improve fragment searching method & library

• issue #11 (closed) developed fragment matching code.
• accepted the fragment file from the original prototype.
• there are some issues with this file:

• file format - switch to using a normal multimolecule SMILES .smi file format.
• it would be useful to generate pictures of fragment library molecules
• the single cif command line script would be very useful to test what fragments are in an individual ccd cif. Need issue #19 to be done!
• The tools need to be usable by other people #18 (closed) needs to be done.
• needs to improved to support SMARTS as well as SMILES alter the fragment library file to tsv with columns name, smarts?, query, comment.
• peptide fragment is not a peptide bond - is it an attempt to search for amino acid? replace with Daylight tutorial amide
• steroid needs to pick up all steroids.
• deoxyribose fragment needs to not pick up ribose.
• pyranose fragment is wrong
• A.M. wants to add additional fragments - provide tools for him to be able to take over the work.

it would be useful to run a search for a SMILES or SMARTS fragment against the complete CCD.

• This would help developing checking the fragment library but is a reasonably big task.
  • thinking of a simple interactive command line 'server'
  • that processes the components.cif holding all PDBCCD in memory
  • then waits for user to enter a SMILES or SMARTS string (or fragment name) on keyboard
  • does a substructure search against the PDBCCD
  • then waits for the next string or to switch mode - S=SMILES T=SMARTS F=fragment

Question: do we really want SMILES substrings to define fragments?

• currently the deoxyribose fragment matches every ribose because deoxyribose is a substructure of ribose. Can SMILES be used to say that C2' is CH2? Does it matter. SMART could be used. Daylight>SMARTS Examples 27-Sept-2017