Hi
I found two issues when reading files:
1) I might be getting something wrong here, but it seems as if
SmilesMolSupplier misses the very first Smiles:
input smiles file "test.smi":
C mola
CC molb
CCC molc
CCCC mold
# python script
from rdkit import Chem
suppl = Chem.SmilesMolSupplier('test.smi');
print "TEST-1 : %s %s"
%(Chem.MolToSmiles(suppl[0]),suppl[0].GetProp("_Name"))
print ""
for mol in suppl:
print "TEST-2 : %s %s" %(Chem.MolToSmiles(mol),mol.GetProp("_Name"))
print ""
for i,mol in enumerate(suppl):
print "TEST-3 : %s %s" %(Chem.MolToSmiles(mol),mol.GetProp("_Name"))
#output
TEST-1 : CC molb
TEST-2 : CC molb
TEST-2 : CCC molc
TEST-2 : CCCC mold
TEST-3 : CC molb
TEST-3 : CCC molc
TEST-3 : CCCC mold
The first molecule "mola" is not available through the supplier (also
happens with other smiles files).
2) SDMolSupplier : I have a script which calculates properties from
SDfiles read in through the corresponding supplier
and RDKIT occassionally reported the following errors:
****
Pre-condition Violation
Atomic number not found
Violation occurred on line 56 in file
/home/dey/Downloads/RDKit_2012_06_1/Code/GraphMol/PeriodicTable.h
Failed Expression: atomicNumber<byanum.size()
****
[12:25:23] Unexpected error hit on line 6
[12:25:23] ERROR: moving to the begining of the next molecule
ERROR for molecule at position 0
It turned out that for the corresponding SD-file the atom elements were
written in all captial letters (e.g. CL) - if these
were changed to the proper format (Cl) RDKIT passed without throwing an
error. Although I can preprocess the SD-files
with a script, it would be nice if RDKIT could handle these cases
internally.
Best
Fabian
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