Hi All
In a recent list of about 100,000 smiles, I ran into 512 that caused
some problems.
Basically, the stereochemistry of the canonicalized (isomericSmiles=True) smiles
gets reversed. I saw some discussion of this topic a while back, but it seems
it had not been resolved.
[15:07:50] Warning: ring stereochemistry detected. The output SMILES
is not canonical.
Any help or input on this?
Some offending smiles are below along with the code
I used to test this. I can provide a file of 512 if you'd like.
I'm using 2012.09.1, freshly compiled from svn
and passing all tests
TJ O'Donnell
-------------------
from rdkit import Chem
import sys
for line in sys.stdin:
smi = line.split(None,1)[0]
mol = Chem.MolFromSmiles(smi)
if mol:
print smi
print Chem.MolToSmiles(mol, isomericSmiles=True)
else:
print "can't parse smiles"
---------------- my truncated input --------
CC1(c2cc(C(F)(F)F)cc(C(F)(F)F)c2)CCN([C@@]2(c3ccccc3)CC[C@H](N3CCN(c4ccccc4Cl)C(=O)C3)CC2)C1=O
Fc1ccc2[nH]cc([C@H]3CC[C@H](N4CCN(c5cccc6c5OCCO6)CC4)CC3)c2c1
Fc1ccc2[nH]cc([C@H]3CC[C@H](N4CCN(c5cccc6c5OCCO6)CC4)CC3)c2c1
Fc1ccc2[nH]cc([C@H]3CC[C@@H](N4CCN(c5cccc6c5OCCO6)CC4)CC3)c2c1
Fc1ccc2[nH]cc([C@H]3CC[C@@H](N4CCN(c5cccc6c5OCCO6)CC4)CC3)c2c1
c1ccc(CCN[C@H]2CC[C@H](Nc3cccc4cnccc43)CC2)cc1
c1ccc(CCN[C@H]2CC[C@H](Nc3cccc4cnccc43)CC2)cc1
c1ccc(CCN[C@@H]2CC[C@H](Nc3cccc4cnccc43)CC2)cc1
c1ccc(CCN[C@@H]2CC[C@H](Nc3cccc4cnccc43)CC2)cc1
CCCn1c2[nH]c(C3CCC(NC(C)=O)CC3)nc2c(=O)n(CCC)c1=O
CCCn1c2[nH]c(C3CCC(NC(C)=O)CC3)nc2c(=O)n(CCC)c1=O
CCCn1c2[nH]c([C@@H]3CC[C@H](NC(C)=O)CC3)nc2c(=O)n(CCC)c1=O
CCCn1c2[nH]c([C@@H]3CC[C@H](NC(C)=O)CC3)nc2c(=O)n(CCC)c1=O
CCCn1c2[nH]c([C@H]3CC[C@H](NC(C)=O)CC3)nc2c(=O)n(CCC)c1=O
CCCn1c2[nH]c([C@H]3CC[C@H](NC(C)=O)CC3)nc2c(=O)n(CCC)c1=O
O=C(O)[C@H]1CC[C@H](Oc2cccc(Sc3ccc(/C=C/C(=O)N4CCOCC4)c(C(F)(F)F)c3C(F)(F)F)c2)CC1
O=C(O)[C@H]1CC[C@H](Oc2cccc(Sc3ccc(/C=C/C(=O)N4CCOCC4)c(C(F)(F)F)c3C(F)(F)F)c2)CC1
