element <reactionStep> (global)

Namespace:	http://www.xml-cml.org/schema/cml2/react
Type:	anonymous complexType
Content:	complex, 7 attributes, 5 elements
Defined:	globally in cmlreact.xsd; see XML source
Includes:	definitions of 5 elements
Used:	at 1 location

XML Representation Summary

<reactionStep

convention	=	xsd:string
dictRef	=	xsd:string
id	=	xsd:string
ratio	=	xsd:float
ref	=	xsd:string
title	=	xsd:string
yield	=	xsd:float

Content:

metadataList*, (name | label)*, (reactionScheme | reaction)*

</reactionStep>

Content model elements (5):

label, metadataList, name, reaction, reactionScheme

Included in content model of elements (1):

reactionStepList

Known Usage Locations

Within anonymous complexTypes of elements (1):
reactionStepList [ref]

Annotation

<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"/>

Anonymous Type Detail

Annotation

<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>

XML Source (see within schema source)

<xsd:element id="el.reactionStep" name="reactionStep">

<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:sequence>

<xsd:element maxOccurs="unbounded" minOccurs="0" ref="metadataList"/>

<xsd:choice maxOccurs="unbounded" minOccurs="0">

<xsd:element ref="name"/>

<xsd:element ref="label"/>

</xsd:choice>

<xsd:choice maxOccurs="unbounded" minOccurs="0">

<xsd:element ref="reactionScheme"/>

<xsd:element ref="reaction"/>

</xsd:choice>

</xsd:sequence>

<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:complexType>

</xsd:element>

Attribute Detail (all declarations; 7/7)

convention

Type:	namespaceRefType
Use:	optional
Defined:	locally within convention attributeGroup

<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" href="convGroup1.xml" id="ex"/>

XML Source (see within schema source)

<xsd:attribute id="att.convention" name="convention" type="namespaceRefType">

<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" href="convGroup1.xml" id="ex"/>

</xsd:documentation>

</xsd:annotation>

</xsd:attribute>

dictRef

Type:	namespaceRefType
Use:	optional
Defined:	locally within dictRef attributeGroup

<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"/>

XML Source (see within schema source)

<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"/>

</xsd:documentation>

</xsd:annotation>

</xsd:attribute>

Type:	idType
Use:	optional
Defined:	locally within id attributeGroup

<h:div class="summary">An attribute providing a unique ID for an element.</h:div> <h:div class="description"/>

XML Source (see within schema source)

<xsd:attribute id="att.id" name="id" type="idType">

<xsd:annotation>

<xsd:documentation>

<h:div class="summary">

An attribute providing a unique ID for an element.

</h:div>

<h:div class="description"/>

</xsd:documentation>

</xsd:annotation>

</xsd:attribute>

ratio

Type:	occupancyType
Use:	optional
Defined:	locally within ratio attributeGroup

<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>

XML Source (see within schema source)

<xsd:attribute id="att.ratio" name="ratio" type="occupancyType">

<xsd:annotation>

<xsd:documentation>

<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>

</xsd:documentation>

</xsd:annotation>

</xsd:attribute>

ref

Type:	refType
Use:	optional
Defined:	locally within ref attributeGroup

<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 document. 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/> 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"/>

XML Source (see within schema source)

<xsd:attribute id="att.ref" name="ref" type="refType">

<xsd:annotation>

<xsd:documentation>

<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 document. 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.

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"/>

</xsd:documentation>

</xsd:annotation>

</xsd:attribute>

title

Type:	xsd:string, predefined
Use:	optional
Defined:	locally within title attributeGroup

<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"/>

XML Source (see within schema source)

<xsd:attribute id="att.title" name="title" type="xsd:string">

<xsd:annotation>

<xsd:documentation>

<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"/>

</xsd:documentation>

</xsd:annotation>

</xsd:attribute>

yield

Type:	occupancyType
Use:	optional
Defined:	locally within yield attributeGroup

<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>

XML Source (see within schema source)

<xsd:attribute id="att.yield" name="yield" type="occupancyType">

<xsd:annotation>

<xsd:documentation>

<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>

</xsd:documentation>

</xsd:annotation>

</xsd:attribute>

Content Element Detail (all declarations; 5/5)

label

Type:	anonymous complexType, complex content
Defined:	by reference within (this) reactionStep element

XML Source (see within schema source)

<xsd:element ref="label"/>

metadataList

Type:	anonymous complexType, complex content
Defined:	by reference within (this) reactionStep element

XML Source (see within schema source)

<xsd:element maxOccurs="unbounded" minOccurs="0" ref="metadataList"/>

name

Type:	anonymous complexType (extension of xsd:string), simple content
Defined:	by reference within (this) reactionStep element

XML Source (see within schema source)

<xsd:element ref="name"/>

reaction

Type:	anonymous complexType, complex content
Defined:	by reference within (this) reactionStep element

XML Source (see within schema source)

<xsd:element ref="reaction"/>

reactionScheme

Type:	anonymous complexType, complex content
Defined:	by reference within (this) reactionStep element

XML Source (see within schema source)

<xsd:element ref="reactionScheme"/>

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