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Two-dimensional chemical structure diagrams

  • Subject: Two-dimensional chemical structure diagrams
  • From: Brian McMahon <bm@xxxxxxxx>
  • Date: Thu, 14 Sep 2000 13:26:26 +0100 (BST)
Acta Cryst. C has for some time required from authors a two-dimensional
diagram of the chemical structures it reports, and the forthcoming
all-electronic journal Acta Cryst. E will also carry this requirement.
Typically such diagrams are produced by authors using software such
as ChemDraw, ISIS Draw or ChemWindows (and many others). A small set of
data names in the coreCIF dictionary (the _chem_conn_* categories) exists
to codify in standard format the connectivity information in such diagrams;
a slightly larger set of data names exists in the MIF core dictionary
[Allen, F.H., Barnard, J.M., Cook, A.P.F. & Hall, S.R. (1995),
J. Chem. Inf. Comput. Sci. 35, 412-427] to serve the same purpose.

It would be useful to have software that can convert from standard chemical
drawing file formats to the CIF or MIF representation (and vice versa), and
to have software capable of reading the CIF connection tables and rendering
the diagram in bitmap formats and ideally as PostScript vector graphics. For
Acta purposes, it would be ideal if any such software could run from a Unix
command line.

(a) Does anyone have such software? :-)
(b) Has anyone shareable software or code fragments suitable for doing
    some part of the job?
(c) Can anyone provide pointers to public specification of the file formats
    used by ChemDraw or other such packages?

Any help or suggestions will be greatly appreciated.

Brian

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