Re: [Rdkit-discuss] RDKit molecule standardization/normalization protocol

after neutralizing charges in the pipeline above? Many thanks, On Thu, 24 Jun 2021 at 18:58, Paolo Tosco wrote: > Hi JP, > > the problem is caused by the reaction SMARTS that standardizes pyridine > *N*-oxides being not very specific and also hitting your molecule, which > is not

Re: [Rdkit-discuss] RDKit molecule standardization/normalization protocol

slightly weird going on. A (successfully) sanitized mol from SMILES "Cn1c(=O)c2nc[nH][n+](=O)c2n(C)c1=O", which when passed to Cleanup(...) starts spitting out can't kekulize errors. I have created a jupyter notebook to highlight this; https://nbviewer.jupyter.org/

[Rdkit-discuss] RDKit molecule standardization/normalization protocol

github.com/susanhleung/rdkit/blob/dev/GSOC2018_MolVS_Integration/rdkit/Chem/MolStandardize/tutorial/MolStandardize.ipynb (thanks!). This is not exactly a cleaning pipeline, but still quite helpful to understand these methods. Many thanks, JP ___ Rdk

Re: [Rdkit-discuss] Sanitization of molecules breaks something for conformer gen (Possible Bug?)

> It would be great if you (or your student) could create a github issue for this, I will go ahead and take a look. I will, thanks for looking into this. On Thu, 15 Nov 2018 at 06:35, Greg Landrum wrote: > Hi JP, > > I am able to reproduce this. > It's not dir

[Rdkit-discuss] Sanitization of molecules breaks something for conformer gen (Possible Bug?)

oblem here: https://nbviewer.jupyter.org/gist/jp-um/528a300f6b46251377f3129576b61616 Also, a list of other molecules which exhibit this same behaviour (just the ones we came across, as we only looked at a small subset of DUDE targets): Adenosine A2a receptor (GPCR)/ 28499( C1=CC2=c3nn/c(=N\N=C\[C@ @

[Rdkit-discuss] RDKit 2018.03.1, python 3, Postgresql and conda cocktail

Dear all, Long time, no type. I am on Debian 9.4 (stretch) and I want to install RDKit latest and greatest (2018.03.1 -- as I am after the excellent ETKDGv2), and the Postgresql cartridge all in python3 (as python2 is for the damned! :-) ). Reading the install instructions at

Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

Joining the fray, +1 for MolVS On 16 January 2018 at 16:00, Brian Cole wrote: > +1 to the MolVS project as well. > > Perhaps an easy bite-size project is to incorporate the open source mae > parser code into core RDKit: https://github.com/schrodinger/maeparser > > > On Mon,

Re: [Rdkit-discuss] Docker with (latest) rdkit+jupyter

cairo cairocffi jupyter RUN mkdir /notebooks CMD jupyter-notebook --ip="*" --no-browser --allow-root --notebook-dir=/notebooks On 21 November 2017 at 18:51, Markus Sitzmann <markus.sitzm...@gmail.com> wrote: > Hi JP, > > From the Docker log you posted it is obvious that the

[Rdkit-discuss] Docker with (latest) rdkit+jupyter

t;conda info " to see the dependencies for each package. The command '/bin/sh -c conda install -y nomkl rdkit pandas cairo cairocffi jupyter' returned a non-zero code: 1 Any ideas? JP -- Check out the vibrant tech comm

Re: [Rdkit-discuss] Is python 2.6(.6) still supported?

Thanks for the eye opener Greg! Will investigate anaconda. I have always somewhat resisted ... Have a good evening! And thanks for the impressive <5min time_to_reply On 19 July 2017 at 22:09, Greg Landrum <greg.land...@gmail.com> wrote: > Hi JP, > > Python 2.6 is no long

[Rdkit-discuss] Is python 2.6(.6) still supported?

. Thanks, JP -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss

Re: [Rdkit-discuss] Installation woes: Ubuntu 16.04, Boost 1.61, and RDKit not living so peacefully together after all ...

, LD_LIBRARY_PATH, and removing the boost-related cmake flags. So this is certainly an issue with wrong libraries being picked up. On 21 June 2017 at 07:29, Greg Landrum <greg.land...@gmail.com> wrote: > did you build boost serialize? > > On Mon, Jun 19, 2017 at 12:03 PM, J

Re: [Rdkit-discuss] Installation woes: Ubuntu 16.04, Boost 1.61, and RDKit not living so peacefully together after all ...

t. > > -greg > > > On Mon, Jun 19, 2017 at 9:39 AM, JP <jeanpaul.ebe...@inhibox.com> wrote: > >> HI Paul, >> >> Funny you should mention that. I have boost 1.61 (installed manually in >> /opt) and system boost I installed via sudo apt-get install >&g

Re: [Rdkit-discuss] Installation woes: Ubuntu 16.04, Boost 1.61, and RDKit not living so peacefully together after all ...

