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

Same here. I would also add the standardisation work done by Francis Atkinson at the EBI as an additional starting point. George. Sent from my giPhone > On 16 Jan 2018, at 17:19, JP wrote: > > Joining the fray, +1 for MolVS > >> On 16 January 2018 at 16:00,

Re: [Rdkit-discuss] Default behavior of certain calls

Great example of functools.partial. For those who like functional programming, it can also be used with map and imap when a function needs more than one parameters. George. Sent from my giPhone > On 12 Oct 2017, at 19:04, Andy Jennings wrote: > > Hi Paolo, > >

Re: [Rdkit-discuss] RDKit-fingerprints set all bits for complex molecules?

Example: https://www.surechembl.org/chemical/SCHEMBL1895 George. Sent from my giPhone > On 1 Jun 2017, at 17:05, Greg Landrum wrote: > > Hi Nils, > > Can you please send me the SMILES for those structures (or point me to an > easy way to lookup a SCHEMBL id)? > > I

Re: [Rdkit-discuss] substructure of a fingerprint position

https://iwatobipen.wordpress.com/2017/01/08/get-bit-information-with-rdkit/ George. Sent from my giPhone > On 26 Jan 2017, at 11:02, Gonzalo Colmenarejo > wrote: > > Hi, > > is there a way in RDKit to retrieve the substructure(s) corresponding to a > (hashed

Re: [Rdkit-discuss] Extracting SMILES from text

:) George. Sent from my giPhone > On 2 Dec 2016, at 22:11, Dimitri Maziuk <dmaz...@bmrb.wisc.edu> wrote: > >> On 12/02/2016 03:12 PM, George Papadatos wrote: >> Here's a pragmatic idea: > ... would it not be safe to >> assume that *any *word containing more t

Re: [Rdkit-discuss] Extracting SMILES from text

Here's a pragmatic idea: If Alexis wants to search for valid SMILES strings representing typical *organic *molecules among text of plain English words, would it not be safe to assume that *any *word containing more than 4 'C' or 'c' characters would only be a SMILES string? This simple filter

Re: [Rdkit-discuss] Extracting SMILES from text

I think Alexis was referring to converting actual SMILES strings found in random text. Chemical entity recognition and name to structure conversion is another story altogether and nowadays one can quickly go a long way with open tools such as OSCAR + OPSIN in KNIME or with something like this:

Re: [Rdkit-discuss] comparing two or more tables of molecules

HI Stephen, Further to Greg's excellent reply, see this paper on how InChI strings and keys can be used in practice to map together tautomer (ones covered by InChI at least), isotope, stereo and parent-salt variants. http://rd.springer.com/article/10.1186/s13321-014-0043-5 Francis (cc'ed) has a

Re: [Rdkit-discuss] Fingerprints_calculation

Hi Sahil, You'll find the same documentation as a Jupyter Notebook here: http://nbviewer.jupyter.org/github/chembl/mychembl/blob/master/ipython_notebooks/02_myChEMBL_RDKit_tutorial.ipynb#Morgan-Fingerprints-(Circular-Fingerprints) Cheers, George On 1 October 2016 at 04:17, Greg Landrum

Re: [Rdkit-discuss] OCEAN: Our Target Prediction Paper (including Source Code)

Hi guys, Congrats - great use of ChEMBL and myChEMBL too :) George On 27 September 2016 at 05:13, Paul Czodrowski < paul.czodrow...@merckgroup.com> wrote: > Dear RDKitters, > > > > Our target prediction method – fully based on RDKit – has become online: > > OCEAN: *O*ptimized *C*ross

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

Axel, this is seriously cool! Many thanks! George On 2 July 2015 at 13:31, Axel Pahl axelp...@gmx.de wrote: Dear fellow RDKitters, the RDKit community is always so helpful that I wanted share back two functions that I use in the IPython Notebook from which I thought that they could be of

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

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* *activity* space. This threshold varies depending on the fingerprint and the dataset of course. See here for some generalised insights: (1)

Re: [Rdkit-discuss] generating scaffold trees

Hi all, Coincidentally, we had a chat about this with James the other day. Maybe the good colleagues at the ICR have implemented this already with RDKit? Nick? Cheers, g On 22 May 2015 at 13:38, Axel Pahl axelp...@gmx.de wrote: Dear RDKitters, has someone used the RDKit to generate

