Thank you, Pavel.
Indeed, in this case the substructure is deleted properly and substitution
gives only variant - clearly, the query knows that the side-atom is not
aromatic and doesn't match it with the ring atom. I wonder why that doesn't
happen when I create molecule from smiles or use other notation for smarts
(C-C1:C:C:C:C:C:1).
Actually, in my case the substructure is created automatically with FindMCS
method, with smarts like this: [#6]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1 and
reading to use as substructure still produces two options for substitution and
wrong result (chipping away part of the ring) for deletion.
Maxim
From: Pavel Polishchuk [mailto:pavel_polishc...@ukr.net]
Sent: Freitag, 31. März 2017 08:18
To: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] DeleteSubstructs vs ReplaceSubstructs
Hi Maxim,
if you change your query to SMARTS it would be possible to delete what you
want
m=Chem.MolFromSmiles('C1(C2=NC=CC=C2)=CC=CC(C)=C1')
ss = Chem.MolFromSmarts('c1ccccc1C')
frag = AllChem.DeleteSubstructs(m, ss)
print(Chem.MolToSmiles(frag))
Pavel.
On 03/31/2017 07:41 AM, Popov, Maxim (Ext) wrote:
Dear RDKit users,
I am trying to remove a common substructure from a number of molecules (with
AllChem.DeleteSubstructs). My problem is best illustrated by this short code:
from rdkit import Chem
from rdkit.Chem import AllChem
m=Chem.MolFromSmiles('C1(C2=NC=CC=C2)=CC=CC(C)=C1')
ss = Chem.MolFromSmiles('C1=CC=CC(C)=C1')
hyd=Chem.MolFromSmiles('[H]')
print("Substituting substructure with hydrogen")
frags = AllChem.ReplaceSubstructs(m, ss,hyd)
for frag in frags:
print(Chem.MolToSmiles(frag))
print("\nDeleting substructure")
frag = AllChem.DeleteSubstructs(m, ss)
print(Chem.MolToSmiles(frag))
I create a toluene connected to pyridine and try to remove toluene.
When replacing toluene substructure with hydrogen (AllChem.ReplaceSubstructs),
I receive two sets of results: pyridine (with explicit hydrogen) and single
carbon plus single hydrogen plus aromatic open chain (what is left from
pyridine after removing one ring atom).
When deleting the toluene substructure (AllChem.DeleteSubstructs), I receive
just the open chain of ex-pyridine (corresponding to second set of the
ReplaceSubstructs results).
Is there a way of directing DeleteSubstructs method to a specific variant (in
this case, leaving pyridine as a ring seems to be logical).
Best regards,
Maxim
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