LD_LIBRARY_PATH. Thanks for your help and time. I really appreciate it. Cheers On 16 June 2017 at 14:12, Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote: > On 16/06/2017 12:08, JP wrote: > >> Hi Folks, >> >> Must have been eons ago last time I posted to this mailing

[Rdkit-discuss] Installation woes: Ubuntu 16.04, Boost 1.61, and RDKit not living so peacefully together after all ...

mplate_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") I know, I know, not the most glamorous of a comeback ... Beers and Cheers, JP --

Re: [Rdkit-discuss] [off topic] What comes next

May the force be with you! (Looking forward to some excellent and very exciting times for the RDKit community!) On 8 December 2015 at 06:06, Greg Landrum wrote: > TL;DR: I'm leaving Novartis at the end of January. Starting in February I > will be splitting my time

Re: [Rdkit-discuss] RDKit Tools for the IPython Notebook

Just WOW Axel. This is useful. Perhaps they will be merged in some future version of RDKit? - Jean-Paul Ebejer Early Stage Researcher On 2 July 2015 at 15:20, George Papadatos gpapada...@gmail.com wrote: Axel, this is seriously cool! Many thanks! George On 2 July 2015 at 13:31, Axel

Re: [Rdkit-discuss] Memory management during conformer generation

molecule (set name / remove similar confs etc / remove high energy stuff), write it to file and release it ? in the if mol: clause... Cheers JP - Jean-Paul Ebejer Early Stage Researcher On 24 June 2015 at 16:47, az adam.zalew...@mail.com wrote: Hi Using the cookbook code as basis (apologies if I

Re: [Rdkit-discuss] Molecular dis / similarity using fingerprints

with a set of numbers. - Jean-Paul Ebejer Early Stage Researcher On 26 May 2015 at 12:57, George Papadatos gpapada...@gmail.com wrote: Hi JP, Aha, so you're looking for a threshold that will exhibit the optimal balance between the false positives and false negatives in the *biological

Re: [Rdkit-discuss] Molecular dis / similarity using fingerprints

of similarity. But that is a tricky number to get right - too high and you remove nothing, too low and you start catching different molecules. I guess the best thing is try a few values (0.5, 0.6, 0.7, 0.8, 0.9) and have a visual look at the remaining compounds. - JP

[Rdkit-discuss] Molecular dis / similarity using fingerprints

the two? (say using n bits gives same results as GetMorganFingerprint). How come the GetMorganFingerprint method has no user-defined length for the fingerprint? What are the hashed equivalents of these fingerprints (e.g. GetHashedMorganFingerprint) ? Take care, JP ps A small suggestion, if I am

[Rdkit-discuss] Help building the RDKit cookbook

Yo Folks, I need some help building the RDKit documentation (how meta, I need documentation on the documentation). I go in $RDBASE/Docs/Book and I 'make html' which barfs the following: mkdir -p _build/html/api mkdir -p _build/html/cppapi cp /opt/RDKit_master/rdkit/docs/* _build/html/api cp:

Re: [Rdkit-discuss] Clustering in RDKit (take 2 - missing wiki link)

This is now at: https://github.com/rdkit/rdkit/blob/master/Docs/Book/Cookbook.rst - Jean-Paul Ebejer Early Stage Researcher On 11 April 2015 at 10:46, JP jeanpaul.ebe...@inhibox.com wrote: Hi RDKitters! I have a bit of python RDKit clustering code using Butina which is commented

[Rdkit-discuss] Clustering in RDKit (take 2 - missing wiki link)

Hi RDKitters! I have a bit of python RDKit clustering code using Butina which is commented with: # Ripped off from https://code.google.com/p/rdkit/wiki/ClusteringMolecules Sadly, and as it happens I need to refer back to this. This was written by Greg, I think as a result of this nudge:

Re: [Rdkit-discuss] RDKit, Inchi, Stereochemistry !

there is a problem in RDKit which is always detecting one of the rings as aromatic (the Inchi doesn't seem to agree on the aromaticity). I hope this is helpful. JP - Jean-Paul Ebejer Early Stage Researcher On 20 February 2015 at 08:00, Greg Landrum greg.land...@gmail.com wrote: A general comment

[Rdkit-discuss] RDKit, Inchi, Stereochemistry !

