Well yes I have this line indeed, I did not put the whole file for
clarity purpose. The thing is tools as MOE, Pymol read it without
problem but RDock for example can't read it properly and returns a
neutral N which is not the case. And if I open it with pymol and save it
back in mol format, the 3 appears on the N line and Rdock has no trouble
anymore...
I was just wondering if there was a trick in RDKit to also save it this
way.
On 25/09/18 17:18, Greg Landrum wrote:
Hi Colin,
The RDkit outputs charge information to mol blocks using the CHG line:
In [3]: m = Chem.MolFromSmiles('C[NH3+]')
In [4]: print(Chem.MolToMolBlock(m))
RDKit 2D
2 1 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2990 0.7500 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
M CHG 1 2 1
M END
I expect that you will find one of those in your mol file and that it
should be properly read in by other tools.
Is this not the case for you?
Best,
-greg
On Tue, Sep 25, 2018 at 4:39 PM Colin Bournez
<colin.bour...@univ-orleans.fr <mailto:colin.bour...@univ-orleans.fr>>
wrote:
Hey everyone,
I have a question concerning the Chem.MolToMolFile() function.
When I open this file containing a N+ (here is the line
corresponding in the mol file) :
11.3700 3.4360 -11.8300 N 0 3 0 0 0 0 0 0 0 0 0 0
And I just save it back withotu any modification, the line is then :
11.3700 3.4360 -11.8300 N 0 0 0 0 0 0 0 0 0 0 0 0
The problem is that for some software this mol file causes trouble
and the N+ is transformed to N with 4 bonds.
I tried several tricks but I was not able to save it as the
original line, does anyone has suggestion?
Thanks,
--
*Colin Bournez*
PhD Student, Structural Bioinformatics & Chemoinformatics
Institut de Chimie Organique et Analytique (ICOA), UMR
CNRS-Université d'Orléans 7311
Rue de Chartres, 45067 Orléans, France
T. +33 238 494 577
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--
*Colin Bournez*
PhD Student, Structural Bioinformatics & Chemoinformatics
Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université
d'Orléans 7311
Rue de Chartres, 45067 Orléans, France
T. +33 238 494 577
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