MOL:
Attributes
Convention for reserved names. This will normally be the name of a glossary
or of a standard. It is expected that all chemical/x-* can be identied through
this attribute. If omitted its value is "" which is interpreted as "LOCAL"
(i.e. no communal semantics are imposed, though collaborating partners may
use this if appropriate.) It is likely that a standard list of conventions
will become available.
In certain contexts the CONVENTION defaults to a TecML-specific value. Thus
DICTNAME within TERMENTRY refers to ISO12620 by default, and within the
UNITS glossary to that glossary. In general, however, authors cannot assume
any default other than the reserved values "" or LOCAL.
Value(s)
CDATA
Default Value
#IMPLIED
Reserved name (in a dictionary or glossary). XVAR, ARRAY and XLIST are made
specific through the use of DICTNAME, which should be in a dictionary
or glossary. These may be 'official' (e.g. from a standards body, learned
society, etc.) and some may be specifically mentioned in CML (e.g.
every chemical/x-* type should have its own glossary). The glossary/dictionary
should be identified through the CONVENTION attribute.
Processing applications are under no obligation to process DICTNAME, but
in that case should pass it to other applications.
Value(s)
CDATA
Default Value
#IMPLIED
The HREF attribute is inherited from HTML2.0 and is used consistently
throughout CML. It serves as the tail of a hyperlink, whose semantics
are being developed by Murray Maloney and others of the HTML-WG as an
Internet draft.
Here is some more information.
Value(s)
CDATA
Default Value
#IMPLIED
Operations on destination (advisory) (HTML 2.0) (I don't understand or use this)
Value(s)
NAMES
Default Value
#IMPLIED
NAME specifies the target of a hyperlink and must be unique
within a document. It is used in the same way as in HTML, but note
that whereas the A element appears to refer to a point in a document,
all CML elements are containers and their extent is clearly defined.
Here is some more information.
Value(s)
CDATA
Default Value
#IMPLIED
The REL attribute is inherited from HTML2.0 and is used consistently
throughout CML. It describes the target of a hyperlink, whose semantics
are being developed by Murray Maloney and others of the HTML-WG as an
Internet draft.
The use of REL is under review (Jan 1997). At present it has not been used
as the CML addressing mechanisms are more advanced.
Value(s)
NAMES
Default Value
#IMPLIED
The REV attribute is inherited from HTML2.0 and is used consistently
throughout CML. It describes the backwards relationship of a hyperlink,
whose semantics
are being developed by Murray Maloney and others of the HTML-WG as an
Internet draft.
At present CML does not specify a use and it should evolve in parallel with
what the WWW community decides.
Value(s)
NAMES
Default Value
#IMPLIED
The TITLE attribute is inherited from HTML2.0 and is used consistently
throughout CML. In HTML 2.0 it is advisory only, but you are encouraged to
use it in CML since it is used to label many of the displays, tables, etc.
Virtually all CML elements have this attribute.
The attribute value of TITLE is searchable, but may be better as contents
of an XVAR in some cases.
Value(s)
CDATA
Default Value
#IMPLIED
By default (TYPE="") MOL represents an observed (or calculated) 'molecule',
but it can be extended to cover additional uses.:
- FUZZY. The 'molecule' is imprecisely defined (perhaps because
some atoms cannot be clearly indentified). This is likely to involve
the FUZZY attribute of ARRAY in ATOMS or BONDS.
- QUERY. The 'molecule' is intended as a query. It may be
precise (i.e. define an 'exact' search) but it may also have FUZZY attributes
(e.g. a range of bond orders, etc.).
- FRAGMENT. The 'molecule' is part of a larger 'molecule' or other
ensemble. In this way polymers can be built up (although there is no
'cloning' or macro facility - I have to think this out.) Note that by
using ATIDx in the BONDS element it is possible to specify and ID in another
MOL - thereby linking two fragments. Example:
<MOL NAME=MOL-glucose1>
<ATOMS>
<ARRAY BUILTIN="ATOMID">C1 C2 ... O5</ARRAY>
<ARRAY BUILTIN="PARIDS">"C2 O5 H1 MOL-glucose:ATOMS:O4" ...""</ARRAY>
...
<BONDS>
<ARRAY BUILTIN="ATID1">... C1 ...</ARRAY>
<ARRAY BUILTIN="ATID2">... MOL-glucose2:ATOMS:O4 ...</ARRAY>
...
This could describe a glucosyl-1-4-glucose and indicate the stereochemistry
at the C1 atom.. AT present glucose1 and glucose2 would have to be explicitly
included. (However, SGML entities can be used so that the same
component was re-used - essentially a macro. An example will be provided
shortly.)
Value(s)
CDATA
Default Value
#IMPLIED
Permanent address of destination (HTML 2.0) (I don't use this)
Value(s)
CDATA
Default Value
#IMPLIED
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cml DTD