/gist.githubusercontent.com/anonymous/7c158926a0f3bf9a4978/raw/d91cc808ac91eccc8bf0e45d9eacd2af382e5105/gistfile1.txt I appreciate if anyone could shed some light. I'd just like to understand. Thank you for your time! - JP -- Download

Re: [Rdkit-discuss] RDKit compile is successful, but python does see RDKit?

-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.uk wrote: Hi, On one our Ubuntu machines, I’ve installed RDKit (compiled from source to get the latest version); ctest passed all tests

[Rdkit-discuss] Inchi installation in postgresql database driving me mad

Hi there RDKitters, I am trying to install inchi functionality from the database, and all I keep getting is: testdb=# select mol_inchi('CCC'::mol); mol_inchi - InChI not available (1 row) SO what I have done till now... From external/INCHI-API - I execute

Re: [Rdkit-discuss] Inchi installation in postgresql database driving me mad

')); mol_inchi - InChI not available (1 row) BOOM !!! - Jean-Paul Ebejer Early Stage Researcher On 12 February 2015 at 15:52, Riccardo Vianello riccardo.viane...@gmail.com wrote: Hi Jean-Paul, On Thu, Feb 12, 2015 at 3:37 PM, JP jeanpaul.ebe...@inhibox.com wrote: cd

Re: [Rdkit-discuss] Inchi installation in postgresql database driving me mad

of the window. Thanks Greg and Roccardo for your ideas -- I wouldn't have noticed this if you hadn't pointed me in the right direction! - Jean-Paul Ebejer Early Stage Researcher On 12 February 2015 at 16:57, JP jeanpaul.ebe...@inhibox.com wrote: On 12 February 2015 at 16:31, JP jeanpaul.ebe

[Rdkit-discuss] molecule not draw well

Just a FYI The following molecule: Cc1ccc(C[NH+]2C32CC(NC(=S)Nc2c2C)C3)cc1 looks broken when drawn with 2014.09.1 (attached). Thanks, - Jean-Paul Ebejer Early Stage Researcher -- Dive into the World of Parallel

Re: [Rdkit-discuss] Ridiculously easy problem - capture RDKit's error messages

-shared-library-to-a-variable - but this isn't very pythonesque and/or understandable. So all in all an unproductive afternoon fighting with 6 to 8 lines of code, but I can say the python has been finally tamed. For today. Have a good weekend folks and thanks for all your answers. Beertime, JP

Re: [Rdkit-discuss] Error in reading sdf format

The problem is in the data file -- I added an example, benzene, from wikipedia, and fixed the first one of your molecules for you (attached). Amongst other things - the first three lines are header lines ( http://en.wikipedia.org/wiki/Chemical_table_file), you only have two of those. I find the

Re: [Rdkit-discuss] Explicit valence error when reading sdf files

On 11 July 2014 23:41, Wendy Carande wcara...@gmail.com wrote: 10104489 TRC 05231419153D PM6 optimization, min free energy conformation 14 14 0 0 0 0 0 0 0 0999 V2000 -0.43072.08890.2792 H 0 0 0 0 0 0 0 0 0 0 0 0 0.04071.10710.2148 C 0 0

[Rdkit-discuss] Minimizing a Boron containing molecule with MMFF94 ... surprising

in conformer_ids: ff = AllChem.MMFFGetMoleculeForceField(mol_h, prop, conf_id) print ff # for boron none emin(CCC(C)(C)C) # works emin(BCC(C)(C)C) # doesnt work Output: jp@jp-Galago-UltraPro:~/tmp$ ./emin.py rdkit.ForceField.rdForceField.ForceField object at 0x7fcb96e72ec0

[Rdkit-discuss] Behaviour change between RDKit versions (HasSubstructMatch)

yo RDKitters, writing this email while waiting eagerly for the Uruguay-England match in an hour or so (blame the beer for any lack of consistency beneath). Can someone explain which changes in the new RDKit result in the following behaviour change. Somehow all (as in all five of them) my tests

Re: [Rdkit-discuss] Opposite of GetSubstructureMatches()

On 16 April 2014 19:13, Christos Kannas chriskan...@gmail.com wrote: Chem.PathToSubmol(mol, path) Hi there Christos, Many thanks for your reply (and idea of using nbviewer) There is still something strange happening which I cannot figure out - my atom index is a tuple with six elements - and

[Rdkit-discuss] Opposite of GetSubstructureMatches()

Hi there RDKitters, This is probably an easy one, but I cannot find anything in the docs or the mailing list. I have a tuple of atom Ids (e.g. 21,22,24,26,27) and a mol and I would like to extract the substructure (molecule) which matches those indices. Note that in my case this will be a

Re: [Rdkit-discuss] An ultimate way to compute 3D coordinates?

