Re: [Rdkit-discuss] Extracting SMILES from text

I could be wrong but I believe IBM system had a preprocessing step which removed all known dictionary words - which would get rid of "submarine" etc. I also believe this problem has been solved multiple times in the past, NextMove software comes to mind, chemical tagger -

Re: [Rdkit-discuss] library name change?

static library as an option or an easy way to get a list of libs to add to the linker command. Igor On Fri, Aug 19, 2016 at 11:22 AM, Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote: > > I'd like to pick apart this comment: > > On 19/08/2016 15:45, Igor Filippov wrote: > >

Re: [Rdkit-discuss] library name change?

If we are talking about the changes to the way the libs are build is there a chance to get a (possibly optional) monolithic static library? It is sometimes a bit of a pain to collect the list of the dependencies. Alternatively some easier way to discover what belongs to what library would be

Re: [Rdkit-discuss] GetMol and GetMolFrags in C++

Did you want std::vector> > RDKit::MolOps::getMolFrags ( const ROMol & *mol*, bool *sanitizeFrags* = true, by any chance? This will return a vector of ROMol's which

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

JP, A bit of self-advertisement if I may - our Diversity Genie, which uses RDKit on the background by the way - was initially created to answer this exact question. www.diversitygenie.com - hope it may come useful. Igor On Wed, May 27, 2015 at 4:05 AM, JP jeanpaul.ebe...@inhibox.com wrote:

Re: [Rdkit-discuss] A RDKit/Scikit-learn question

Oops, sorry, got into a wrong branch! I am just repeating Maciek's answer it looks like! Igor On Fri, Feb 20, 2015 at 7:50 AM, Igor Filippov igor.v.filip...@gmail.com wrote: Maciek, I think scikit-learn is using numpy arrays and not plain Python lists. They look very similar

Re: [Rdkit-discuss] A RDKit/Scikit-learn question

Maciek, I think scikit-learn is using numpy arrays and not plain Python lists. They look very similar, but are not quite the same thing. Maybe post a bit more complete code sample for people to play with? Igor On Fri, Feb 20, 2015 at 4:06 AM, Maciek Wójcikowski mac...@wojcikowski.pl wrote:

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

with rudeness and condescension. If you are unable to present your arguments in a civilized manner then please cease this discussion. Best regards, Igor On Thu, Feb 19, 2015 at 2:53 PM, Dimitri Maziuk dmaz...@bmrb.wisc.edu wrote: On 02/19/2015 01:24 PM, Igor Filippov wrote: Markus also spelled out

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

No. there's only one definition if unique This is way too simplistic. The definition of unique depends on the application. Not only in chemistry but other fields as well. The way you just defined unique is appropriate for integer numbers, but not everything is quite so trivial. Is human face

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

update the bug report and work on tracking down the wrong problem That's how I sometimes do it too... ;) Igor On Wed, Feb 18, 2015 at 12:35 PM, Greg Landrum greg.land...@gmail.com wrote: Yep, you guys are right. I diagnosed that too quickly. Thanks for pointing out the mistake. I'll

Re: [Rdkit-discuss] Tests failing on Windows: more info

Not that I use it or recommend it but a bit of googling brought me this: http://www.appveyor.com/ Also, perhaps something is possible with azure cloud and visual studio online? HTH, Igor On Tue, Feb 10, 2015 at 11:52 PM, Greg Landrum greg.land...@gmail.com wrote: This particular problem was

Re: [Rdkit-discuss] Tests failing on Windows

I think this kind of errors pops up when the environment variables haven't been set up - RDBASE, PYTHONPATH and LD_LIBRARY_PATH. Also, make sure you run make install (or its equivalent for MSVC, I only used Linux/MSYS/OSX versions) before running the tests. Hope this helps, Igor On Fri, Jan 23,

Re: [Rdkit-discuss] ubuntu 14.04 hangs on building SLNAttribs.cpp.o

-DRDK_BUILD_SLN_SUPPORT=OFF there is an additional bonus when getting rid of sln support - boost can be used as headers-only library, it does not have to be compiled prior to rdkit compilation. Igor On Thu, Oct 9, 2014 at 10:07 AM, Michał Nowotka mmm...@gmail.com wrote: Hi, I'm trying to

Re: [Rdkit-discuss] Having problems with installing RDKit_2014_03_1 in Ubuntu

Why are you linking with a static libpyton in /usr/local/lib? Ubuntu does not come with packaged libpyton? I would try either compiling RDKit as a set of static libraries (since you're linking to a static libpyton), or getting a shared libpython.so. Or/and also try to recompile with -fPIC as the

Re: [Rdkit-discuss] MaxMin Picker and Python

Matthew, Two lines of shameless self-promotion: This is exactly the kind of problem for Diversity Genie - http://www.diversitygenie.com/ It is using RDKit library underneath, but wraps it in a simple, easy to use GUI front-end. Best regards, Igor On Wed, Jul 16, 2014 at 6:18 PM, Matthew Lardy

[Rdkit-discuss] boost::regex

Dear Greg et al, I was wondering if the only binary dependency on boost is boost::regex used in SLN reader/writer? If that is the case would it be possible to ifdef this code with a flag - I never had a need to use SLN but compiling the correct version of boost::regex and caring around associated

Re: [Rdkit-discuss] boost::regex

Fantastic! You're ahead of the curve as always! Igor On Wed, Feb 12, 2014 at 10:55 AM, Greg Landrum greg.land...@gmail.comwrote: Hi Igor, On Wed, Feb 12, 2014 at 4:42 PM, Igor Filippov igor.v.filip...@gmail.comwrote: Dear Greg et al, I was wondering if the only binary dependency

[Rdkit-discuss] RDKit+InChI on MinGW64

I ran into a small problem compiling InChI (as part of RDKit) on 64-bit Windows using MinGW64 - _strdup was defined in util.c and it also seems to be available from some default Windows library. The attached tiny patch fixed the problem for me, perhaps it will be useful to someone else as well.

