I notice that if I pass a mol object (derived from a molblock with the
chiral flag set) through GetMolFrags(), the resulting chiral molecules do
not have the chiral flag set when new molblocks are generated. I include a
molfile at the end that can be used to demonstrate this with the code
below. Am I missing a flag somewhere to preserve the chiral information?
Please note that I am aware that I can manually set the chiral flag with
SetProp() after fragments are generated, however I want to preserve the
user's original input and not force everything to have the chiral flag set.
mmol = Chem.MolFromMolBlock(open("C:\\Users\\...\\blahblah.mol","r").read())
print(Chem.MolToMolBlock(mmol, includeStereo=True))
# confirm we see chiral flag set in molblock header
frags = list(Chem.GetMolFrags(mmol,asMols=True))
print(Chem.MolToMolBlock(frags[0],includeStereo=True))
# confirm chiral flag missing in molblock header
print(Chem.MolToMolBlock(frags[0],includeStereo=True))
# confirm chiral flag missing in molblock header
-------------------------
ChemDraw06052017572D
15 15 0 0 1 0 0 0 0 0999 V2000
-3.7695 -0.7508 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.7695 0.0742 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.0550 -1.1633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.3405 -0.7508 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.3405 0.0742 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-3.0550 0.4867 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.0550 1.3117 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6260 -0.8992 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6260 -0.0742 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.3405 -1.3117 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.0550 -0.8992 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.0550 -0.0742 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
2.3405 0.3383 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.3405 1.1633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.7695 0.3383 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 3 1 0
3 4 1 0
4 5 1 0
5 6 1 0
6 2 1 0
6 7 1 1
8 9 1 0
8 10 1 0
10 11 1 0
11 12 1 0
12 13 1 0
13 9 1 0
13 14 1 6
12 15 1 0
M END
-------------------------
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