cmljitter

CML Jitter

A little tool that reads a cml file from stdin, assigns random position to each atom found and writes the result to stdout.

Usage Example

% cat mymolecule.cml | cmljitter > myrandomizedmolecule.cml

Installation

% git clone https://notabug.org/grindhold/cmljitter
% cd cmljitter
% python3 setup.py build
# python3 setup.py install

Purpose

IUPAC parsers like libopsin know how to derive the topological structure from a IUPAC conformant molecule name, but not its actual structure in threedimensional space. If you let it parse a molecule name, it will output a CML file in which each atom will be placed at coordinates (0,0,0). Tools like avogadro are able to calculate this structure using forcefield algorithms, but this only works properly if all atoms are in different places. Cmljitter fills the gap and is able to prepare a cml file to be optimized by avogadro.

License

GPL-3.0