Hello all,
I have got a bunch of SDF-files with molecules and some long descriptions in
SDF-tags on them that include stuff like "->" inside.
These files have been produced by ChemAxon's software and are handled fine by
their software.
Such files can be written out also from RDKit 2014_09_02, but they fail when
you try to read them in.
Here is an example code:
1. Generate t.sdf in Python:
from rdkit import Chem
mol = Chem.MolFromSmiles("CC")
mol.SetProp("TESTFIELD","This should not work -> Let's see\n\nI guess this is
not visible\n")
mol.SetProp("TESTFIELD2","Beep")
mol2 = Chem.MolFromSmiles("CCC")
mol2.SetProp("TESTFIELD","Added another molecule -> Here the same thing\n\nI
guess this is not visible\n")
mol2.SetProp("TESTFIELD2","Beep")
w = Chem.SDWriter("t.sdf")
w.write(mol)
w.write(mol2)
w.close()
2. Trying to read the file in Python fails:
from rdkit import Chem
s = Chem.SDMolSupplier("t.sdf")
for mol in s:
print mol.GetProp("TESTFIELD")
// The TESTFIELD text is cropped and TESTFIELD2 is skipped completely
// so the line below will fail:
// print mol.GetProp("TESTFIELD2")
[10:29:43] ERROR: Problems encountered parsing data fields
[10:29:43] ERROR: moving to the begining of the next molecule
I guess in this case I will do some pre-processing for the files before reading
them in SDMolSupplier, but I just wanted to point out this special case.
Apologies if this was old news, but at least I was unable to find it after
quick look.
Best regards,
Tuomo
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