Module createfragments

This script will break up a set of input molecules into fragments
based on some simple rules, similar to those described in the original
RECAP paper. Run with -h to see the basic rules.

If -murcko option is specified, then Murco Assembly scaffolds are generated
instead of fragments. This is done by removing terminal from each "branch"
until reacing a ring.

If -recap option is specified, then rules are as follows:
I. Only break the bonds matching the RECAP SMARTS patterns.
     1 = Amide
     2 = Ester
     3 = Amine
     4 = Urea
     5 = Ether
     6 = Olefin
     7 = Quarternary nitrogen, 
     8 = Aromatic nitrogen - aliphatic carbon
     9 = Lactam nitrogen - aliphatic carbon
     10 = Aromatic carbon - aromatic carbon
     11 = Sulphonamide
  II. Do not break ring bonds
  III. Do not break bonds that would yield one of the following fragments: 
  hydrogen, methane, ethane, prone, butane.
  NOTE: -recap_use can be used to specify which RECAP rules to use. The value
  must be a list of comma-separated numbers (no spaces).

Example usage::
    from schrodinger.structutils import createfragments
    frag_creator = createfragments.FragmentCreator(atoms=options.atoms,
                            bonds=options.bonds, smarts=options.smarts,
                            carbon_hetero=options.carbon_hetero,
                            maxatoms=options.maxatoms,
                            removedup=options.removedup, murcko=options.murcko,
                            recap=options.recap, recap_use=recap_list,
                            complete=options.complete,
                            add_h=options.add_h, verbose=True)
    for struct in my_structures:
        # fragments is a list of Structure objects
        fragments = frag_creator.fragmentStructure(struct)

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