Re: [Rdkit-discuss] rdkit.version()

Hi Soren, from rdkit import rdBase print rdBase.rdkitVersion Cheers, George On 11 December 2014 at 18:22, Soren Wacker swac...@ucalgary.ca wrote: Hi, I would like to find out the currently installed version on my System. However, I cannot find a version string in RDKit. Something like

[Rdkit-discuss] myChEMBL

Hi all, Further to Michał's announcement earlier, let me use this opportunity to announce the new release of myChEMBL, as I'm sure it will be relevant to many of you. myChEMBL is an open platform which consists of a Linux (Ubuntu) Virtual Machine featuring a PostgreSQL schema with the latest

Re: [Rdkit-discuss] flexmatch in RDKit cartridge?

-- Jan On 2014-02-20 13:46, George Papadatos wrote: Hi there, Wouldn't that be (at least partly) possible with an exact structure search? - @= : returns whether or not two molecules are the same. Cheers, George On 20 February 2014 11:59, Greg Landrum greg.land...@gmail.com wrote

Re: [Rdkit-discuss] flexmatch in RDKit cartridge?

Hi there, Wouldn't that be (at least partly) possible with an exact structure search? - @= : returns whether or not two molecules are the same. Cheers, George On 20 February 2014 11:59, Greg Landrum greg.land...@gmail.com wrote: Sounds interesting. Can anyone provide a pointer to a doc

Re: [Rdkit-discuss] InChI roundtrip

OK just to add some fuel to this fire: A colleague of mine and I looked at the inchi roundtrip using KNIME 2.9 and the latest versions of indigo and rdkit nodes. We used ~90,000 inchis from chembl_17, converted them to mols (sanitise + remove Hs), removed the ones that fail to convert, and then we

Re: [Rdkit-discuss] InChI roundtrip

difference for the examples I've tried. Igor On Thu, Jan 30, 2014 at 2:07 PM, George Papadatos gpapada...@gmail.comwrote: OK just to add some fuel to this fire: A colleague of mine and I looked at the inchi roundtrip using KNIME 2.9 and the latest versions of indigo and rdkit nodes. We used

[Rdkit-discuss] MDS using RDKit, SciKit and Pandas

Hi RDKitters, This is not a question, more like an FYI. Inspired by Noel's related post: http://baoilleach.blogspot.co.uk/2014/01/convert-distance-matrix-to-2d.html, I've put together an iPython Notebook example that performs MDS on a bunch of ChEMBL compounds (i.e. visualises their chemical

[Rdkit-discuss] postgres FPs in python

Hi there, DB-related question again: When I retrieve fps from a postgres db, they look like this: \x020c00102204810001040001981408420180400040048088c020800423a192001814002021044200092400040208 Is there are way to convert them to RDKit bitvector fingerprint

[Rdkit-discuss] Friday pandas q

Question to rdkit pandas users (pandaskitters?): I managed to have the mol_send(m) object in a pandas frame: [image: Inline images 1] if I do this: data['mol'].map(str).map(Chem.Mol) I get the mol in base64 PNG: [image: Inline images 2] How do I display the column as rendered images (and keep

Re: [Rdkit-discuss] Friday pandas q

= pd.DataFrame(d,columns=('molregno','pkl')) df2['romol']=df2.apply(lambda x:Chem.Mol(str(x['pkl'])),axis=1) PandasTools.RenderImagesInAllDataFrames() del df2['pkl'] df2.head(2) -greg On Fri, Oct 25, 2013 at 4:43 PM, George Papadatos gpapada...@gmail.comwrote: Question to rdkit pandas

Re: [Rdkit-discuss] Notes from the 2013 UGM

Hi all, I'd also like to thank you all for attending this UGM at the EBI and contributing to its success. And, of course, a big thanks to Greg for, well, you know. :) See you all next year - or sooner! George On 22 October 2013 09:09, Greg Landrum greg.land...@gmail.com wrote: Hi, Looks

[Rdkit-discuss] rdkit mol objects from sql

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 generated by the cartridge, is there a way to retrieve them using a psycopg2 connection within python - ideally inside a pandas dataframe? I've got this snippet: import pandas

