Tool for finding "fragments" in each CCD molecule.
Requirements From PDBe confluence: 16 June 2016
SV wants a tool to produce a file that lists the fragments present in each of the chemical compounds:
read in the chemical component definition cif file.
read in file smi.txt that contains lines like:
cyclopentane:C1CCCC1 cyclopropane:C1CC1 cytosine:C1=CNC(NC1N)O
- use rdkit to find which of the fragments is in the ccd.
- write results as a csv format file with the contents: 3 letter code eg. "ATP", fragment name from smi.txt, atom names comma delimited e.g. "C1,C2,C3,C4,O5"
- Producing this tool is a priority.
- name for tool ccd_find_fragments.py (provisional)