Hi Chris, Sorry for the delay.
The only detail is whatever you get when you type "obabel -L" and the name of the descriptor. To answer some of the questions, descriptors that return 'true' or 'false' are really filters, e.g. the "-s". They are handled by the same code that handles true descriptors. And I agree about Lipinski - this should have returned the number of failures, rather than a true or false - it has always bugged me. Making this change breaks any code relying on this, but it's almost useless as it is. We also need a HAC (heavy atom count) and 'atoms' should always return the same results regardless of whether hydrogens or explicit or not (this should be true for all descriptors). Regarding cansmi (the following example probably makes more sense where the input is not SMILES): obabel -:CO -:OC --filter "cansmi=CO" -osmi CO OC Actually, this should be fixed as the following should really give the same result: obabel -:CO -:OC --filter "cansmi=OC" -osmi but currently gives 0 results. There's no reason why OB can't convert OC to CO before doing the search. Formula would be similar. As you hint, it would be good to extend 'nF' to arbitary atoms. There's nothing special about fluorine. Maybe this is an area worth refreshing over the next while, both in terms of documentation and functionality. Regards, - Noel On Fri, 20 Mar 2020 at 15:11, Chris Swain via OpenBabel-discuss < openbabel-discuss@lists.sourceforge.net> wrote: > Hi > > I’m looking at the —filter option and as I read the docs the available > descriptors are and I’ve added, in brackets, a comment/question/guess about > options for filtering based on the descriptors. Does anyone know if these > are described in detail anywhere, otherwise I guess I’ll be spending a > while wit trial and error. > > obabel -L descriptors > abonds Number of aromatic bonds (integer,>, <, =) > atoms Number of atoms (integer,>, <, =) > bonds Number of bonds (integer,>, <, =) > cansmi Canonical SMILES (is this for SMARTS matching? include/exclude?) > cansmiNS Canonical SMILES without isotopes or stereo > dbonds Number of double bonds (integer,>, <, =) > formula Chemical formula (not sure how to filter) > HBA1 Number of Hydrogen Bond Acceptors 1 (JoelLib) (integer,>, <, =) > HBA2 Number of Hydrogen Bond Acceptors 2 (JoelLib) (integer,>, <, =) > what is the difference to above? > HBD Number of Hydrogen Bond Donors (JoelLib) (integer,>, <, =) > InChI IUPAC InChI identifier (matches or is this a text string > comparison?) > InChIKey InChIKey (matches, or is this a text string comparison?) > L5 Lipinski Rule of Five (how is this implemented? According to > Lipinski you can violate one property?) > logP octanol/water partition coefficient (float,>, <, =) > MP Melting point (is this a calculated property?) > MR molar refractivity (float ,>, <, =) > MW Molecular Weight filter (float ,>, <, =) > nF Number of Fluorine Atoms (Integer ,>, <, =, only Fluorine, or does > it work with other elements eg nCl, nPo) > rotors Rotatable bonds filter Is this a totable bond count? > s SMARTS filter (how is this a descriptor of a molecule?) > sbonds Number of single bonds (integer ,>, <, =) > smarts SMARTS filter (is this different to above?) > tbonds Number of triple bonds (integer ,>, <, =) > title For comparing a molecule's title (exact text match, case > sensitive, can use wild cards) > TPSA topological polar surface area (float ,>, <, =) > > Cheers, > > Chris > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >
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