Perfect, thanks so much for the help Greg.
Best,
Nick
On 6 Feb 2012, at 12:36, Greg Landrum wrote:
I'm not sure why it should produce this particular error, but what you
should be doing is:
-L$RDBASE/lib
-greg
On Mon, Feb 6, 2012 at 10:45 AM, Nicholas Firth
nicholas.fi...@icr.ac.uk
because of the same error above, and when I
put in an arbitrary depth and managed to get some output, however it seemed
only to output a huge amount of zero's
Thanks,
Nick
On 8 Mar 2012, at 13:07, Greg Landrum wrote:
Hi Nick,
On Thu, Mar 8, 2012 at 1:10 PM, Nicholas Firth
nicholas.fi
having issue with these functions because I'm writing in C++ and
want to return this value, so don't have any pointers as this results in a
memory leak.
Any help, whether it be programming advice or RDKit function advice would be
very helpful.
Best,
Nick
Nicholas Firth, Ph.D. Student
Institute
:33, Paul Emsley wrote:
On 06/06/12 14:06, Nicholas Firth wrote:
Well I'm not quite sure what the issue is to be honest (also not very sure if
this fix will even work, so thought it best to ask).
The work round is:
ROMol *tempMol= static_castROMol *(new RWMol(mol));
tempMol = MolOps::addHs
Hi everyone,
As some one asked today about the Multiple conformations in one molecule, I
thought I would give it a crack, I've managed to get the conformations in to
one molecule (with what looks like a memory leak, that I can't seem to shift)
but I can't seem to write them back out again, I
for this mistake, so Greg you can direct all hate mail to him.
Best,
Nick
From: Greg Landrum [greg.land...@gmail.com]
Sent: 05 October 2012 05:19
To: Nicholas Firth
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Multiple Conformations SD Reader
, the decompose works (although it takes quite some time),
however the GetLeaves().keys() function seems to get stuck. I wondered if
anyone had experienced this and has a fix/workround?
Best,
Nick
Nicholas Firth, Ph.D. Student
Ph.D. Student
Institute of Cancer Research
15 Cotswold Road
Belmont
,
Nick
Nicholas Firth, Ph.D. Student
Ph.D. Student
Institute of Cancer Research
15 Cotswold Road
Belmont
Surrey
SM2 5NG
[http://upload.wikimedia.org/wikipedia/en/c/c5/Institute_of_Cancer_Research_logo.jpg]http://icr.ac.uk
[http://www.wordtracker.com/attachments/LinkedIn-Logo.png]
http
** and **' (where stars are numbers), that
would be fine if I could work round the error, however it seems to get caught
in an infinite loop of these error messages, which I can't seem to get around.
Any ideas greatly appreciated.
Best,
Nick
Nicholas Firth, Ph.D. Student
Ph.D. Student
Institute
] or
[A]. Is there anyway the smiles reader can read [R] molecules? It's pretty
simple to work round, but I thought it might be nice to go in RDKit
Thanks in advance.
Best,
Nick
Nicholas Firth, Ph.D. Student
Ph.D. Student
Institute of Cancer Research
15 Cotswold Road
Belmont
Surrey
SM2 5NG
[http
Hi RDKitters,
I'm sure this must of been covered somewhere else but I can't find it in the
forum or the source.
I am manipulating SMILES strings and wonder whether I can use RDKit as a
shortcut, so my question is does the order of occurrence in a SMILES string of
an atom match the atom index
Hi RDKitters,
I've just been made aware that the PAINS filters have been nicely put into
SMARTS (http://www.macinchem.org/reviews/pains/painsFilter.php), my question is
how do people think would be the most efficient way to implement this in RDKit?