O=C(O)[C@@H]1CC[C@H](Oc2cccc(Sc3ccc(/C=C/C(=O)N4CCOCC4)c(C(F)(F)F)c3C(F)(F)F)c2)CC1
O=C(O)[C@@H]1CC[C@H](Oc2cccc(Sc3ccc(/C=C/C(=O)N4CCOCC4)c(C(F)(F)F)c3C(F)(F)F)c2)CC1
N#Cc1ccc2[nH]cc([C@@H]3CC[C@H](N4CCN(c5cccc6nccnc65)CC4)CC3)c2c1
N#Cc1ccc2[nH]cc([C@@H]3CC[C@H](N4CCN(c5cccc6nccnc65)CC4)CC3)c2c1
N#Cc1ccc2[nH]cc([C@@H]3CC[C@@H](N4CCN(c5cccc6nccnc65)CC4)CC3)c2c1
N#Cc1ccc2[nH]cc([C@@H]3CC[C@@H](N4CCN(c5cccc6nccnc65)CC4)CC3)c2c1
O=C(NC1CCC(CCN2CCN(c3cccc(Cl)c3Cl)CC2)CC1)c1cccs1
O=C(N[C@@H]1CC[C@@H](CCN2CCN(c3cccc(Cl)c3Cl)CC2)CC1)c1cccs1
Cn1ccc2ccc3c4[nH]c5c(cccc5CCN[C@H]5CC[C@H](O)CC5)c4c4c(c3c21)C(=O)NC4=O
N=C(N)Nc1ccc(CNC(=O)N2CCN(C(=O)O[C@@H]3CCC[C@H](OC(=O)N4CCN(C(=O)CCCCn5ccnc5)CC4)CCC3)CC2)cc1
CC(C)c1cc(C(C)C)c(S(=O)(=O)NC[C@H]2CC[C@H](C(=O)NNC(=O)c3cc4ccccc4s3)CC2)c(C(C)C)c1
O=C(CCC[C@@H]1OO[C@H](CCCC(=O)c2ccccc2)OO1)c1ccccc1
------ my truncated output ; input smiles/output smiles pairs of lines ------
N#Cc1ccc2[nH]cc([C@H]3CC[C@@H](N4CCN(c5cccc6nccnc65)CC4)CC3)c2c1
N#Cc1ccc2[nH]cc([C@@H]3CC[C@H](N4CCN(c5cccc6nccnc65)CC4)CC3)c2c1
N#Cc1ccc2[nH]cc([C@H]3CC[C@@H](N4CCN(c5cccc6nccnc65)CC4)CC3)c2c1
N#Cc1ccc2[nH]cc([C@@H]3CC[C@@H](N4CCN(c5cccc6nccnc65)CC4)CC3)c2c1
N#Cc1ccc2[nH]cc([C@H]3CC[C@H](N4CCN(c5cccc6nccnc65)CC4)CC3)c2c1
N#Cc1ccc2[nH]cc([C@@H]3CC[C@@H](N4CCN(c5cccc6nccnc65)CC4)CC3)c2c1
N#Cc1ccc2[nH]cc([C@H]3CC[C@H](N4CCN(c5cccc6nccnc65)CC4)CC3)c2c1
O=C(NC1CCC(CCN2CCN(c3cccc(Cl)c3Cl)CC2)CC1)c1cccs1
O=C(NC1CCC(CCN2CCN(c3cccc(Cl)c3Cl)CC2)CC1)c1cccs1
O=C(N[C@@H]1CC[C@@H](CCN2CCN(c3cccc(Cl)c3Cl)CC2)CC1)c1cccs1
O=C(N[C@H]1CC[C@H](CCN2CCN(c3cccc(Cl)c3Cl)CC2)CC1)c1cccs1
Cn1ccc2ccc3c4[nH]c5c(cccc5CCN[C@H]5CC[C@H](O)CC5)c4c4c(c3c21)C(=O)NC4=O
Cn1ccc2ccc3c4[nH]c5c(cccc5CCN[C@@H]5CC[C@@H](O)CC5)c4c4c(c3c21)C(=O)NC4=O
N=C(N)Nc1ccc(CNC(=O)N2CCN(C(=O)O[C@@H]3CCC[C@H](OC(=O)N4CCN(C(=O)CCCCn5ccnc5)CC4)CCC3)CC2)cc1