I don't know about the ultimate way: but this works for me (to generate n conformers): writer = Chem.SDWriter('some_file.sdf') # add Hydrogens molH = Chem.AddHs(mol) # create n conformers for molecule confIds = AllChem.EmbedMultipleConfs(molH, n) # E optimize for confId in confIds:

Re: [Rdkit-discuss] Possible rotatable bonds replacement

). This does not come for free either, as the API becomes slightly less clean (and what to do in the future when, for example, someone finds a non-SMARTS based way to do this -- add another parameter?). Still I think this is the less of all evils. Thanks Toby Greg! JP On 31 January 2014 06:54

Re: [Rdkit-discuss] PDB reader and bond perception

Thanks Greg! Much appreciated. - Jean-Paul Ebejer Early Stage Researcher On 15 January 2014 08:38, Greg Landrum greg.land...@gmail.com wrote: On Tue, Jan 14, 2014 at 11:48 AM, Greg Landrum greg.land...@gmail.comwrote: ok, it looks like something bad happened[1] when the PDB branch was

[Rdkit-discuss] Add a charge to an atom and modify Hs accordingly (protonation)

Hi there, This must be really easy -- but anything I am trying is failing and I am losing my mind. I want to add a charge (+ / -) to an atom and add or delete a connected H accordingly. I thought an easy way to do this was to remove all Hs from the molecule (removeHs), add a charge

[Rdkit-discuss] PDB reader and bond perception

RDKitters! Finally back on the mailing list! I am sure we've been through this at the UGM (my mind must have wandered off!), but a quick question about the PDB reader and bond perception. Is this supported with the current PDB reader? I remember that someone (PaulE, perhaps?) was saying bond

Re: [Rdkit-discuss] PDB reader and bond perception

by these days) in the PDB. For posterity: I have found a post in the mailing list started by James which sheds some light on this: https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg03481.html On 13 January 2014 19:46, sereina riniker sereina.rini...@gmail.com wrote: Hi JP

Re: [Rdkit-discuss] atom coordinates

Yes, of course - try this: conf = mol.GetConformer() pt = conf.GetAtomPosition(0) Cheers JP On 8 November 2013 12:01, Michal Krompiec michal.kromp...@gmail.com wrote: Hello, In the Python API, is it possible to read the 3D coordinates of an atom (from a Mol object created from an SDF file

Re: [Rdkit-discuss] rdkit mol objects from sql

Does the following help you george? http://comments.gmane.org/gmane.science.chemistry.rdkit.user/860 On 23 October 2013 17:11, George Papadatos gpapada...@gmail.com wrote: Hi RDKitters, I must have seen this in an ipython notebook but can't find it right now: If I have a table of rdkit mols

Re: [Rdkit-discuss] New MMFF-enabled RDKit branch

On 21 September 2013 13:55, Greg Landrum greg.land...@gmail.com wrote: Something JP is particularly going to like is that Paolo also added the out-of-plane term to the RDKit UFF implementation. This means that this bug: https://github.com/rdkit/rdkit/issues/62 which was formerly this bug

Re: [Rdkit-discuss] New MMFF-enabled RDKit branch

Well done Paolo! During last year's UGM, when Greg asked for an RDKit wishlist from the audience, this functionality was suggested by more than one person. Thanks! JP On 23 August 2013 04:28, Greg Landrum greg.land...@gmail.com wrote: Thanks Paolo! I think it will be great for the RDKit

Re: [Rdkit-discuss] How to specify similarity threshold for single query?

I may have an idea for a workaround, and not a solution ... Why not try to set the parameter rdkit.tanimoto_threshold in a stored procedure and call the stored procedure from python? Instead of trying set xxx=yyy on the cursor directly. Just an idea, JP On 11 July 2013 16:52, Michał Nowotka

[Rdkit-discuss] A question of GitHub Issue tracking for RDKit

in the issue list in github? Many Thanks, JP -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev___ Rdkit-discuss mailing list Rdkit

Re: [Rdkit-discuss] aromatic nitrogens

On 25 June 2013 17:00, Igor Filippov igor.v.filip...@gmail.com wrote: Histidine How about: N[C@@H](Cc1c[nH]cn1)C(O)=O Chem.MolFromSmiles('N[C@@H](Cc1c[nH]cn1)C(O)=O') rdkit.Chem.rdchem.Mol object at 0x27ef0c0 -- This

