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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