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

...@inhibox.com wrote: 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

Re: [Rdkit-discuss] RDKit UGM 2013 - a few pictures

Lovely pics Paul. Many thanks, g On 14 October 2013 16:56, Paul Emsley pems...@mrc-lmb.cam.ac.uk wrote: https://www.dropbox.com/sh/a3s55kmxa37yx7e/vLC5uea1xP Paul. -- October Webinars: Code for Performance

Re: [Rdkit-discuss] Problem drawing molecules under windows

Hi Andrea, Seems like a font problem to me, which could indicate the lack of cairo/pango libraries. George On 26 September 2013 17:29, Greg Landrum greg.land...@gmail.com wrote: Hi Andrea, On Thu, Sep 26, 2013 at 10:59 AM, Andrea Volkamer volka...@bio.mx wrote: ** I am relatively new

[Rdkit-discuss] failed tests for github master version on ubuntu

Hi there, I tried to install RDKit on a fresh Ubuntu 13.04 VM today. I checkout out the source from GitHub master but I got the following errors after ctest: 65% tests passed, 28 tests failed out of 79 Total Test time (real) = 23.19 sec The following tests FAILED: 4 - pyBV (Failed) 5 -

Re: [Rdkit-discuss] failed tests for github master version on ubuntu

- pythonTestDirChem (Failed) Errors while running CTest Do you have any ideas why that might be? Is it safe to ignore it? George On 25 September 2013 10:04, George Papadatos gpapada...@gmail.com wrote: Hi there, I tried to install RDKit on a fresh Ubuntu 13.04 VM today. I checkout out the source from

Re: [Rdkit-discuss] failed tests for github master version on ubuntu

to try $ cd rdkit/Chem $ python test_list.py and see what is actually failing. HTH, Paolo On 09/25/2013 11:27 AM, George Papadatos wrote: Hello again, Sorry for the false alarm - that was me messing up with the env variables and not having enough coffee to realise it earlier! However

Re: [Rdkit-discuss] name generator

I think this is not an actual structure to name converter but a look-up service based on a a predefined dictionary. If this is true, then it won't return anything for any novel/unseen structures. Give it a try and let us know. George. Sent from my giPhone On 27 Aug 2013, at 18:39, David

Re: [Rdkit-discuss] MMP analysis - active vs. inactive compounds

Hi Paul, I guess you firstly have to generate the list of MMPs as per Jameed's code, secondly you join your property values for MolID1 and MolID2 and finally you calculate the property difference/ratio for each MMP. Best regards, George On 3 May 2013 12:10, paul.czodrow...@merckgroup.com

[Rdkit-discuss] Cartridge problems (again) Ubuntu 64-bit

Hi RDKitters, So I've successfully installed RDKit from the *svn trunk* on a brand new Ubuntu Server 12.10 64-bit VM. All 77/77 tests passed. Yay. When I tried to build the cartridge against psql 9.1.8, 4/8 tests failed: ## Build RDKit Cartridge cd $RDBASE/Code/PgSQL/rdkit make sudo make

Re: [Rdkit-discuss] Cartridge problems (again) Ubuntu 64-bit

in the rdkit fingerprint. Don't worry about them. I will fix those tests after the fingerprint changes settle down, definitely before the next release. -greg On Mar 21, 2013, at 1:22 PM, George Papadatos gpapada...@gmail.com wrote: Hi RDKitters, So I've successfully installed RDKit from

Re: [Rdkit-discuss] problems with RDKit and Mountain Lion

if it's relevant or not: I have not yet done an rdkit build with boost 1.51, so I am not sure that the problem isn't there -greg On Tuesday, October 9, 2012, George Papadatos wrote: Hi James, You're right. I checked out the true HEAD which is 2234 but it still failed! This is the make

Re: [Rdkit-discuss] problems with RDKit and Mountain Lion

On 10 October 2012 02:35, Greg Landrum greg.land...@gmail.com wrote: Just an FYI, not sure if it's relevant or not: I have not yet done an rdkit build with boost 1.51, so I am not sure that the problem isn't there -greg On Tuesday, October 9, 2012, George Papadatos wrote: Hi James