Re: [Rdkit-discuss] aromatic nitrogens

On 25 June 2013 17:47, Igor Filippov igor.v.filip...@gmail.com wrote: I'm getting an exception at sanitizeMol - can't kekulize with this SMILES (and many many others) :( Thank you, Igor On Tue, Jun 25, 2013 at 12:14 PM, JP jeanpaul.ebe...@inhibox.com wrote: On 25 June 2013 17:00, Igor

Re: [Rdkit-discuss] Could not embed molecule. (The Anthony Conundrum)

On 21 June 2013 10:10, Greg Landrum greg.land...@gmail.com wrote: Do you mind doing a bug report on github for this? Not at all. Done. I cannot assign labels or milestones to it - I assume this is on purpose, so you can organize the issues list yourself (mind you, this is a good idea to have

[Rdkit-discuss] Could not embed molecule. (The Anthony Conundrum)

the following error: --- ValueErrorTraceback (most recent call last) /home/jp/ipython-input-30-f4834f0dae19 in module() 11 mol = Chem.MolFromSmiles('C(=O)(O)c1cncs1') 12 --- 13

Re: [Rdkit-discuss] Counting neighboring atoms including H (both implicit and explicit)

print a.GetTotalDegree() On 18 June 2013 15:54, Syeda Sabrina sus364...@gmail.com wrote: Thanks a lot JP. So the number of neighbors for an atom, does not include only the the directly connected atoms while the GetNeightbors will return atoms directly connected to the atom of interest

Re: [Rdkit-discuss] sudo apt-get install python-rdkit not working

Merci Greg, This needs an update then: https://github.com/rdkit/rdkit/blob/master/Docs/Book/Install.rst Ubuntu 12.04 and later On 15 May 2013 04:49, Greg Landrum greg.land...@gmail.com wrote: Hi JP, On Tue, May 14, 2013 at 3:43 PM, JP jeanpaul.ebe...@inhibox.com wrote: On: jpebe@ned

Re: [Rdkit-discuss] sudo apt-get install python-rdkit not working

On Wed, May 15, 2013 at 10:58 AM, JP jeanpaul.ebe...@inhibox.com wrote: Merci Greg, This needs an update then: https://github.com/rdkit/rdkit/blob/master/Docs/Book/Install.rst Ubuntu 12.04 and later On 15 May 2013 04:49, Greg Landrum greg.land...@gmail.com wrote: Hi JP, On Tue, May

[Rdkit-discuss] sudo apt-get install python-rdkit not working

On: jpebe@ned:~/dphil/ligity_vs_es_tests$ lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 12.04.2 LTS Release: 12.04 Codename: precise Fresh rdkit install via: sudo apt-get install python-rdkit librdkit1 rdkit-data Gives: import rdkit from rdkit

Re: [Rdkit-discuss] Building rdkit on Ubuntu 12.10

Trying to be helpful... A few weeks ago I wrote a blog entry on how to install RDKit on Ubuntu (tested on 12.04, 12.10): http://blopig.com/blog/?p=315 - Jean-Paul Ebejer Early Stage Researcher On 26 April 2013 03:39, Paul Emsley pems...@mrc-lmb.cam.ac.uk wrote: On 25/04/13 23:43, hari

[Rdkit-discuss] Coding convention/style?

A soft question, RDKitters. Is there an official coding convention/style when contributing to RDKit? Just wondering. Of course, it is easy to copy whatever is in https://github.com/rdkit/rdkit/tree/master/Code (but one hopes to pick some of the beautiful looking code!) And just to confirm,

[Rdkit-discuss] Feature definition of cations and anions ... a question of semantics.

Hi there RDKitters, I was wondering if there is any reason why the feature factory detects NegIonizable (or PosIonizable) as a feature - but not the actual charges i.e. Anion (or cation). If you are doing feature extraction, to build pharmacophoric models, this electrostatics data is important.

Re: [Rdkit-discuss] looking for suggestions: github vs bitbucket vs google code

I have used cvs and later svn, and never really have needed DVCS. Still, I have projects in both GitHub and BitBucket using Git (I never got around using mercurial - so I don't know which is better). CVS was quirky and buggy, but I never had any problems with SVN which is straightforward and

Re: [Rdkit-discuss] Depicting R groups follow-up

26 20-28 order: 2 conj?: 0 aromatic?: 0 27 9-10 order: 1 conj?: 0 aromatic?: 0 28 9-29 order: 2 conj?: 0 aromatic?: 0 I am quite lost, anyone knows what this actually means - any help/idea what I am doing wrong? Many Thanks, JP - Jean-Paul Ebejer Early Stage Researcher On 1 February 2013 04:04

[Rdkit-discuss] Depicting R groups follow-up

I am trying to depict R groups using a labels like R1, R2 etc. From a previous discussion: http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01793.html Here's what's going on currently: By default the rendering code uses atom.GetSymbol() to determine what should show up in the

Re: [Rdkit-discuss] computing all possible molecular descriptors from a smile string rather than .sdf file

I think this is what you need: http://www.rdkit.org/docs/GettingStartedInPython.html#descriptor-calculation - Jean-Paul Ebejer Early Stage Researcher On 31 January 2013 16:52, Leela Velautham leela.velaut...@exeter.ox.ac.ukwrote: Hey, I'm in Python and have a molecule in a smile string

Re: [Rdkit-discuss] Detecting R groups using RDKit and the MCS code (R group decomposition).

