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:

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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