Hi,
Am Freitag, den 18.02.2011, 17:43 +0000 schrieb JP:
> I have a set of molecules in a mol2 file (DUD set) and I would like to
> read them ALL at one go (MolFromMol2File gives me only one molecule,
> possible the first).
>
>
> Any ideas how to do this solely with RDKit ?
simply use python for this task.
attached is a example script where you possibly have to adapt the
delimiter.
regards
uwe
import rdkit.Chem
def RetrieveMol2Block(fileLikeObject, delimiter="@<TRIPOS>MOLECULE"):
"""generator which retrieves one mol2 block at a time
"""
mol2 = []
for line in fileLikeObject:
if line.startswith(delimiter) and mol2:
yield "".join(mol2)
mol2 = []
mol2.append(line)
if mol2:
yield "".join(mol2)
if __name__ == "__main__":
import sys
import rdkit.Chem.Descriptors as descr
with open(sys.argv[1]) as fi:
for mol2 in RetrieveMol2Block(fi):
rdkMolecule = rdkit.Chem.MolFromMol2Block(mol2)
print descr.MolWt(rdkMolecule)
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