I've started to add the fmcs MCS search code to RDKit.
By that I mean it does not include the command-line driver
which is part of the fmcs distribution; just the MCS search code.

The interface to it is a single function which takes these

def MCS(mols, min_num_atoms=2,
        maximize = Default.maximize,
        atom_compare = Default.atom_compare,
        bond_compare = Default.bond_compare,
        match_valences = Default.match_valences,
        ring_matches_ring_only = False,
        complete_rings_only = False,

The steps I've done so far are:
  - rename all other functions and classes to use the
      "_" prefix to indicate that they are internal
  - remove the command-line driver code
  - removed all code uses of the word 'fmcs'

The steps still to do are:
  - use the right module name
  - reformat the doc strings
  - make it build properly
  - add basic tests
  - add the above to SVN and commit to SF

I have some questions about those steps.

1) What is the right module name? Greg and I talked
about it a couple of months ago. I can't find the
paper where I wrote it down.

Right now it is "rdkit.Chem.MCS", so that the actual
function to call is "rdkit.Chem.MCS.MCS".

2) Is there any other documentation I should update
other than the docstrings?

I'll have more questions which I get to the build system.

I'm not sure of the long-term coordination between
the RDKit and fmcs code bases. Greg would like to
push more of the RDKit code into C++ while I would
like fmcs to be portable across other toolkits.

My hope is that excepting API names, future code
will be portable across both futures. My other hope
is to get funding for the work. :)


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