bondArray[el.bondArray]
A container for a number of bond

bondArray is a child of molecule and contains bond information. There are two strategies:

  • Create individual bond elements under bondArray (in any order). This gives the greatest flexibility but is the most verbose.
  • Create *Array attributes (e.g. of orderArrayType under bondArray. This requires all arrays to be of identical lengths with explicit values for all bonds in every array. This is NOT suitable for complexType bond children such as stereo , nor can IDs be added to bonds.. It also cannot be checked as easily by schema- and schematron validation. The atomRef1Array and atomRef2Array attributes are then mandatory. It is allowed (though not yet recommended) to add *Array children such as floatArray

The attributes are directly related to the scalar attributes under atom which should be consulted for more info.

example

Example - these are exactly equivalent representations

<stm:list xmlns:stm="http://www.xml-cml.org/schema/stmml">
  <bondArray>
    <bond id="b1" atomRefs2="a1 a2" 
        order="1"/>
    <bond id="b2" atomRefs2="a1 a3" order="2"/>
    <bond id="b3" atomRefs2="a3 a5" order="1"/>
  </bondArray>
  <bondArray
    atomRef1="a1 a1 a3"
    atomRef2="a2 a3 a5"
    order="1 2 1"/>
</stm:list>
Content Model
(bond+|(
cannot contain stereo as array. attributes required in array mode
|stm:array)*)
id[att.id]
A unique ID for an element

This is not formally of type ID (an XML NAME which must start with a letter and contain only letters, digits and .-_:). It is recommended that IDs start with a letter, and contain no punctuation or whitespace. The function generate-id() in XSLT will generate semantically void unique IDs.

It is difficult to ensure uniqueness when documents are merged. We suggest namespacing IDs, perhaps using the containing elements as the base. Thus mol3:a1 could be a useful unique ID. However this is still experimental.

[xsd:string]
Pattern: [A-Za-z0-9_-]+(:[A-Za-z0-9_-]+)?
An attribute providing a unique ID for an element
title[att.title]
A title on an element.
No controlled value.

example

<action title="turn on heat" start="T09:00:00" convention="xsd"/>
convention[att.convention]
A string referencing a dictionary, units, convention or other metadata.

The namespace is optional but recommended where possible

Note: this convention is only used within STMML and related languages; it is NOT a generic URI.

example

<list>
<!-- dictRef is of namespaceRefType -->
  <scalar dictRef="chem:mpt">123</scalar>  
<!-- error -->
  <scalar dictRef="mpt23">123</scalar>  
</list>
[xsd:string]
Pattern: [A-Za-z][A-Za-z0-9_]*(:[A-Za-z][A-Za-z0-9_]*)?
A reference to a convention

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 molecule would by default extend to its bond and atom children. This can be overwritten if necessary by an explicit convention.

It may be useful to create conventions with namespaces (e.g. iupac:name). Use of convention 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.

There is no default, but the conventions of STMML or the related language (e.g. CML) will be assumed.

example

<bond convention="fooChem" order="-5"
   xmlns:fooChem="http://www.fooChem/conventions"/>
dictRef[att.dictRef]
A string referencing a dictionary, units, convention or other metadata.

The namespace is optional but recommended where possible

Note: this convention is only used within STMML and related languages; it is NOT a generic URI.

example

<list>
<!-- dictRef is of namespaceRefType -->
  <scalar dictRef="chem:mpt">123</scalar>  
<!-- error -->
  <scalar dictRef="mpt23">123</scalar>  
</list>
[xsd:string]
Pattern: [A-Za-z][A-Za-z0-9_]*(:[A-Za-z][A-Za-z0-9_]*)?

A reference to a dictionary entry.

Elements in data instances such as scalar may have a dictRef 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.

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.

