="summary">A ratio in the range 0 to 1.</h:div>
<h:div class="description">Currently used for ratios between brached reactions but re-usable for other concepts.</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"/>
yield occupancyType optional
<h:div class="summary">Yield of a reaction or reactionStep.</h:div>
<h:div class="description">Yields can be given on either element. They should lie in the range 0 to 1 inclusive (i.e. percentages will need to be converted). Software may use yield to calculate amounts of substances created during a reaction or series of reactions.</h:div>
Wildcard: ANY attribute from ANY namespace OTHER than 'http://www.xml-cml.org/schema'

Source

<xsd:element name="reactionStep" id="el.reactionStep" substitutionGroup="anyCml">
  <xsd:annotation>
    <xsd:documentation>
      <h:div class="summary">A child of reactionStepList and a container for reaction or reactionScheme.</h:div>
      <h:div class="description">
        <h:p>
          <h:tt>reactionStep</h:tt>is always contained within reactionStepList and is designed to manage "sub-reactions" which have close relationships. These will often involve reactions which, taken together, describe a higher level reaction or reaction type. Examples are:
          <h:ul>
            <h:li>biochemical pathways</h:li>
            <h:li>synthetic reaction schemes</h:li>
            <h:li>multi-step reactions</h:li>
            <h:li>parallel and/or coupled reactions</h:li>
          </h:ul>. A reactionStep normally contains a single reaction or reactionScheme. It can have attributes such as yield and ratio which can be used by the parent reactionStepList.</h:p>
      </h:div>
      <h:div class="example" href="reactionStepList4.xml"/>
      <h:div class="example" href="reactionStepList5a.xml"/>
      <h:div class="example" href="reactionStepList5b.xml"/>
    </xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:annotation>
      <xsd:documentation>
        <h:div>
          <h:p>The
            <h:tt>name</h:tt>applies to the overall schema of reactions.
            <h:tt>label</h:tt>is for additional textual information and classification.
            <h:tt>reactionStepList</h:tt>normally contains
            <h:tt>reaction</h:tt>s but we make provision for nested reactionSchemes if required.</h:p>
        </h:div>
      </xsd:documentation>
    </xsd:annotation>
    <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="dictRef"/>
    <xsd:attributeGroup ref="convention"/>
    <xsd:attributeGroup ref="title"/>
    <xsd:attributeGroup ref="id"/>
    <xsd:attributeGroup ref="ref"/>
    <xsd:attributeGroup ref="yield">
      <xsd:annotation>
        <xsd:documentation>
          <h:div class="specific">
            <h:p>The yield of the reactionStep. Note that this lies in the range 0-1.</h:p>
          </h:div>
        </xsd:documentation>
      </xsd:annotation>
    </xsd:attributeGroup>
    <xsd:attributeGroup ref="ratio">
      <xsd:annotation>
        <xsd:documentation>
          <h:div class="specific">
            <h:p>The ratio of this step to one or more sibling steps. Note that this lies in the range 0-1. It is meaningless to use this unless there are siblings, in which case it refers to the relative molar fluxes through each. The "percentage yields" will need to be transformed to this range. There is no requirement that the sum of fluxes through a group of siblings sum to 1.0, though they should not sum to more.</h:p>
          </h:div>
        </xsd:documentation>
      </xsd:annotation>
    </xsd:attributeGroup>
    <xsd:anyAttribute namespace="##other" processContents="lax"/>
  </xsd:complexType>
</xsd:element>

Sample