I don't have much experience with SMARTS
/theinstituteofcancerresearch
Making the discoveries that defeat cancer
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On 15 May 2013, at 05:10, Greg Landrum
greg.land...@gmail.commailto:greg.land...@gmail.com wrote:
Hi Nick,
On Tue, May 14, 2013 at 12:19 PM, Nicholas Firth
nicholas.fi...@icr.ac.ukmailto:nicholas.fi
Also to add to my previous email, when I started out with C++ RDKit I found it
really useful to dig into the source code. Especially look through the code
written to test the descriptors, more often than not you can adapt what Greg
and co. have done already to do what you want.
Best,
Nick
Hi Gonzalo,
I shamelessly only have an example using PBF. Forgive the slightly dirty C++
coding, but you can get the idea of descriptor calculation.
using namespace std;
using namespace RDKit;
int main(int argc, char *argv[]){
string fileName = argv[1];
SDMolSupplier
| Twitter
@ICRnews
From: Nicholas Firth
Sent: 03 October 2013 16:13
To: Greg Landrum
Cc: rdkit-discuss@lists.sourceforge.net
Subject: RE: [Rdkit-discuss] ambiguous detail
Hi Greg,
As you were so worried about about the size of the RDKit dist due
Hi RDKitters,
I am seeing some weird behaviour from the adding an atom and a bond to an
EditableMol. It works fine in most cases however for this particular fragment
I'm getting an extra hydrogen being added on for some reason.
mol = Chem.MolFromSmiles('O=C1NC2=C(N1)C(=O)NC(=O)N2')
Hi RDKitters,
This may be a silly question, but I'm wondering if there's any functionality in
RDKit to add two molecules together? I've been writing to SMILES and joining
with a '.' and then reading back in. This feels very cludgy.
Basically I have two fragments of molecules and I want to add
On 11/29/2013 05:03 PM, Nicholas Firth wrote:
Hi RDKitters,
This may be a silly question, but I'm wondering if there's any functionality
in RDKit to add two molecules together? I've been writing to SMILES and
joining with a '.' and then reading back in. This feels very cludgy.
Basically I
Hi RDKitters,
This isn't strictly an RDKit based issue, but I guess someone here will be able
to help me. I'm trying to identify the index of atoms in a molecule which have
one or more hydrogen bonded to them but are not bonded to a dummy atom ([*]).
mol = Chem.MolFromSmiles('[*]CCC[*]')
From: Adrian Jasiński [jasinski.adr...@gmail.com]
Sent: 27 March 2014 19:30
To: Jameed Hussain
Cc: Nicholas Firth; rdkit-discuss@lists.sourceforge.net Discuss
Subject: Re: [Rdkit-discuss] SMARTS behaviour
you can allways visualise yours SMARTS by using http
Hi RDKitters,
When using RECAP in RDKit I want to get the smallest set of non-overlapping
fragments using the RECAP rules, so for the example in the docs
CCC(=O)OCCOc1c1, I would expect to get the following [*]C(CC)=O, [*]CCO[*],
[*]OC1=CC=CC=C1.
However this isn't the case as I get the
Hi RDKitters,
I have (yet another) question about the handling of SMARTS. I have a set of
SMARTS (http://www.macinchem.org/reviews/pains/painsFilter.php) which I have
been using to perform PAINS filters but I've just discovered some strange
behaviour, I would expect a match to happen in the
://www.facebook.com/theinstituteofcancerresearch
Making the discoveries that defeat cancer
[cid:image001.gif@01CE053D.51D3C4E0]
On 1 May 2014, at 14:44, Greg Landrum
greg.land...@gmail.commailto:greg.land...@gmail.com wrote:
Hi Nick,
On Thu, May 1, 2014 at 2:07 PM, Nicholas Firth
nicholas.fi
Hi RDKitters,
I'm trying to update my RDKit verso, using brew. I go through the steps that
Matthew Swain emailed about previously but I'm getting an error.
$ brew untap edc/rdkit
Untapped 1 formula
$ brew tap rdkit/rdkit
Cloning into '/usr/local/Library/Taps/rdkit-rdkit'...
remote: Reusing
the correct formula.
