I've had similar problems; none of the claimed methods to switch off RDKit
logging of warnings has worked for me.
I ended up just re-directing stderr when running the script like this:
python myfile.py 2> myErrorLog.txt
Dr. Steve O'Hagan,
-Original Message-
Hi folks,
This looks as if HasSubstructMatch should return TRUE, so why is it FALSE?
[Python 3.6, RDKit 2017.09.3]
from rdkit import Chem
from rdkit.Chem import Draw
patt =
paper, though not inclined to use
a web service for what I want to do.
Cheers,
Steve.
From: George Papadatos [mailto:gpapada...@gmail.com]
Sent: 01 December 2016 14:26
To: Greg Landrum <greg.land...@gmail.com>
Cc: Stephen O'hagan <soha...@manchester.ac.uk>;
rdkit-discuss@lists.sou
Has anyone come up with fool-proof way of matching structurally equivalent
molecules?
Unique Smiles or InChI String comparisons don't appear to work presumable
because there are different but equivalent structures, e.g. explicit vs
non-explicit H's, Kekule vs Aromatic, isomeric forms vs
o: Stephen O'hagan <soha...@manchester.ac.uk>
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] MolWt of substructure hit?
On Sep 7, 2016, at 11:53 AM, Stephen O'hagan wrote:
> How would I find the molecular weight (fraction) of that substructure within
> a compounds
Hi,
Supposing I have identified a substructure as a SMARTS string, e.g.
[#6](:,-[#6]:,-[#6](-[#6]):,-[#6]-[#6](:[#6]:[#7]):[#6]:[#6]):,-[#6]:,-[#6]
- In general, this may have wild card atoms.
How would I find the molecular weight (fraction) of that substructure within a
compounds expressed
14.04):
http://www.blopig.com/blog/2013/02/how-to-install-rdkit-on-ubuntu-12-04/
Take Care,
JP
-
Jean-Paul Ebejer
Early Stage Researcher
On 17 February 2015 at 17:20, Stephen O'hagan
soha...@manchester.ac.ukmailto:soha...@manchester.ac.uk wrote:
Hi,
On one our Ubuntu machines, I’ve installed
81:pythonTestDirML
86:pythonTestDirChem
Cheers,
Steve.
From: Riccardo Vianello [mailto:riccardo.viane...@gmail.com]
Sent: 18 November 2014 19:46
To: Stephen O'hagan
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] conda-rdkit fails to install Win7.
Hi Steve,
On Tue, Nov 18
Trying to install conda-rdkit on win7 64-bit as per instructions
https://github.com/rdkit/conda-rdkit
'conda build boost' appears to work.
'conda build rdkit' appears to download and re-install boost during
installation.
It then fails with cmake unable to find boost, and subsequently 'nmake
OK, thanks for this – I’ll have a go and see it works for me.
Cheers,
Steve.
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 13 June 2014 13:23
To: Stephen O'hagan
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] remove redundant bits from bitvector fingerprints
hmm
...@gmail.com]
Sent: 04 June 2014 04:40
To: Stephen O'hagan
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] remove redundant bits from bitvector fingerprints
Hi Steve,
On Tue, Jun 3, 2014 at 2:08 PM, Stephen O'hagan
soha...@manchester.ac.ukmailto:soha...@manchester.ac.uk wrote:
I have
I have a fragment of code generating fingerprints for a long list of molecules
(length ~ 1000)
for index in range(0,len(smi)):
smiles=smi[index]
mol=Chem.MolFromSmiles(smiles)
AllChem.EmbedMolecule(mol)
AllChem.UFFOptimizeMolecule(mol)
dm = Chem.Get3DDistanceMatrix(mol)
fp =
It appears that Eclipse PyDev code completion and syntax colouring was fooling
me!
Get3DDistanceMatrix is flagged as “undefined”, but code runs just fine!?
Cheers,
Steve.
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 08 May 2014 02:52
To: Stephen O'hagan
Cc: rdkit-discuss
I still don’t see it in the beta of the Q1 2014 release?
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 02 May 2014 15:00
To: Stephen O'hagan
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] 3D-Pharmacophore fingerprints ?
I can find no Get3DDistanceMatrix defined
done here as the documentation is a bit Spartan.
Is there any reference to a journal article?
Cheers,
Steve.
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 01 May 2014 14:57
To: Stephen O'hagan
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] 3D-Pharmacophore
Would it be possible to generate 3D-pharmacophore fingerprints similar to the
existing 2D ones?
Dr. Steve O'Hagan,
Computer Officer,
Bioanalytical Sciences Group,
School of Chemistry,
Manchester Institute of Biotechnology,
University of Manchester,
131, Princess St,
OK,
Adding:
AllChem.EmbedMolecule(m1)
AllChem.UFFOptimizeMolecule(m1)
Fixed the problem. Now to work out what it all means!
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 24 April 2014 04:39
To: Stephen O'hagan
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss
I'm trying to understand how the RDKit pharmacophore features work; tried this
fragment from a previous post:
import os
from rdkit import Chem
from rdkit.Chem import ChemicalFeatures
from rdkit import Geometry
from rdkit import RDConfig
from rdkit.Chem import AllChem
from rdkit.Chem.Pharm3D
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