Babel
Babel is a program for the conversion of molecular data formats,
written by Pat Walters and Matt Stahl (Dolata research group, Department of
Chemistry, University of Arizona, Tucson). The implementation in
ChemShell has been achieved by adding the capability to
read and write the ChemShell internal data format to Babel (currently
version 1.03), and adding a simple Tcl interface consisting of
two commands, (import_file and export_file to read and write external
data files.
The coords= argument specified the internal coordinate structure to
read from or write to, the file= argument specified the external file.
For both import_file and export_file it is necessary for Babel to be passed information on the format
of the external file. This can be passed via Tcl using the format= argument,
but is also determined by import_file and export_file from certain file
suffixes (e.g. .pdb, .mac. and .gin). See the on-line help (help babel for
a list of supported file types). It is a trivial matter to modify src/babel/babel.tcl
to recognise further suffixes automatically.
The following example effectively converts from a .mmod file (macromodel format) to
an XYZ format example file:
import_file file=test.mmod coords=temp
export_file file=junk.xyz coords=temp
The following example generates a ChemDraw connection table from an existing
structure (from the previous example):
export_file format=d file=chemdraw.dat coords=temp
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