[*]c1c1.[2*]C.[2*]c1c1 chains [*]OC Now, where is the number label on each first entry? Not a big deal of course, but wrecks havoc with my regex. Also should these lists be uniquified or not? Take a look at the first example (e.g. [2*]C.[2*]C)? Thank-you, JP

[Rdkit-discuss] Detecting R groups using RDKit and the MCS code (R group decomposition).

Hola RDkitters, I have a number of analogue molecules (how lucky) - from which I can extract a scaffold using Dalke's MCS code (great piece of work, btw). I would like to identify each R group from each molecule. My current idea which I wanted to bounce with you was, for every molecule that I

[Rdkit-discuss] Volume Overlap using RDKit

RDKitters, Long time no type, I've been busy with that little chestnut of my PhD... I would like to align two molecules and calculate the shape tanimoto with ShapeTanimotoDist(...). The issue is that this method requires a pre-defined alignment - which I do not have. Is there a way how to do a

Re: [Rdkit-discuss] Volume Overlap using RDKit

January 2013 14:10, Stiefl, Nikolaus nikolaus.sti...@novartis.comwrote: Hi JP, Do you want to do a shape align or just any sort of alignment? There is a MolAlign in All.Chem which will give you an RMSD align. This works well if you have reasonably similar molecules (do a GetSubstructMatch

[Rdkit-discuss] kekulize form not matching aromatic equivalent

Hi there RDkitters, I have a molecule defined in aromatic form (c1n[nH]nn1) and I am trying to do a replace substructs on it using the equivalent kekule form as a query ('C1=N[NH1]N=N1). However the substitution does not happen. As shown by the following code: from rdkit import Chem from

[Rdkit-discuss] better error messages (vol 3)

the m = Chem.MolFromMol2Block(mol_block, sanitize=False) m.Debug() trick -- but I am none wiser. Thanks for your attention, JP #!/usr/bin/env python import rdkit from rdkit import Chem mol_block=@TRIPOSMOLECULE 2oc2_RX3 7882 1 SMALL NO_CHARGES @TRIPOSATOM 1 O1

Re: [Rdkit-discuss] better error messages (vol 3)

Please disregard this bad hair day message. I am, allegedly, a computer scientist, and I should know that counting starts from 0. Bleh, Sorry, - Jean-Paul Ebejer Early Stage Researcher On 8 November 2012 15:33, JP jeanpaul.ebe...@inhibox.com wrote: Hi there RDkitters, Poll season: Does

Re: [Rdkit-discuss] Location of C++ UFFOptimizeMolecule() function?

Finally, a question I [think I] can answer and Greg hasn't beaten me to it. Now what is the chance of that happening? So, Hans, the method is in a wrapper in $RDBASE/Code GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp: int UFFOptimizeMolecule(ROMol mol, int maxIters=200, double

Re: [Rdkit-discuss] ForwardSDMolSupplier::atEnd bug

On 10 October 2012 14:24, Greg Landrum greg.land...@gmail.com wrote: On Tue, Oct 9, 2012 at 4:44 PM, Toby Wright toby.wri...@inhibox.com wrote: Working in C++, I am calling ForwardsSDMolSupplier's method atEnd(), expecting that it returns false if there are more molecules and true if

Re: [Rdkit-discuss] parallel conformation generation

This is great Andrew (especially the subsequent explanation)! Many Thanks. Considering that this is a task lots of people will want to do - is this code CONTRIB dir material? (perhaps max_workers should be a fourth command line argument defaulting to 1) A few months (years?) back Greg

[Rdkit-discuss] Molecule equality (override == in python)

So excited for next week folks! Now to a real issue. I must be really missing something basic... I understand the below returns false because of the different Mol instances, but is there an easyish way (without comparing inchis, fingerprints, converting to canonical Smiles etc) how to override

Re: [Rdkit-discuss] RDKIT installation issue on Centos 5.6

in your LD_LIBRARY_PATH env variable? If not then you have to rebuild boost with the python library as well as the regex one. Cheers, JP -- Live Security Virtual Conference Exclusive live event will cover all the ways today's

[Rdkit-discuss] Missing GetLastItemText ?

