Babel

Introduction

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.

Examples

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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