Re: [Rdkit-discuss] problems with RDKit and Mountain Lion

...@gmail.com wrote: George- My templating fix was submitted as 2155, and HEAD in SVN is at 2234. I'm not terribly familiar with homebrew, or why it thinks 2148 is HEAD James On Tue, Oct 9, 2012 at 2:27 PM, George Papadatos gpapada...@gmail.comwrote: Hi James, Many thanks

Re: [Rdkit-discuss] parallel conformation generation

Hi Andrew, Thanks for this. I didn't know about the futures and progressbar modules. You wrote: --- *I have to use the zip because map(f, iterable, [chunksize=None]) only takes a single iterable. This also means I need to change the generateconformations function so that it takes a single

Re: [Rdkit-discuss] Reading files (SmilesMolSupplier, SDMolSupplier

Hi Fabian, The first one is easy: the function expects a header in the file by default. There is a parameter that toggles this but I don't have access to a computer right now. There is an example in the documentation. Best regards, George Sent from my gPad On 7 Sep 2012, at 13:34, Fabian

Re: [Rdkit-discuss] Faulty valence for nitrogen in aromatic ring

Wow, this almost makes me wanting to re-write my thesis in LaTeX. Almost! :) George On 15 August 2012 16:26, Greg Landrum greg.land...@gmail.com wrote: On Wed, Aug 15, 2012 at 5:10 PM, Michael Palmer mpal...@uwaterloo.ca wrote: Now that I've at least tried to clear up what is going on,

Re: [Rdkit-discuss] windows binary install

Hi Alan, You're almost there but it seems now that you need to upgrade your numpy from 1.4 to 1.6. Regards, George P. Sent from my gPhone On 11 Aug 2012, at 21:38, stanley5101 stanley5...@yahoo.co.uk wrote: I've gone to this archived message and installed the library mentioned. It

Re: [Rdkit-discuss] cartridge problems

, George On 29 May 2012 23:27, George Papadatos gpapada...@gmail.com wrote: Hi Jan, Many thanks for the reply. Yes, I used apt-get and the default repositories to install postgresql on a Ubuntu 12.04. I'll follow your guidelines and the new repos tomorrow and I'll let you know. Many

Re: [Rdkit-discuss] cartridge problems

On 30 May 2012 12:48, Jan Holst Jensen j...@biochemfusion.com wrote: On 2012-05-30 13:24, George Papadatos wrote: Thanks to both of you. I do not know how to check for the PG_VERSION_NUM. I tried to edit to guc.c by removing the conditional check of the PG_VERSION but with the same results

Re: [Rdkit-discuss] cartridge problems

Compare it with this one: georgep@george-VB:~/local/rdkit/rdkit_trunk/Code/PgSQL/rdkit$ make installcheck /usr/lib/postgresql/9.1/lib/pgxs/src/makefiles/../../src/test/regress/pg_regress --inputdir=. --psqldir='/usr/lib/postgresql/9.1/bin' --dbname=contrib_regression rdkit-91 props btree molgist

[Rdkit-discuss] Python 2.7 binaries for WinXP VirtualBox - FYI

! Regards, George Papadatos -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint

Re: [Rdkit-discuss] Failed Expression: pick = 0

for each parent structure, try (mysql-specific): select cs.molregno, group_concat(mh.molregno), cs.molfile, cs.canonical_smiles from compound_structures cs, molecule_hierarchy mh where cs.molregno = mh.parent_molregno group by cs.molregno I hope it hels. Best regards, George Papadatos EMBL-EBI

[Rdkit-discuss] Strange SMILES behaviour

Hello all, Could anyone please explain this: In [21]: Chem.CanonSmiles('C1=CC=C2C(=C1)NC=S2') Out[21]: 'c1[nH]c2c2s1' In [22]: Chem.MolFromSmiles(Out[21]) [16:47:14] Can't kekulize mol In other words, how is it possible that a valid RDKit SMILES output fails to be converted to molecule

Re: [Rdkit-discuss] Strange SMILES behaviour

Thanks for the prompt reply Greg; this is what I suspected too! Regards, George On 12 March 2012 17:22, Greg Landrum greg.land...@gmail.com wrote: Hi George, On Mon, Mar 12, 2012 at 5:58 PM, George Papadatos gpapada...@gmail.com wrote: Could anyone please explain this: In [21