Hi there, Using RDKit latest+greatest version of RDKit 2012_06_1. I am trying to use GetLastItemText - which has been announced in Q1 2012 - Suppliers support GetLastItemText() (http://sourceforge.net/projects/rdkit/files/rdkit/Q1_2012/). I cannot find documentation for this method. I was

Re: [Rdkit-discuss] Missing GetLastItemText ?

On 12 July 2012 18:36, Greg Landrum greg.land...@gmail.com wrote: Hi JP, On Thu, Jul 12, 2012 at 1:52 PM, JP jeanpaul.ebe...@inhibox.com wrote: hmm, that's highly embarrassing. NO IT IS NOT Sorry about that, You don't have to be. You do an incredible job at pretty much maintaining

Re: [Rdkit-discuss] Detecting rings and bond types from PDB HETATM record

Forgot to include the mailing list. doh! - Jean-Paul Ebejer Early Stage Researcher On 9 July 2012 09:23, JP jeanpaul.ebe...@inhibox.com wrote: On 6 July 2012 21:07, Paul Emsley paul.ems...@bioch.ox.ac.uk wrote: On 06/07/12 10:27, JP wrote: The SMILES is in fact, a wget call away - since

Re: [Rdkit-discuss] Detecting rings and bond types from PDB HETATM record

atoms). - Jean-Paul Ebejer Early Stage Researcher On 6 July 2012 07:33, Stiefl, Nikolaus nikolaus.sti...@novartis.com wrote: Hi JP, Not sure if this is of any help. If it's an pdb file from rcsb or an in-house one where you have a corresponding smiles available maybe you could use

Re: [Rdkit-discuss] Announcement: 1st RDKit User Group Meeting scheduled

I just noticed that this is a user meeting and not a dev one - so perhaps such a topic is out of scope... - Jean-Paul Ebejer Early Stage Researcher On 4 July 2012 16:52, Greg Landrum greg.land...@gmail.com wrote: On Wed, Jul 4, 2012 at 3:38 PM, JP jeanpaul.ebe...@inhibox.com wrote

Re: [Rdkit-discuss] Announcement: 1st RDKit User Group Meeting scheduled

...@bioch.ox.ac.uk wrote: On 06/07/12 10:06, JP wrote: I just noticed that this is a user meeting and not a dev one - so perhaps such a topic is out of scope... What's the difference? A user uses python and a dev uses python, boost.python and c++? Anyway, I too (AFAICS ATM) would be interested

[Rdkit-discuss] Detecting rings and bond types from PDB HETATM record

Hi there at RDKit, I generate a RWMol instance from the HETATM portion of a PDB file. My atoms are currently only joined by a single bond as defined in the connect portion of the pdb file, e.g. CONECT 2235 2234 2236 CONECT 2236 2231 2235 2251 CONECT 2237 2238 2242 Are there any obvious

Re: [Rdkit-discuss] Overview of clustering in RDKit

On 15 June 2012 04:36, Greg Landrum greg.land...@gmail.com wrote: Hi JP, On Wed, Jun 13, 2012 at 12:03 PM, JP jeanpaul.ebe...@inhibox.com wrote: hmm, nice idea. How about this: http://code.google.com/p/rdkit/wiki/ClusteringMolecules -greg Bravo! Many thanks Greg -- this is really helpful

[Rdkit-discuss] Molecule substructure replacement gives interesting results (fragmented)

Hi there, I have a list of molecules of which I want all to be in the same tautomeric (does this word even exist?) form. This cheat works fine using ReplaceSubstructs on my 100+ molecule with the exception of one case, where the resulting molecule is being fragmented. Can someone explain why

Re: [Rdkit-discuss] Molecule substructure replacement gives interesting results (fragmented)

Researcher On 15 June 2012 11:06, JP jeanpaul.ebe...@inhibox.com wrote: Hi there, I have a list of molecules of which I want all to be in the same tautomeric (does this word even exist?) form. This cheat works fine using ReplaceSubstructs on my 100+ molecule with the exception of one case

[Rdkit-discuss] Largest Common Substructure

Excuse the Cheminformatics 101 question. I have two molecules. Is there a way in RDKit how I can get the largest possible substructure between the two input molecules? I understand this can be done with subgraph isomorphism techniques, is there some out-of-the-box functionality for this? Does

Re: [Rdkit-discuss] Largest Common Substructure

wrote: On Fri, May 25, 2012 at 4:13 PM, JP jeanpaul.ebe...@inhibox.com wrote: Excuse the Cheminformatics 101 question. I have two molecules.  Is there a way in RDKit how I can get the largest possible substructure between the two input molecules? I understand this can be done with subgraph

[Rdkit-discuss] Is this expected/correct behaviour?

