Re: [Rdkit-discuss] DeleteSubstructs vs ReplaceSubstructs

2017-04-03 Thread Popov, Maxim (Ext) 
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('c1c1C')
  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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Re: [Rdkit-discuss] DeleteSubstructs vs ReplaceSubstructs

2017-03-31 Thread Pavel Polishchuk 

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('c1c1C')
  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:


fromrdkit importChem

fromrdkit.Chem importAllChem

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)

forfrag infrags:

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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[Rdkit-discuss] DeleteSubstructs vs ReplaceSubstructs

2017-03-30 Thread Popov, Maxim (Ext) 
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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