Re: [Rdkit-discuss] 2011.09 (Q3 2011) RDKit release

Hi James, This looks like there are missing dlls from the lib folder. The easiest solution would to be copy all the files from the lib folder of the previous (working) RDKit version and paste them in the lib folder of the current one (without overwriting them). Regards, George On 16 October

Re: [Rdkit-discuss] 2011.09 (Q3 2011) RDKit release

Hi Greg, This should work - this is how I solved a similar problem with the latest RDKit version for Windows. Cheers, George On 16 October 2011 16:32, Greg Landrum greg.land...@gmail.com wrote: I'm traveling and don't have access to the machine where I normally do windows builds, but I

Re: [Rdkit-discuss] Partial/Rooted/Anchored Morgan Fingerprint

Hi Greg, That's great , thanks a lot for your help. Regards, George On 30 September 2011 07:01, Greg Landrum greg.land...@gmail.com wrote: Hi George, On Thu, Sep 29, 2011 at 1:11 PM, George Papadatos gpapada...@gmail.com wrote: I'd like to calculate the *rooted* Morgan fingerprint

Re: [Rdkit-discuss] label properties on 2D depiction

Hi all, On a related topic, is it possible to depict an arbitrary string on a cairo canvas? I am thinking particularly depicting the name or ID of a molecule below its structure. Regards, George On 12 July 2011 06:36, Peter Schmidtke pschmid...@ub.edu wrote: Thanks Greg, I'll give it a try

Re: [Rdkit-discuss] random forest in RDKit

Hi guys, I'd also be interested in some ML examples. Regards, George On 2 May 2011 20:52, Igor Filippov igor.v.filip...@gmail.com wrote: Hi Greg, Yes, actually for this project I'm interested in Python specifically! Time to learn me some new tricks :) I was looking through the docs

Re: [Rdkit-discuss] Python 2.7 binaries for win32

caused the problem for me. Removing the '90' from the 2 dlls in lib folder seems to do the trick. Regards, George On 18 April 2011 08:17, George Papadatos gpapada...@gmail.com wrote: Hi Uwe, Thanks for the reply. Perhaps I did not make it clear but what I meant is that I appended %RDBASE%\lib

Re: [Rdkit-discuss] Python 2.7 binaries for win32

Hi Uwe, Thanks for the reply. Perhaps I did not make it clear but what I meant is that I appended %RDBASE%\lib to the PATH variable. Regards, George Sent from my gPhone On 18 Apr 2011, at 07:49, Uwe Hoffmann chemis...@uwe-hoffmann.de wrote: Hi George, Am 17.04.2011 12:03, schrieb George

Re: [Rdkit-discuss] Python 2.7 binaries for win32

Cheers, Greg. George On 17 April 2011 06:14, Greg Landrum greg.land...@gmail.com wrote: Dear all, After a couple of requests, I just uploaded a win32 build of the 2011.03 release that supports Python 2.7 to both the google code and sourceforge download sites. Best Regards, -greg

Re: [Rdkit-discuss] Installation driving me mad (RDKit on Centos 5.4 final)

Landrum greg.land...@gmail.com wrote: I'm not convinced of that. I'm pretty sure that I have built numpy on redhat and ubuntu systems without ever installing lapack. -greg On Wed, Feb 23, 2011 at 12:06 PM, George Papadatos gpapada...@gmail.com wrote: ...yet you need them to build

[Rdkit-discuss] KNIME + Java RDKit library

folder, I included all the .jar files and the RDKFuncs.dll. Any ideas??? Regards, George Papadatos -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM

[Rdkit-discuss] Antwort: Installation fails for KNIME nodes

Hi Paul, No worries! :) Regards, George -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3. Spend less time writing and rewriting code

[Rdkit-discuss] KNIME + Java RDKit library problem

folder, I included all the .jar files and the RDKFuncs.dll. Any ideas??? Regards, George Papadatos -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5

Re: [Rdkit-discuss] KNIME + Java RDKit library problem

Hi Thorsten and Greg, Many thanks for your replies. On 16 November 2010 20:16, Thorsten Meinl thorsten.me...@uni-konstanz.dewrote: Hi George, I installed the RDKit nodes for KNIME (by copying the plugins folder manually, as I too had problems with the 'update from file' feature).