Tool for finding "fragments" in each CCD molecule.

What

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)