N=C(N)Nc1ccc(CNC(=O)N2CCN(C(=O)O[C@H]3CCC[C@@H](OC(=O)N4CCN(C(=O)CCCCn5ccnc5)CC4)CCC3)CC2)cc1
CC(C)c1cc(C(C)C)c(S(=O)(=O)NC[C@H]2CC[C@H](C(=O)NNC(=O)c3cc4ccccc4s3)CC2)c(C(C)C)c1
CC(C)c1cc(C(C)C)c(S(=O)(=O)NC[C@@H]2CC[C@@H](C(=O)NNC(=O)c3cc4ccccc4s3)CC2)c(C(C)C)c1
O=C(CCC[C@@H]1OO[C@H](CCCC(=O)c2ccccc2)OO1)c1ccccc1
O=C(CCC[C@@H]1OO[C@H](CCCC(=O)c2ccccc2)OO1)c1ccccc1
O=C(CCC[C@@H]1OO[C@@H](CCCC(=O)c2ccccc2)OO1)c1ccccc1
O=C(CCC[C@H]1OO[C@H](CCCC(=O)c2ccccc2)OO1)c1ccccc1
CCCn1c2[nH]c([C@@H]3CC[C@@H](CNC(C)=O)CC3)nc2c(=O)n(CCC)c1=O
CCCn1c2[nH]c([C@H]3CC[C@H](CNC(C)=O)CC3)nc2c(=O)n(CCC)c1=O
CCCn1c2[nH]c(C3CCC(CNC(C)=O)CC3)nc2c(=O)n(CCC)c1=O
CCCn1c2[nH]c(C3CCC(CNC(C)=O)CC3)nc2c(=O)n(CCC)c1=O
c1cc2c(cccc2N2CCN([C@H]3CC[C@@H](c4c[nH]c5ccccc54)CC3)CC2)[nH]1
c1cc2c(cccc2N2CCN([C@@H]3CC[C@H](c4c[nH]c5ccccc54)CC3)CC2)[nH]1
c1cc2c(cccc2N2CCN([C@H]3CC[C@@H](c4c[nH]c5ccccc54)CC3)CC2)[nH]1
c1cc2c(cccc2N2CCN([C@@H]3CC[C@H](c4c[nH]c5ccccc54)CC3)CC2)[nH]1
c1cc2c(cccc2N2CCN([C@@H]3CC[C@@H](c4c[nH]c5ccccc54)CC3)CC2)[nH]1
c1cc2c(cccc2N2CCN([C@H]3CC[C@H](c4c[nH]c5ccccc54)CC3)CC2)[nH]1
c1cc2c(cccc2N2CCN([C@@H]3CC[C@@H](c4c[nH]c5ccccc54)CC3)CC2)[nH]1
c1cc2c(cccc2N2CCN([C@H]3CC[C@H](c4c[nH]c5ccccc54)CC3)CC2)[nH]1
CCCCC(=O)N[C@@]1(C(=O)N[C@H](Cc2ccccc2)C(=O)N[C@@H](CCCN=C(N)N)C(=O)N[C@@H](Cc2c[nH]c3ccccc23)C(=O)NCC(N)=O)CC[C@@H](c2ccc(C)cc2)CC1
CCCCC(=O)N[C@]1(C(=O)N[C@H](Cc2ccccc2)C(=O)N[C@@H](CCCN=C(N)N)C(=O)N[C@@H](Cc2c[nH]c3ccccc23)C(=O)NCC(N)=O)CC[C@H](c2ccc(C)cc2)CC1
CC(C)Oc1ccccc1N1CCN([C@H]2CC[C@@H](NS(=O)(=O)c3cnc(Cl)c(Br)c3)CC2)CC1
CC(C)Oc1ccccc1N1CCN([C@@H]2CC[C@H](NS(=O)(=O)c3cnc(Cl)c(Br)c3)CC2)CC1
CC(C)Oc1ccccc1N1CCN([C@H]2CC[C@@H](NS(=O)(=O)c3cnc(Cl)c(Br)c3)CC2)CC1
CC(C)Oc1ccccc1N1CCN([C@@H]2CC[C@H](NS(=O)(=O)c3cnc(Cl)c(Br)c3)CC2)CC1
------------------------------------------------------------------------------
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