position there can be C or H with rdkit?
Thank you very much for your help.
Best regards,
Dr Janusz Petkowski
Research Fellow at MIT EAPS<https://eapsweb.mit.edu/people/jjpetkow>
Tel: +1 (617) 258 - 6910
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Dear RDKit Community,
I have a quick question. Is it possible to return a Z-matrix instead of the
usual, Cartesian coordinates for a molecule in RDKit or do you know of any way
of converting or generating Z-matrix coordinates for a batch of molecules?
Thanks!
Dr Janusz Petkowski
Research
Hi Ling (and Paolo earlier),
Thank you very much for your answers, both work very well.
All the best and happy coding!
Dr Janusz Petkowski
Research Fellow at MIT EAPS<https://eapsweb.mit.edu/people/jjpetkow>
Tel: +1 (617) 258 - 6910<tel:%28857%29%2
)?
Thank you very much for your help,
Best regards,
Dr Janusz Petkowski
Research Fellow at MIT EAPS<https://eapsweb.mit.edu/people/jjpetkow>
Tel: +1 (617) 258 - 6910<tel:%28857%29%20777-6977>
--
Check out the
k you once again!
Janusz
From: Peter Gedeck [peter.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 spec
]
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
FromSmiles('c1c1')
...: m1 = Chem.AddHs(m1, onlyOnAtoms=(2,3,4))
...: Chem.MolToSmiles(m1)
...:
...:
Out[5]: '[H]c1([H])c1[H]'
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl<mailto:mac...@wojcikowski.pl>
2017-01-21 15:54 GMT+01:00 Janusz P
s but I am not a programmer and my python
skills are not yet advanced.
Best regards,
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: [Rdk
[H]C([H])=C([H])[H] converted from C=C using
Chem.AddHs(mol) will not be matched onto
[H]C(=C([H])C([H])([H])[H])C([H])([H])[H] which is correct.
Thank you very much for your help,
Best regards,
Janusz Petkowski
--
Dear Greg and Peter,
Thank you very much for your feedback and I am very sorry if my examples were
not clear enough. Please look at those below, provided in a format Greg
requested. I hope it helps in explaining what I mean.
Thanks a lot!
Best regards,
Janusz Petkowski
As an additional
nd as I mentioned earlier the bonding has higher order of
importance than the hybridization.
I hope that that this clarifies what I would like to achieve, I know that it is
probably highly non-standard problem and an unique one, but I would really
appreciate your help with that matter! Of course the e
burden you with this but I only started learning programming
around two months ago and my python programming skills are still quite limited.
Thanks a lot for all your help!
Janusz Petkowski
From: Greg Landrum [greg.land...@gmail.com]
Sent: Saturday, November 14, 2015 11:37 PM
esRingOnly and completeRingsOnly methods?
With current implementation of ringMatchesRingOnly and completeRingsOnly
methods they treat all the rings the same way, no matter the size.
If not, how would one do that?
Thanks a lot for your help!
Have a great weekend!
Best regards,
Janusz
first post on
RDKit forum, I am new to RDKit and python in general, so I apologize if I
anything is not clear.
I would really appreciate your help!
Best regards,
Janusz Petkowski
--
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