This attribute can also be used on dictionary elements to define the namespace prefix

example

<scalar dataType="xsd:float" title="surfaceArea" 
  dictRef="cmlPhys:surfArea" 
  xmlns:cmlPhys="http://www.xml-cml.org/dict/physical"
  units="units:cm2">50</scalar>

example

<stm:list xmlns:stm="http://www.xml-cml.org/schema/stmml">
  <stm:observation>
    <p>We observed <object count="3" dictRef="#p1"/> 
      constructing dwellings of different material</p>
  </stm:observation>
  <stm:entry id="p1" term="pig">
    <stm:definition>A domesticated animal.</stm:definition>
    <stm:description>Predators include wolves</stm:description>
    <stm:description class="scientificName">Sus scrofa</stm:description>
  </stm:entry>
</stm:list>
bondID[]
An array of references to bonds

The refences cannot (yet) cannot be schema- or schematron-validated. Instances of this type will be used in array-style representation of electron counts, etc. It can also be used for arrays of bondIDTypes such as in complex setereochemistry, geometrical definitions, bond groupings, etc.

example
XSD:LIST of bondRefType
A reference to an existing bond

A reference to a bond may be made by atoms (e.g. for multicentre or pi-bonds), electrons (for annotating reactions or describing electronic properties) or possibly other bonds (no examples yet). The semantics are relatively flexible.

example

<bondArray>
  <bond id="b1" atomRefs2="a3 a8" order="D">
    <electron bondRef="b1"/>
    <stereo>C</stereo>
  </bond>
  <bond id="b2" atomRefs2="a3 a8" order="S">
    <stereo convention="MDL" conventionValue="6"/>
  </bond>
</bondArray>
[xsd:string]
Pattern: \s*\S+\s*

The IDs for the bonds. Required in array mode

atomRef1[]
An array of atomRefs

The atomRefs cannot be schema- or schematron-validated. Instances of this type will be used in array-style representation of bonds and atomParitys. It can also be used for arrays of atomIDTypes such as in complex setereochemistry, geometrical definitions, atom groupings, etc.

example

<molecule id="m1">
  <atomArray atomID="a2 a4 a6"  
      elementType="O N S"/>
</molecule>
XSD:LIST of atomRefType
A reference to an existing atom

example

<molecule id="m1">
  <atomArray>
    <atom id="a1"/>
  </atomArray>
  <electron id="e1" atomRef="a1"/>
</molecule>
[xsd:string]
Pattern: *[A-Za-z_][A-Za-z0-9\-:_]*\s*

The first atoms in each bond. Required in array mode

atomRef2[]
An array of atomRefs

The atomRefs cannot be schema- or schematron-validated. Instances of this type will be used in array-style representation of bonds and atomParitys. It can also be used for arrays of atomIDTypes such as in complex setereochemistry, geometrical definitions, atom groupings, etc.

example

<molecule id="m1">
  <atomArray atomID="a2 a4 a6"  
      elementType="O N S"/>
</molecule>
XSD:LIST of atomRefType
A reference to an existing atom

example

<molecule id="m1">
  <atomArray>
    <atom id="a1"/>
  </atomArray>
  <electron id="e1" atomRef="a1"/>
</molecule>
[xsd:string]
Pattern: *[A-Za-z_][A-Za-z0-9\-:_]*\s*

The second atoms in each bond. Required in array mode

order[]
An array of bond orders

(seeAlso orderType)

XSD:LIST of orderType
Bond order (as a string)

This is purely conventional and used for bond/electron counting. There is no default value. The emptyString attribute can be used to indicate a bond of unknown or unspecified type. The interpretation of this is outside the scope of CML-based algorithms. It may be accompanied by a convention attribute on the bond which links to a dictionary. Example: <bond convention="ccdc:9" atomRefs2="a1 a2"/> could represent a delocalised bond in the CCDC convention.

Allowed values

  • S
    Single bond

  • 1
    Single bond

  • D
    Double bond

  • 2
    Double bond

  • T
    Triple bond

  • 3
    Triple bond

  • A
    Aromatic bond

The bond orders in each bond. Used in array mode