Hi,
I'm trying to read the data lines from an SD file where the CTAB is in
V3000 format. If the file "v3000propIssue.sdf" contains the following:
testMol
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 1 0 0 0 0
M V30 BEGIN ATOM
M V30 1 C 0 0 0 0
M V30 END ATOM
M V30 END CTAB
M END
> <TestProp>
42
$$$$
then it is read by an SDMolSupplier it loads correctly (as shown by the
Debug) apart from the data lines which are not converted to RDKit
properties as the following interactive code snippet show:
>>> import rdkit
>>> from rdkit import Chem
>>> mol = Chem.SDMolSupplier("v3000propIssue.sdf").next()
[10:59:33] ERROR: Problems encountered parsing data fields
[10:59:33] ERROR: moving to the begining of the next molecule
>>> mol.HasProp("_Name")
1
>>> mol.HasProp("TestProp")
0
>>> mol.Debug()
Atoms:
0 6 C chg: 0 deg: 0 exp: 0 imp: 4 hyb: 4 arom?: 0 chi: 0
Bonds:
Any ideas why this might be?
Yours,
Toby Wright
--
InhibOx Ltd
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