**Configuration:**
- RDKit Version: 2019.09.1
**Description:**
I am attempting to perform an r-group decomposition on a set of molecules
which vary slightly within the rings of the MCS (N/O positions within the
ring structure).
I first calculated the MCS using FindMCS function and then filtered based
on a threshold, followed by an attempt to RGD. I did try several different
options for MCS (see the commented out **mcs_varied** line below. I am
wondering if this is the expected behavior and perhaps I am asking too much
of the RGD function to handle SMARTS where multiple atoms are possible? Or
perhaps I am in error in the params I am using? Thank you for any help you
can provide.
---------------------------------------------------------------------------
smiles_list = ['CN(C)CC1CC2c3cc(F)ccc3Cc3ccc(F)cc3N2O1',
'CN(C)CCC1CC2c3ccccc3Cc3ccccc3N2O1',
'CN(C)CC1CC2c3cccnc3Cc3ccccc3N2O1',
'CN(C)CC1CC2c3ccccc3Cc3ccncc3N2O1',
'Cc1ccc2c(c1)N1OC(CN(C)C)CC1c1ccccc1C2',
'CN(C)CC1CC2c3ccccc3Cc3ccc(F)cc3N2O1',
'CN(C)CC1CC2c3ccccc3Cc3ccccc3N2O1',
'CN(C)CC1CC2c3ccccc3Cc3ccc(Cl)cc3N2O1',
'CN(C)CC1CC2c3ccccc3Cc3ccccc3C2O1']
ms = [Chem.MolFromSmiles(m) for m in smiles_list]
#MCS
mcs_varied = rdFMCS.FindMCS(ms,atomCompare=rdFMCS.AtomCompare.CompareAny,
threshold=0.8)
#mcs_varied = rdFMCS.FindMCS(ms, atomCompare=rdFMCS.AtomCompare.CompareAny,
bondCompare=rdFMCS.BondCompare.CompareOrder, ringMatchesRingOnly=True,
completeRingsOnly=True, threshold=0.8)
#filter off those which do not match the thresholded smarts from mcs...
patt = Chem.MolFromSmarts(mcs_varied.smartsString)
matches = []
for mol in ms:
if mol.HasSubstructMatch(patt):
matches.append(mol)
#perform RGD
print (mcs_varied.smartsString)
---------------------------------------------------------------------------
output
>>[#6]-[#7](-[#6])-[#6]-[#6]1-[#6,#8]-[#6,#7]2-[#7,#6](-[#8,#6]-1)-[#6]1:[#6]:[#6,#7]:[#6]:[#6]:[#6]:1-[#6]-[#6]1:[#6]-2:[#6]:[#6]:[#6]:[#7,#6]:1
---------------------------------------------------------------------------
core = Chem.MolFromSmarts(mcs_varied.smartsString)
res, unmatched = rdRGD.RGroupDecompose([core], matches, asSmiles=True)
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)
<ipython-input-271-bb8c2d599741> in <module>
28 core = Chem.MolFromSmarts(mcs_varied.smartsString)
29
---> 30 res, unmatched = rdRGD.RGroupDecompose([core],matches,asSmiles=True)
RuntimeError: Invariant Violation
Duplicate labels in rgroup core!
Violation occurred on line 101 in file
Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp
Failed Expression: atoms.find(rlabel) == atoms.end()
RDKIT: 2019.09.1
BOOST: 1_67
---------------------------------------------------------------------------
In case you want to quickly view the structures on your end...
---------------------------------------------------------------------------
AllChem.Compute2DCoords(core)
for m in matches: AllChem.GenerateDepictionMatching2DStructure(m,core)
Draw.MolsToGridImage(matches,molsPerRow=4,subImgSize=(200,200))
--
Dennis Moccia
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