[Rdkit-discuss] Another Can't kekulize mol question

[Markus Metz]

Hello all:

This might be another FAQ but here it goes.

I am wondering if there is a convenient way to output those structures
throwing errors.

BTW, the molecules were sanitized.

As always, any input is highly appreciated.

Markus
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[Rdkit-discuss] best free protein-ligand structure interaction fingerprint API

[Thomas Evangelidis]

I am sorry for being off-topic. I would like to ask if anyone can suggest
me any good python API that calculates protein-ligand structure interaction
fingerprints as bit arrays. Preferably open source so I can incorporate it
into my own code.

thanks
Thomas

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==

Thomas Evangelidis

Research Specialist
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/1S081,
62500 Brno, Czech Republic

email: tev...@pharm.uoa.gr

  teva...@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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Re: [Rdkit-discuss] GetSubstructMatches

[Greg Landrum]

Hi Jean-Marc,

The answer is in the error message, once you know how to read it, which
isn't really trivial:

On Wed, Dec 14, 2016 at 5:35 PM, Jean-Marc Nuzillard <
jm.nuzill...@univ-reims.fr> wrote:

>
> Traceback (most recent call last):
>File "glmap.py", line 11, in 
>  matches = mol.GetSubstructMatches(skel)
> Boost.Python.ArgumentError: Python argument types in
>  Mol.GetSubstructMatches(Mol, str)
> did not match C++ signature:
>  GetSubstructMatches(class RDKit::ROMol self, class RDKit::ROMol
> query, bool uniquify=True, bool useChirality=False, bool
> useQueryQueryMatches=False, unsigned int maxMatches=1000)
>

It's telling you that you called Mol.GetSubstructMatches was called with a
Mol and a string  (the "Mol" is the object you're calling "mol" and the
string is the  object you are calling "skel"). It expects, however, to be
called with a Mol and a Mol.

If you convert skel into an RDKit molecule everything should work.

-greg
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Re: [Rdkit-discuss] GetSubstructMatches

[Jean-Marc Nuzillard]

Sure, it works!

Thanks, Greg.

Jean-Marc

Le 14/12/2016 à 17:43, Greg Landrum a écrit :

Hi Jean-Marc,

The answer is in the error message, once you know how to read it, 
which isn't really trivial:


On Wed, Dec 14, 2016 at 5:35 PM, Jean-Marc Nuzillard 
> wrote:



Traceback (most recent call last):
   File "glmap.py", line 11, in 
 matches = mol.GetSubstructMatches(skel)
Boost.Python.ArgumentError: Python argument types in
 Mol.GetSubstructMatches(Mol, str)
did not match C++ signature:
 GetSubstructMatches(class RDKit::ROMol self, class RDKit::ROMol
query, bool uniquify=True, bool useChirality=False, bool
useQueryQueryMatches=False, unsigned int maxMatches=1000)


It's telling you that you called Mol.GetSubstructMatches was called 
with a Mol and a string  (the "Mol" is the object you're calling "mol" 
and the string is the  object you are calling "skel"). It expects, 
however, to be called with a Mol and a Mol.


If you convert skel into an RDKit molecule everything should work.

-greg




--
Jean-Marc Nuzillard
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France

Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/ICMR

http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/

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[Rdkit-discuss] GetSubstructMatches

[Jean-Marc Nuzillard]

Hi all,

I have encountered the following problem :

Traceback (most recent call last):
   File "glmap.py", line 11, in 
 matches = mol.GetSubstructMatches(skel)
Boost.Python.ArgumentError: Python argument types in
 Mol.GetSubstructMatches(Mol, str)
did not match C++ signature:
 GetSubstructMatches(class RDKit::ROMol self, class RDKit::ROMol 
query, bool uniquify=True, bool useChirality=False, bool 
useQueryQueryMatches=False, unsigned int maxMatches=1000)

trying to find substructure skel in molecule mol.
I use RDKit under Windows, using Anaconda python and packages.
Presently, I have rdkitVersion 2016.03.1 and boostVersion 1_56.

I get similar messages with GetSubstructMatch and HasSubstructMatch.

Any idea?

All the best,

Jean-Marc

-- 

Dr. Jean-Marc Nuzillard
Institute of Molecular Chemistry
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France

Tel : 33 3 26 91 82 10
Fax :33 3 26 91 31 66
http://www.univ-reims.fr/ICMR

http://eos.univ-reims.fr/LSD/
http://eos.univ-reims.fr/LSD/JmnSoft/


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