On Sat, Sep 1, 2012 at 1:28 AM, Andrew Dalke <da...@dalkescientific.com> wrote:
> 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.

I would have no objection to the command-line driver being there in a
separate file in the package; it could well be useful to people.

> The interface to it is a single function which takes these
> parameters.
> 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,
>         timeout=Default.timeout,
>         times=None,
>         verbose=False,
>         verbose_delay=1.0,
>         ):

Any objection to calling it FindMCS?

> 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".

MCS is fine with me, the function would then be rdkit.Chem.MCS.FindMCS
assuming that you agree with my function renaming suggestion.

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

It would be nice to have something about it in the Getting Started
guide, but I can do that.

> 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.

Since the rest of the list haven't been involved in these discussions,
here's my motivation for that:
having the MCS code in C++ increases the impact of the code: it allows
it to be used from the cartridge, in the knime nodes, from other Java
programs, and from C++ itself. There may also be performance benefits
(I say "may" because I know that Andrew writes really good Python
code), but those are at most a secondary motivation


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