Hi Andrew - that's great - thanks! Maybe SubsetMCS would be good since it will be for a subset of the entire system? Ciao Nik
On 9/25/12 4:44 AM, "Greg Landrum" <greg.land...@gmail.com> wrote: >On Tue, Sep 25, 2012 at 4:30 AM, Andrew Dalke <da...@dalkescientific.com> >wrote: >> The next quarter release is coming soon, which was good incentive for >>me to >> work on the new MCS code for RDKit. > >This is great news. Andrew's MCS code fills an important gap in the >current RDKit functionality. > > >> Here's the API and documentation. >> >> >> def FindMCS(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, >> ): >> """Find the maximum common substructure of a set of molecules >> >> @type mols: molecule iterator >> @param mols: find the MCS of these molecules >> @type min_num_atoms: integer >> @param min_num_atoms: The minimum number of atoms which must be in >>the MCS. >> The minimim value is 2. >> @type maximize: "atoms" or "bonds" >> @param maximize: The default "atoms" maximizes the number of atoms >>in >> the MCS. Use "bonds" to maximize the number of bonds >>instead. >> @type atom_compare: "any", "elements", or "isotopes" >> @param atom_compare: Specify the atom comparison function. The >>default "elements" >> says that two atoms are the same if and only if they have >>the same >> element number. Use "isotopes" if you are using isotope >>labels to >> define your own atom classs. With "any", all atoms match >>each other. >> @type bond_compare: "any" or "bondtypes" >> @param bond_compare: Specify the bond comparison function. The >>default >> "bondtypes" says that two bonds are the same if and only >>if they >> have the same bond type. With "any", all bonds match each >>other. >> @type match_valences: boolean >> @param match_valences: If True, atoms must also have matching >>valences >> to match. By default this is False. >> @type ring_matches_ring_only: boolean >> @param ring_matches_ring_only: If True, then both bonds must either >>be in >> a ring or not in a ring in order to match. By default >>this is False. >> @type ring_matches_ring_only: boolean >> @param ring_matches_ring_only: If True, then both bonds must either >>be in >> a ring or not in a ring in order to match. By default >>this is False. >> @type complete_rings_only: boolean >> @param complete_rings_only: If True, then if a ring bond of a >>molecule >> is in the MCS then the corresponding MCS bond is also in >>a ring. >> @type timeout: float >> @param timeout: stop search after 'timeout' seconds and report the >>current >> best MCS. >> >> @rtype: MCSResult >> @return: Information about the MCS search results. Attributes are >>'completed' >> (0 if timeout reached, otherwise 1), 'num_atoms', 'num_bonds', >>and 'smarts'. >> >> >> Is that too unreadable? I can rewrite that to be more prose than >> this sort of auto-documentation format. > >Is there a python documentation generator that can process that and do >something sensible with it? If so, I'm fine with it. If not, then >maybe the @type bits can be combined into the @param somehow (yes, it >would just be text then). > > >> I wasn't sure of how/where to update the documentation. Greg? Do you >>have >> an idea of where it might go? Or perhaps want to do it yourself? > >The API docs are automatically generated. It would be nice to have a >brief section for the GettingStarted document >($RDBASE/Docs/Book/GettingStartedInPython.rst), but I am willing to >write that if you don't have time. > >> In other news, I'll be presenting the MCS work at the Goslar conference >> this fall, and I've got some funding to work on finding a threshold MCS, >> that is, the maximum common substructure which is in at least some >>percentage >> threshold of the entire system. > >Congrats! That would definitely be useful. > >> Can anyone suggest a good name for that? Threshold MCS? Something else? > >"Threshold MCS" sounds ok to me, but I'm not great at naming things. > >-greg > >-------------------------------------------------------------------------- >---- >Live Security Virtual Conference >Exclusive live event will cover all the ways today's security and >threat landscape has changed and how IT managers can respond. Discussions >will include endpoint security, mobile security and the latest in malware >threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >_______________________________________________ >Rdkit-devel mailing list >Rdkit-devel@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/rdkit-devel ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. 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