Matt
On 27 May 2014, at 08:37, Nicholas Firth
nicholas.fi...@icr.ac.ukmailto:nicholas.fi...@icr.ac.uk wrote:
Hi RDKitters,
I'm trying to update my RDKit verso, using brew. I go through the steps that
Matthew Swain emailed about previously but I'm getting an error.
$ brew
, at 18:57, Dimitri Maziuk
dmaz...@bmrb.wisc.edumailto:dmaz...@bmrb.wisc.edu wrote:
On 06/10/2014 11:34 AM, Nicholas Firth wrote:
... I have been running the job
for about 30 minutes and I've got one process which is using 2.43 GB of
memory (and growing) yet some of the processes don't appear
wrote:
On 06/10/2014 01:48 PM, Nicholas Firth wrote:
I still have plenty of CPU's and memory available though, so this
seems odd. Some of the processes have done nothing and the others seem
to have frozen at different times.
Yeah. Parallel processing is often not quite that straightforward
trying to get out of the analysis? There may be another approach
that will work,
-greg
On Wed, Jun 11, 2014 at 3:25 AM, Nicholas Firth
nicholas.fi...@icr.ac.ukmailto:nicholas.fi...@icr.ac.uk wrote:
I think I have found part of the problem, I tried it on a single processor last
night
Hi RDKitters,
I might be being stupid here, but I'm trying to marry up the bitinfo from a
hashed fingerprint to the actual fingerprint and I can't seem to do it.
from rdkit import Chem, DataStructs
from rdkit.Chem import rdMolDescriptors as rdMD
info = {}
mol = Chem.MolFromSmiles('C')
@ICRnews
From: Greg Landrum [greg.land...@gmail.com]
Sent: 17 July 2014 05:52
To: Nicholas Firth
Cc: RDKit Discuss
Subject: Re: [Rdkit-discuss] Unhashed info in hashed fingerprint
On Wed, Jul 16, 2014 at 6:40 PM, Nicholas Firth
nicholas.fi
/theinstituteofcancerresearch
Making the discoveries that defeat cancer
[cid:image001.gif@01CE053D.51D3C4E0]
On 21 Jul 2014, at 04:28, Greg Landrum
greg.land...@gmail.commailto:greg.land...@gmail.com wrote:
On Thu, Jul 17, 2014 at 10:04 AM, Nicholas Firth
nicholas.fi...@icr.ac.ukmailto:nicholas.fi
Hi,
I personally don't use the inChi support, but I am aware that you have to
install it as an optional package.
Optional packages
If you would like to install the RDKit InChI support (first available in
the Q2 2011 release), follow the instructions in $RDBASE/External/INCHI-API to
get a
Hi RDKitters,
I'm having an issue with running some reactions, I've taken a snapshot of my
IPython notebook. I'm expecting to see some reactants there.
I'm guessing I'm just being stupid, so thanks in advance for the answers!
Best,
Nick
Nicholas C. Firth | PhD Student | Cancer Therapeutics
.51D3C4E0]
On 24 Sep 2014, at 18:47, Greg Landrum
greg.land...@gmail.commailto:greg.land...@gmail.com wrote:
Could it be that you mean ps = rxn.RunReactants((sub,ring)) ?
-greg
On Wed, Sep 24, 2014 at 6:50 PM, Nicholas Firth
nicholas.fi...@icr.ac.ukmailto:nicholas.fi...@icr.ac.uk wrote:
Hi
Hi Christos,
I did a few tweets using #rdkitugm2014 but it's by no means representative of
the excellent presentations.
I guess people will be putting their slides into the repository in the next few
days.
Best,
Nick
Nicholas C. Firth | PhD Student | Cancer Therapeutics
The Institute of
| Belmont | Sutton | Surrey | SM2 5NGT020 8722 4033|Enicholas.fi...@icr.ac.uk|Wwww.icr.ac.uk|Twitter@ICRnewsFacebookwww.facebook.com/theinstituteofcancerresearchMaking the discoveries that defeat cancer
On 28 Oct 2014, at 15:20, Nicholas Firth nicholas.fi...@icr.ac.uk wrote:Hello RDKitters,I'm having
Hi Josh,
I've done a fair bit of breaking bonds and putting things back together, and
I've tended to use the EditableMol class to do this. However I haven't been
breaking any ring bonds.
