Hi Jan,
The below behavior is the result of a bug (
https://github.com/rdkit/rdkit/issues/229).
mol_from_ctab() takes an (undocumented) optional argument that is supposed
to determine whether or not the molecule's conformation is stored in the
database. The default is to not store the conformation; this reduces the
size of the database and the speed at which molecules are depickled. The
bug is that even if you try to keep the conformation the argument is
ignored and the conformation is discarded.
I'll get this fixed tomorrow morning. Alternatively, if you want to fix it
now, the change just needs to be made in the definition of mol_from_ctab()
in rdkit_io.c
-greg
On Wed, Mar 5, 2014 at 10:27 AM, Jan Holst Jensen <j...@biochemfusion.com>wrote:
> Hi,
>
> About ready to push a changeset for implementing mol_to_ctab(), but I
> would like it to play nice and preserve input depictions.
>
> Ideally I would like the following
>
> select mol_to_ctab(mol_from_ctab(<input-molfile>));
>
> to output a molfile where the coordinates of "input-molfile" are preserved.
>
> If I do that in Python it works:
>
> >>> from rdkit import Chem
> >>> m = Chem.MolFromMolBlock("""chiral1.mol
> ... ChemDraw04200416412D
> ...
> ... 5 4 0 0 0 0 0 0 0 0999 V2000
> ... -0.0141 0.0553 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> ... 0.8109 0.0553 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
> ... -0.4266 0.7697 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
> ... -0.0141 -0.7697 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
> ... -0.8109 -0.1583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> ... 1 2 1 0
> ... 1 3 1 0
> ... 1 4 1 1
> ... 1 5 1 0
> ... M END""")
> >>> m
> <rdkit.Chem.rdchem.Mol object at 0x1240980>
> *>>> m.GetNumConformers()*
> *1*
> >>> Chem.MolToMolBlock(m)
> 'chiral1.mol\n RDKit 2D\n\n 5 4 0 0 0 0 0 0 0 0999
> V2000\n -0.0141 0.0553 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
> 0\n 0.8109 0.0553 0.0000 F 0 0 0 0 0 0 0 0 0 0 0
> 0\n -0.4266 0.7697 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0
> 0\n -0.0141 -0.7697 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0
> 0\n -0.8109 -0.1583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n
> 1 2 1 6\n 1 3 1 0\n 1 4 1 0\n 1 5 1 0\nM END\n'
> >>> quit()
>
>
> In the PG cartridge I lose the conformer of the input. My implementation
> looks like this:
>
> rdkit_io.c:
>
> PG_FUNCTION_INFO_V1(mol_to_ctab);
> Datum mol_to_ctab(PG_FUNCTION_ARGS);
> Datum
> mol_to_ctab(PG_FUNCTION_ARGS) {
> CROMol mol;
> char *str;
> int len;
>
> fcinfo->flinfo->fn_extra = SearchMolCache(
> fcinfo->flinfo->fn_extra,
> fcinfo->flinfo->fn_mcxt,
> PG_GETARG_DATUM(0),
> NULL, &mol, NULL);
>
> bool createDepictionIfMissing = PG_GETARG_BOOL(1);
> str = makeCtabText(mol, &len, createDepictionIfMissing);
>
> PG_RETURN_CSTRING( pnstrdup(str, len) );
> }
>
>
> adapter.cpp:
>
> extern "C" char *
> makeCtabText(CROMol data, int *len, bool createDepictionIfMissing) {
> ROMol *mol = (ROMol*)data;
>
> try {
> ereport(NOTICE,
> (errcode(ERRCODE_SUCCESSFUL_COMPLETION),
> errmsg("mol conformer count = %d", mol->getNumConformers())));
>
> if (createDepictionIfMissing && mol->getNumConformers() == 0) {
> RDDepict::compute2DCoords(*mol);
> }
> StringData = MolToMolBlock(*mol);
> } catch (...) {
> ereport(WARNING,
> (errcode(ERRCODE_WARNING),
> errmsg("makeCtabText: problems converting molecule to
> CTAB")));
> StringData="";
> }
>
> *len = StringData.size();
> return (char*)StringData.c_str();
> }
>
>
> If I run the Python example equivalent from psql:
>
> postgres=# select mol_to_ctab(mol_from_ctab('chiral1.mol
> ChemDraw04200416412D
>
> 5 4 0 0 0 0 0 0 0 0999 V2000
> -0.0141 0.0553 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.8109 0.0553 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
> -0.4266 0.7697 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
> -0.0141 -0.7697 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
> -0.8109 -0.1583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0
> 1 3 1 0
> 1 4 1 1
> 1 5 1 0
> M END', false));
> *NOTICE: mol conformer count = 0*
> mol_to_ctab
> -----------------------------------------------------------------------
> +
> RDKit 2D +
> +
> 5 4 0 0 0 0 0 0 0 0999 V2000 +
> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+
> -1.5000 0.0000 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0+
> -0.0000 -1.5000 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0+
> 0.0000 1.5000 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0+
> 1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+
> 1 2 1 6 +
> 1 3 1 0 +
> 1 4 1 0 +
> 1 5 1 0 +
> M END +
>
> (1 row)
>
> postgres=#
>
> Something I missed about querying a mol for conformers ? As of now I lose
> the input conformer and the code will always output a
> calculated-from-scratch depiction.
>
> Cheers
> -- Jan
>
>
>
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