I'was having related problems when manually building an OBMol from external data like
Matthew, so I've tested calculating descriptors, and I found I get a bunch of Nan's, too.
My data contains coordinates, elements and bond orders, so I add to the molecule both
OBAtom's and OBBond's (in between BeginModify() and EndModify()).
Adding hydrogens after that was totally messed up, so I looked into it and I noticed a
difference in the values obtained with GetImplicitValence()/GetValence() when building the
molecule VS reading it with Pybel.
Even adding this didn't solve the problem:
obmol.SetImplicitValencePerceived = False
obmol.SetHybridizationPerceived = False
obmol.UnsetImplicitValencePerceived()
obmol.UnsetHydrogensAdded()
obmol.PerceiveBondOrders()
Thanks,
S
On 08/14/2017 12:27 PM, Matthew Kennedy wrote:
I tested both these cases.
1) If I call mol.ConnectTheDots() then cast the OBMol to a pybel.Molecule, calcdesc()
still returns nan for SMILES/INCHI/SMARTS, but the OBMol.numBonds gets set to the
appropriate number.
2) If I call mol.PerceiveBondOrder() then cast the OBMol to a pybel.Molecule, calcdesc()
still returns nan for SMILES/INCHI/SMARTS, but the OBMol.numBonds doesn't get changed,
still reads 0.
3) If I call pybelMol.write("inchi") it returns the correct (or at least the same one as
Babel command line) inchi string if I have previously called ConnectTheDots().
Thanks for the help!
On Mon, Aug 14, 2017 at 3:07 PM, Geoffrey Hutchison <geoff.hutchi...@gmail.com
<mailto:geoff.hutchi...@gmail.com>> wrote:
> I am attempting to begin using pybel/openbabel to calculate inchi strings
on the fly without having to write temporary files and use command line open babel.
Try this as a workaround:
inchi = pybelmol.write(‘inchi’)
smiles = pybelmol.write(‘can’)
I’m wondering if there’s something subtly wrong with the install - these
should be
able to write the InChI and canonical SMILES.
-Geoff
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