Tks Greg Big big tks you very much It was exactly my answer.
-----Original Message----- From: Greg Landrum [mailto:greg.land...@gmail.com] Sent: mercredi, 26. mai 2010 18:33 To: Cedric MORETTI Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] cycles in RDKIT Dear Cedric, On Wed, May 26, 2010 at 5:12 PM, Cedric MORETTI <cedric.more...@firmenich.com> wrote: > Hello > I'd like to know if it was possible to search in RDKIT which would isolate > any cycles. > I thought the search for chemical moiety "C1" or "C1" and save the file with > these molecules. > The more complicated now. > Is it possible to find fragments containing only the cycle and the cycle? > > Basically I have a database with 70,000 molecules and I want to have the > cyclic fragments contained in the database. > If you have an idea to help me thank you. I'm not sure I've understood the question, but I will try: If you want to identify the cyclic fragements, the simplest thing to do is to use the function Chem.DeleteSubstructs to remove all non-cyclic atoms: [1]>>> from rdkit import Chem [2]>>> p = Chem.MolFromSmarts('[!r]') #<- this query matches any non-ring atoms [3]>>> m=Chem.MolFromSmiles('Cc1ccccc1OCC') [4]>>> m2=Chem.DeleteSubstructs(m,p) [5]>>> Chem.MolToSmiles(m2) Out[5] 'c1ccccc1' In the case of molecules without cycles, this removes everything: [6]>>> m3 = Chem.MolFromSmiles('CCC') [7]>>> m4=Chem.DeleteSubstructs(m3,p) [8]>>> Chem.MolToSmiles(m4) Out[8] '' And for linked rings, it leaves you with multiple pieces: [9]>>> m5 = Chem.MolFromSmiles('C1CC1CCc1ccc(CC)cc1') [10]>>> m6= Chem.DeleteSubstructs(m5,p) [11]>>> Chem.MolToSmiles(m6) Out[11] 'c1ccccc1.C1CC1' Which you could split into separate molecules if you wanted to: [14]>>> frags = Chem.GetMolFrags(m6,asMols=True) [15]>>> frags Out[15] (<rdkit.Chem.rdchem.Mol object at 0xa637e64>, <rdkit.Chem.rdchem.Mol object at 0xa64c064>) [16]>>> [Chem.MolToSmiles(x) for x in frags] Out[16] ['C1CC1', 'c1ccccc1'] Is this what you were looking for? -greg ********************************************************************** DISCLAIMER This email and any files transmitted with it, including replies and forwarded copies (which may contain alterations) subsequently transmitted from Firmenich, are confidential and solely for the use of the intended recipient. The contents do not represent the opinion of Firmenich except to the extent that it relates to their official business. ********************************************************************** ------------------------------------------------------------------------------ _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
