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
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
]
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
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
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
>
> 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
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
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
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
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