Hi,
please see the example below.
Best, Michael
>>> from rdkit import Chem
>>> block = open('truncated.mol').read()
>>> print block
16134395
Marvin 08171214412D
9 8 0 0 0 0 999 V2000
6.4522 4.5670 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
7.1667 4.9795 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
7.8812 4.5670 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.1667 5.8045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.8812 6.2170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.8812 7.0420 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
8.5956 5.8045 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
8.5956 4.9795 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
7.8812 3.7420 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
2 4 1 6 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
5 7 1 0 0 0 0
3 8 1 0 0 0 0
3 9 2 0 0 0 0
M END
# input contains stereo bond between atoms 2 and 4
>>> m=Chem.MolFromMolBlock(block)
>>> from rdkit.Chem import AllChem
>>> block2 = AllChem.MolToMolBlock(m)
>>> print block2
16134395
RDKit 2D
9 8 0 0 0 0 0 0 0 0999 V2000
6.4522 4.5670 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
7.1667 4.9795 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.8812 4.5670 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.1667 5.8045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.8812 6.2170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.8812 7.0420 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
8.5956 5.8045 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
8.5956 4.9795 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
7.8812 3.7420 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 6
2 4 1 0
4 5 1 0
5 6 2 0
5 7 1 0
3 8 1 0
3 9 2 0
M END
# stereo bond has migrated to atoms 2 and 3 in the output
--
Michael Palmer
University of Waterloo
Waterloo, Canada
science.uwaterloo.ca/~mpalmer
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