As I'm sure you can see by looking at the molecule the reason you're getting
this behaviour is because
/theinstituteofcancerresearch
Making the discoveries that defeat cancer
[cid:image001.gif@01CE053D.51D3C4E0]
On 9 Dec 2014, at 14:54, Nicholas Firth
nicholas.fi...@icr.ac.ukmailto:nicholas.fi...@icr.ac.uk wrote:
Hi Josh,
I've done a fair bit of breaking bonds and putting things back together, and
I've
in the shortest path.
Kind regards
James
-Original Message-
From: Nicholas Firth [mailto:nicholas.fi...@icr.ac.ukhttp://icr.ac.uk]
Sent: 21 April 2015 17:44
To: James Davidson;
rdkit-discuss@lists.sourceforge.netmailto:rdkit-discuss@lists.sourceforge.net
Subject: RE: Python GetShortestPath()?
Dear
Dear James,
I tried to be helpful and show you how I do it with GetAdjacencyMatrix, however
I ran into my old friend the segmentation fault 11 as there is still some weird
error with this function.
Here's what I have though, should work for you.
from rdkit import Chem
m =
will be truncated to just 1. Based on the specifications, if you
want to include a blank line, it should actually be either a or a \t,
rather than being completely blank.
Cheers,
Paolo
On 04/29/15 12:16, Nicholas Firth wrote:
I use SD files with new lines in the properties quite frequently (inherited
Is this not a case of Schrodingers aromaticity? Until we know what the dummy
atom is, it is both aromatic and not?
Best,
Nick
Nicholas C. Firth | PhD Student | Cancer Therapeutics
The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | Surrey
| SM2 5NG
T 020 8722 4033 | E
Hi Axel,
I was sure there was something in the core that did this but I can't seem to
find it now! I have a function that uses isotope labelled dummy atoms to attach
fragments if it's of any use? As with most the code I write, it doesn't have
the greatest error handling, or rational use of
Axel,
This is excellent. I may actually be able to get other people to use my work
now I can use a nice interface!
Best,
Nick
Nicholas C. Firth | PhD Student | Cancer Therapeutics
The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | Surrey
| SM2 5NG
T 020 8722 4033 | E
Hi Eric,
I don't know if there is a recommended way, but there's an easy way for sure!
from rdkit import Chem
m = Chem.Mol() #creates a blank molecule, can use an existing RDKit molecule
though
em = Chem.EditableMol(m)
idx1 = em.AddAtom(Chem.Atom(6)) #this returns the RDKit index of the atom
We have an as yet unpublished method which is similar (but performs better)
implemented in RDKit. However we use MOE for the scaffold tree. It would be
quite easy to implement in RDKit , but I have a thesis to write!
My suggestion would be to ask Nathan to write up the paper and then give you
Looks like the problem opening the file with the extra parameters used ('t+')
as the gzip module just sticks a 'b' on the end of the opening mode
if mode and 'b' not in mode:
mode += 'b'
The test should run if line 3033 is changed from
outf = gzip.open(tempfile.mktemp(),'wt+')
to
outf =
ikely to want to see highlighting at all, it's easier to just
> turn if off:
>
> In [12]: IPythonConsole.highlightSubstructs=False
>
> In [13]: m.GetSubstructMatch(Chem.MolFromSmiles('CO'))
> Out[13]: (1, 2)
>
> In [14]: m.__sssAtoms
> Out[14]: []
>
>
>
> I hope thi
Howdy RDKitters,
Been a while since I used this list, so forgive me if my question is silly.
I'm seeing some weird behaviour from drawing molecules. I've got some
wrapper classes that I'm using to write some de novo design code, which
involves fragmenting molecules, and I've obviously been
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