| atomRefs2 |
atomRefs2Type |
|
|
optional |
|
<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>
|
|
| 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>
|
|
| moleculeRefs2 |
moleculeRefs2Type |
|
|
optional |
|
<h:div class="summary">References to two different molecules.</h:div>
<h:div class="description">Available for any reference to molecules but normally will be the normal reference attribute on the join element. The order of molecules is preserved and may matter.</h:div>
<h:div class="curation">2006-11-24: PMR created</h:div>
|
|
| order |
orderType |
|
|
optional |
|
<h:div class="summary">The order of the bond.</h:div>
<h:div class="description">There is NO default. This order is for bookkeeping only and is not related to length, QM calculations or other experimental or theoretical calculations.</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"/>
|
|
| Wildcard: ANY attribute from ANY namespace OTHER than 'http://www.xml-cml.org/schema'
|
