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 as
:10
To: Stephen O'hagan
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 expressed as
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 non-iso
I think fingerprint based comparison will still not cope with equivalent
structures – and I doubt that they’re guaranteed to be ‘collision’ free.
Cheers,
Steve.
From: Christos Kannas [mailto:chriskan...@gmail.com]
Sent: 28 November 2016 17:32
To: Stephen O'hagan
Cc: rdkit-di
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
Cc: Stephen O'hagan ;
rdkit-discuss@lists.sourceforge.net; Francis Atkinson
Subject: Re: [Rdkit-di
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 =
Chem.MolFromSmarts("[*,#1]-[#7]-1-[#6]-[#6]-[#7](-[#6]-[#6]-1)-[#6](\[*,#1])=[#7]\[#6]-1=[#6]-[#6](-[*,#1])=[#6](-[*,#1])
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-
From
problem is more to know which molecules cause problems than avoiding the
printing of warning messages in the console window.
I am looking for an option that would turn warnings into errors, if any.
Jean-Marc
Le 21/01/2019 à 13:44, Stephen O'hagan a écrit :
> I've had similar proble
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 impo
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-di
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,
MANCHESTE
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-Pharmaco
Let me know when it’s available.
Cheers,
Steve.
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 ?
On Fri, May 2, 2014 at 3:52 PM, Stephen O&
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 de
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-di
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 = Gene
...@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
mailto:soha...@manchester.ac.uk>> wrote:
I have a
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
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 er
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, N
Hi,
On one our Ubuntu machines, I've installed RDKit (compiled from source to get
the latest version); ctest passed all tests.
Cmake seemed to detect the correct python version and boost libs.
However, python does not see the RDkit module(s).
Any ideas what might be going wrong?
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
mailto:soha...@manchester.ac.uk>> wrote:
Hi,
On one our Ubuntu machines, I’ve installed RDKit (co
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