Hi there, I have hit on some surprising behaviour (to me at least), and I thought to ask for further clarification. I create a molecule without sanitization (red flag) - because, oh well, I downloaded this sd file from the web so it must be perfectly curated and what not. When I try Chem.AddHs,

Re: [Rdkit-discuss] Trying to load a large mol2 file (protein)...

ARGH Forgot to post to the group. On 9 May 2012 10:23, JP jeanpaul.ebe...@inhibox.com wrote: On 9 May 2012 05:12, Greg Landrum greg.land...@gmail.com wrote: one last question: Could this be due to the problem discussed on this thread? http://www.mail-archive.com/rdkit-discuss

[Rdkit-discuss] Trying to load a large mol2 file (protein)...

Hi for the second time today, I am trying to generate a mol instance from the attached mol2 file (which can be read by other tools). This is a format-converted receptor from the DUD set - so huge in size compared to your average ligand (around 9000 atoms). When I Chem.MolFromMol2File the file I

[Rdkit-discuss] More postgresql cartridge woes.

Just installed RDKit 2012_03_1 on Debian 6.0.4, squeeze. RDKit works fine. I also built and installed the RDKit extension for postgresql in the following manner: % cd $RDBASE/Code/PgSQL/rdkit % make % sudo make install (I also did create extension rdkit in my database) Which also seemed to

Re: [Rdkit-discuss] More postgresql cartridge woes.

: pthread_mutexattr_settype I've been playing with LD_LIBRARY_PATH ... to no avail... - Jean-Paul Ebejer Early Stage Researcher On 27 April 2012 17:03, Greg Landrum greg.land...@gmail.com wrote: On Fri, Apr 27, 2012 at 5:11 PM, JP jeanpaul.ebe...@inhibox.com wrote: Just installed RDKit 2012_03_1

[Rdkit-discuss] Keeping only parts of a molecule (a set of atom ids)

Hi there at RDKit, I have a set of atom indices from a molecule I want to keep, and any atom which is not in this list I want to discard. I thought of implementing this as follows: #!/usr/bin/env python from rdkit import Chem mol = Chem.MolFromSmiles(CCC1CNCC1CC) keep_atoms = [2,3,4] #

Re: [Rdkit-discuss] Keeping only parts of a molecule (a set of atom ids)

And as a follow up - running this: #!/usr/bin/env python from rdkit import Chem mol = Chem.MolFromSmiles(CCC1CNCC1CC) edit_mol = Chem.EditableMol(mol) edit_mol.RemoveAtom(0) for atom in edit_mol.GetMol().GetAtoms(): print atom.GetIdx() gives seg fault... jp@xxx:~/tmp$ test.py

Re: [Rdkit-discuss] Keeping only parts of a molecule (a set of atom ids)

Thanks to both of you, nice trick... - Jean-Paul Ebejer Early Stage Researcher On 22 March 2012 16:34, Eddie Cao cao.yi...@gmail.com wrote: Hi JP, Sarah was right on the trick of deleting atoms in the descending order of atom index. Regarding the segment fault, this is very likely

Re: [Rdkit-discuss] Where is my H dude? (in GetNeighbors)

Indeed - as shown in RDKit 2012.01 by: #!/usr/bin/env python from rdkit import Chem mol = Chem.MolFromSmiles(C[NH]C) for atom in mol.GetAtoms(): neighbours = [x.GetSymbol() for x in atom.GetNeighbors()] # where is my H dude? print %s has neighbours %s % (atom.GetSymbol(), ',

Re: [Rdkit-discuss] Where is my H dude? (in GetNeighbors)

represented. - Jean-Paul Ebejer Early Stage Researcher On 14 March 2012 10:46, Greg Landrum greg.land...@gmail.com wrote: Dear Jean-Paul, On Wed, Mar 14, 2012 at 11:11 AM, JP jeanpaul.ebe...@inhibox.com wrote: Indeed - as shown in RDKit 2012.01 by: #!/usr/bin/env python from rdkit import

[Rdkit-discuss] Difference between Recap and Molecular Fragments (Chapter 1.9, RDKit documentation)

Hi there everyone, A high level question. Can anyone highlight the main advantages/disadvantages of fragmenting molecules using FragmentCatalog (Chap 1.9, RDKit documentation) vs RDKit.Chem.Recap ? Probably the fragmenting rules are different, but what are the use cases for these two different

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