Sorry, hit send prematurely.
I'd define a separate function FindMCSWithTimeout for the timeout parameter
unless a majority of users will be concerned with this method's running
time, but I'm not familiar with the algorithm's details.
On Sat, Sep 1, 2012 at 8:57 AM, James Swetnam <jswet...@gmail.com> wrote:
> Some pendantic and unsolicited API critiques, but as a user I figured I
> should chime in.
> Agree with Greg's assertion to rename to FindMCS.
> def MCS(mols, min_num_atoms=2,
> maximize = Default.maximize,
> // Rename Default to something like MCSParams, and have a factory
> function returning a DefaultMCSParams I assume this is the command pattern?
> atom_compare = Default.atom_compare,
> bond_compare = Default.bond_compare,
> match_valences = Default.match_valences,
> ring_matches_ring_only = False,
> complete_rings_only = False,
> // Could you remove timeout? This is OpenBabel likeIt's orthogonal to
> the method itself. You could define an additional method with
> // Logging should really be separated from API methods. You should be
> using the python logging framework
> <http://docs.python.org/library/logging.html>such that users
> // can modify these globally and not through the API
> // Also remove from this function
> On Fri, Aug 31, 2012 at 8:37 PM, Greg Landrum <greg.land...@gmail.com>wrote:
>> On Sat, Sep 1, 2012 at 1:28 AM, Andrew Dalke <da...@dalkescientific.com>
>> > 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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