Re: [Rdkit-discuss] adding custom number of explicit H to specified non-hydrogen atoms

2017-01-22 Thread Maciek Wójcikowski
ter.ged...@gmail.com] > *Sent:* Saturday, January 21, 2017 3:44 PM > *To:* Janusz Petkowski; Maciek Wójcikowski > > *Cc:* rdkit-discuss@lists.sourceforge.net > *Subject:* Re: [Rdkit-discuss] adding custom number of explicit H to > specified non-hydrogen atoms > > Looks like

Re: [Rdkit-discuss] adding custom number of explicit H to specified non-hydrogen atoms

2017-01-21 Thread Janusz Petkowski
ay, January 21, 2017 3:11 PM To: Janusz Petkowski Cc: rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net> Subject: Re: [Rdkit-discuss] adding custom number of explicit H to specified non-hydrogen atoms Cześć, Following code will add Hs to atoms 2,3,4. These are the usual

Re: [Rdkit-discuss] adding custom number of explicit H to specified non-hydrogen atoms

2017-01-21 Thread Janusz Petkowski
] Sent: Saturday, January 21, 2017 3:46 PM To: Janusz Petkowski Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] adding custom number of explicit H to specified non-hydrogen atoms Which RDKit version do you have? "print rdkit.__version__" Pozdrawiam, | Be

Re: [Rdkit-discuss] adding custom number of explicit H to specified non-hydrogen atoms

2017-01-21 Thread Maciek Wójcikowski
cikowski.pl] > *Sent:* Saturday, January 21, 2017 3:11 PM > > *To:* Janusz Petkowski > *Cc:* rdkit-discuss@lists.sourceforge.net > *Subject:* Re: [Rdkit-discuss] adding custom number of explicit H to > specified non-hydrogen atoms > > Cześć, > > Following code will add Hs to atoms 2,3,4

Re: [Rdkit-discuss] adding custom number of explicit H to specified non-hydrogen atoms

2017-01-21 Thread Janusz Petkowski
Petkowski Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] adding custom number of explicit H to specified non-hydrogen atoms Cześć, Following code will add Hs to atoms 2,3,4. These are the usual RDKit indices which you get from "Atom.GetIdx()". In [5]: m1 = Chem.Mol

Re: [Rdkit-discuss] adding custom number of explicit H to specified non-hydrogen atoms

2017-01-21 Thread Maciek Wójcikowski
> > Janusz Petkowski > -- > *From:* Maciek Wójcikowski [mac...@wojcikowski.pl] > *Sent:* Saturday, January 21, 2017 5:35 AM > *To:* Janusz Petkowski > *Cc:* rdkit-discuss@lists.sourceforge.net > *Subject:* Re: [Rdkit-discuss] adding custom

Re: [Rdkit-discuss] adding custom number of explicit H to specified non-hydrogen atoms

2017-01-21 Thread Janusz Petkowski
it-discuss] adding custom number of explicit H to specified non-hydrogen atoms Hi Janusz, AddHs has a parameter "onlyOnAtoms" which takes a list of indices of atoms to include. [http://www.rdkit.org/Python_Docs/rdkit.Chem.rdmolops-module.html#AddHs] Pozdrawiam, | Best regards

Re: [Rdkit-discuss] adding custom number of explicit H to specified non-hydrogen atoms

2017-01-21 Thread Maciek Wójcikowski
Hi Janusz, AddHs has a parameter "onlyOnAtoms" which takes a list of indices of atoms to include. [http://www.rdkit.org/Python_Docs/rdkit.Chem.rdmolops- module.html#AddHs] Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2017-01-20 23:21 GMT+01:00 Janusz Petkowski

[Rdkit-discuss] adding custom number of explicit H to specified non-hydrogen atoms

2017-01-20 Thread Janusz Petkowski
Dear RDKit Community, By default H atoms are not explicit in the molecular graph and because of that the substructure matching is ignoring them when searching for substructures. It is possible to use Chem.AddHs(mol) to add explicit hydrogens to all atoms in the molecule and then perform