BONDS

BONDS contains an arbitrary number of arrays (ARRAY) for carrying bond information. The following BUILTINs are provided.

• BONDID ID of the bond. (optional).
• ATID1 ATOMID of the first atom in the bond. The direction of the bond is irrelevant and the two atoms can therefore be in any order.
• ATID2 ATOMID of the second atom in the bond. See above. Note that ATID1 and ATID2 must be present for any bond (not checkable by SGML parser.).
• ORDEROrder of the bond (convention yet to be agreed).
• CYCLICThe cyclicity of the bond. +1 (acyclic), -1 (cyclic) and 0 (unknown, etc).
• PARITYParity of the bond ('cis' or 'trans'). Convention (+1, 0, -1) yet to be worked out.
• PARIDSATOMIDs used to reference the parity
• SUBSTITUTE(Only in LINK version of BONDS). Can take values of 0 or 1 for (no) substitution. See below

Normally BONDS corresponds to the contents of an accompanying ATOMS - i.e. all ATIDs or other addresses in BONDS point to ATOMS. However, a MOL can contain an additional BONDS which describes links to other MOLs (e.g. for building macromolecules, combinatorial libraries, etc.). These are contained within a BONDS with the LINK attribute set to 1 (or YES).

Note that it is perfectly valid to have ATOMSs without any BONDSs (after all, bonds are merely 'opinions').

BONDS may have CONVENTION and DICTNAME attributes and these can be used to resolve problems of convention (e.g. 'order', 'stereochemistry'). It is assumed that the contained ARRAYs use the same convention unless overridden.

Content Model

• An optional XHTML description.
• An arbitrary number of ARRAYs with the bond properties.
• An arbitrary number of XVARs or XLISTs for additional information.

Note that BONDS can be used for isolated bonds.

Content

• array -- A very flexible matrix/array/geometry container.
• xhtml -- A hypertext container for use in TecML and CML.
• xlist -- A very flexible generic list/tree/table container.
• xvar -- A generic, flexible, container for scalar information.

ATTRIBUTES
CONTENT DECLARATION

Tag Minimization

Open Tag: REQUIRED
Close Tag: REQUIRED

Parent Elements

• mol -- Toplevel container for molecular information.

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