Hi RDKitters,
I wonder why the InChI strings generated by RDKit differ from the ones
generated by the standard IUPAC inchi-1 executable.
I have used the IUPAC inchi-1 executable from a command line to generate
IUPAC InChI strings (the executable that comes pre-built with the InChI
1.04 binary download).
RDKit InChI strings were generated with the RDKit KNIME nodes, this version:
RDKit KNIME integration 2.1.0.201302211506
I constructed a KNIME workflow that reads in an SD-file, uses the
"Molecule to RDKit" node and then the "RDKit To InChI" node with default
options to generate RDKit InChI strings.
I ran the standard InChI example file Samples.sdf through the KNIME
workflow and compared with the InChIs generated from the IUPAC
executable. A number of InChI strings are different; it seems to be
almost all stereo-related.
For example: InChI strings generated for spiro.mol (spiro.mol - attached):
IUPAC:
InChI=1S/2C9H14Cl2/c2*1-7(10)3-9(4-7)5-8(2,11)6-9/h2*3-6H2,1-2H3/t2*7-,8-,9-/m10/s1
RDKit: InChI=1S/2C9H14Cl2/c2*1-7(10)3-9(4-7)5-8(2,11)6-9/h2*3-6H2,1-2H3
and stertaut.mol (stertaut.mol - attached):
IUPAC:
InChI=1S/C6H6O5/c7-1-2-3(5(8)9)4(2)6(10)11/h1,3-4,7H,(H,8,9)(H,10,11)/b2-1-/t3-,4+/m0/s1
RDKit:
InChI=1S/C6H6O5/c7-1-2-3(5(8)9)4(2)6(10)11/h1,3-4,7H,(H,8,9)(H,10,11)/t3-,4-/m1/s1
OK, now those InChI samples look like they are heavy on fringe cases and
perhaps thus likely to really stress toolkits.
So I took something more peaceful and ran a peptide from PubChem
through (pubchem_71296070.mol - attached).
IUPAC:
InChI=1S/C33H55N9O10/c1-18(43)26(37)31(49)40-23(16-20-10-4-3-5-11-20)30(48)39-21(12-6-8-14-34)28(46)38-22(13-7-9-15-35)29(47)42-27(19(2)44)32(50)41-24(33(51)52)17-25(36)45/h3-5,10-11,18-19,21-24,26-27,43-44H,6-9,12-17,34-35,37H2,1-2H3,(H2,36,45)(H,38,46)(H,39,48)(H,40,49)(H,41,50)(H,42,47)(H,51,52)/t18-,19-,21+,22+,23+,24+,26+,27+/m1/s1
RDKit:
InChI=1S/C33H55N9O10/c1-18(43)26(37)31(49)40-23(16-20-10-4-3-5-11-20)30(48)39-21(12-6-8-14-34)28(46)38-22(13-7-9-15-35)29(47)42-27(19(2)44)32(50)41-24(33(51)52)17-25(36)45/h3-5,10-11,18-19,21-24,26-27,43-44H,6-9,12-17,34-35,37H2,1-2H3,(H2,36,45)(H,38,46)(H,39,48)(H,40,49)(H,41,50)(H,42,47)(H,51,52)/t18-,19-,21+,22+,23+,24+,26+,27+/m0/s1
The "only" difference in this case is that IUPAC outputs an InChI string
with /m0 and RDKit an InChI with /m1. As far as I can understand from
the InChI FAQ the /m0 /m1 difference indicates that these are different
enantiomers.
I converted the InChIs back to molecule with the "InChI to RDKit" KNIME
node. The molecule generated from the IUPAC InChI (from-iupac-inchi.mol
- attached) faithfully reconstructs the original PubChem molecule. When
I construct a molecule from the RDKit InChI (from-rdkit-inchi.mol -
attached), all the stereo centers have been inverted (as expected -
different enantiomer).
Is there a good explanation for this ?
Cheers
-- Jan
71296070
-OEChem-04201305312D
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ACD/Labs0709041010
22 24 0 0 0 0 0 0 0 0 1 V2000
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M END
> <NAME>
spiro
$$$$
-ISIS- 12270110152D
11 11 0 0 0 0 0 0 0 0999 V2000
3.2267 -1.8596 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
5.6630 -3.2662 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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M END
> <Name>
stertaut
$$$$
Mrv0541 04251323112D
52 52 0 0 0 0 999 V2000
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M END
Mrv0541 04251323112D
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M END
------------------------------------------------------------------------------
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