Re: [Rdkit-discuss] Exhaustive fragmentation of molecules

2020-01-08 Thread Francois Berenger
On 08/01/2020 20:47, Paolo Tosco wrote: Dear Puck, You may break a bond by creating a Chem.RWMol out of your Chem.Mol, and then calling the RemoveBond() method on your Chem.RWMol, or you may use dedicated functions in the rdmolops module. Individual fragments can then be obtained by calling

[Rdkit-discuss] (no subject)

2020-01-08 Thread Victor Viterbo
Dear rdkit community, I would like to assign to atoms in a molecule membership to fragments like the one detected by |rdkit.Chem.Fragments.fr_Al_COO(). I was hence wondering if by any chance there was a way to |||either|: | |a) test membership like for the GetIsAromatic() type of

Re: [Rdkit-discuss] Exhaustive fragmentation of molecules

2020-01-08 Thread Paolo Tosco
Dear Puck, You may break a bond by creating a Chem.RWMol out of your Chem.Mol, and then calling the RemoveBond() method on your Chem.RWMol, or you may use dedicated functions in the rdmolops module. Individual fragments can then be obtained by calling rdmolops.GetMolFrags(). I have put

[Rdkit-discuss] Exhaustive fragmentation of molecules

2020-01-08 Thread Puck van Gerwen
Dear rdkit community, I am looking to start from a mol object (loaded from an .xyz file) and return all possible fragments (as mol objects) generated from breaking one bond (any bond order). I don't want any pre-encoded rules about which bonds to break as in BRICS. I saw some discussions on the

[Rdkit-discuss] Exhaustive fragmentation of molecules

2020-01-08 Thread Puck van Gerwen
Dear rdkit community, I am looking to start from a mol object (loaded from an .xyz file) and return all possible fragments generated from breaking one bond (any bond order). I don't want any pre-encoded rules about which bonds to break as in BRICS. I sa -- Puck van Gerwen Doktorandin Gruppe von