Re: [Rdkit-discuss] InChI roundtrip

, 2014 at 5:05 AM, Igor Filippov igor.v.filip...@gmail.com wrote: Thank you, Greg! Very nice explanation and I think this issue has confused people before me as well. I am going to have to keep reminding myself about it as the subject comes up every now and then. Igor On Jan 29, 2014 10:59 PM

Re: [Rdkit-discuss] InChI roundtrip

29, 2014 at 2:04 PM, Igor Filippov igor.v.filip...@gmail.comwrote: Greg et al, Here is a little script that demonstrates a problem with fingerprints after the roundtrip through InChI. My input mol file is also attached. As you can see the similarity between before and after is not 1 in 45

[Rdkit-discuss] InChI roundtrip

I noticed that if I convert mol to inchi and then back to mol in quite a few cases the stereochemistry information gets lost. Is it something that is handled completely by InChI library or is RDKit not reading the mols produced from InChI correctly? Igor

Re: [Rdkit-discuss] InChI roundtrip

file? -greg On Tue, Jan 28, 2014 at 5:22 AM, Igor Filippov igor.v.filip...@gmail.comwrote: Here are some examples - original InChI were created from the original SD file, then a new SD file was created from those and new InChI calculated, called here InChI. It's a tab-separated table

Re: [Rdkit-discuss] Upcoming patch release

Are you planning V3000 support included in this release or is it slated for a later date? Igor On Sat, Jan 25, 2014 at 1:42 AM, Greg Landrum greg.land...@gmail.comwrote: Dear all, I'm just about done with the patch release to fix the PDB bond-order perception bug and am looking for any

Re: [Rdkit-discuss] Upcoming patch release

want to give it a try now. -greg On Sat, Jan 25, 2014 at 3:16 PM, Igor Filippov igor.v.filip...@gmail.comwrote: Are you planning V3000 support included in this release or is it slated for a later date? Igor On Sat, Jan 25, 2014 at 1:42 AM, Greg Landrum greg.land...@gmail.comwrote

[Rdkit-discuss] MaxMin picker

I was wondering if anyone might have a simple example how to use MaxMin picker from C++? The source code doesn't seem to have a helpful test file for this functionality and I am a bit stuck figuring out if I need to use pick or lazypick and how to construct the distance matrix in the form suitable

Re: [Rdkit-discuss] structure to IUPAC name made on RDkit?

OPSIN is doing the reverse - converts name to structure, perhaps it's possible to re-use the algorithm? Igor On Tue, Jan 14, 2014 at 1:29 PM, David Hall li...@cowsandmilk.net wrote: Certainly, RDKit can help, any cheminformatics toolkit with SMARTS/substructures to quickly classify something

Re: [Rdkit-discuss] Faster RDKit builds when you're not interested in running the tests

But this would disable static libraries as well, right? Just to make sure. I actually use more static libs than shared. Igor On Wed, Jan 1, 2014 at 2:26 AM, Greg Landrum greg.land...@gmail.com wrote: Dear all, I just checked in a small change that makes building the RDKit much faster in

Re: [Rdkit-discuss] mol 3000

. There aren't that many examples of v3000 mol files I can find in the wild and to this point I have been relying solely on Marvin sketch to confirm that things are reasonable. -greg On Saturday, December 28, 2013, Igor Filippov wrote: Greg, I remember you mentioned that adding v3000 mol

Re: [Rdkit-discuss] error: can't copy 'rdkit/rdBase.so': doesn't exist or not a regular file

chmod 700 setup.py ./setup.py build How was it ever going to work? I don't think it's in any of the build instructions. And the build instructions aren't exactly hard to find these days - unlike the old procedure with bjam, etc. RTFM seems like an appropriate response here. On Mon, Dec 16,

Re: [Rdkit-discuss] docker.io - container for fully fledged rdkit installation on linux?

independent of the Linux distribution of the host). On Wed, Nov 27, 2013 at 4:20 PM, Igor Filippov igor.v.filip...@gmail.com wrote: Not to criticize or anything, but I've seen this issue quite a few times - perhaps the problem is actually with me and everybody else is in the know? I've spent

Re: [Rdkit-discuss] Announcement: ChemicalToolBox

Looks very interesting. I will definitely check it out! Igor On Wed, Nov 20, 2013 at 3:49 AM, Greg Landrum greg.land...@gmail.comwrote: Bjoern, Congrats on the CTB and thanks for letting us know about it! -greg On Tue, Nov 19, 2013 at 9:30 PM, bjoern.gruen...@googlemail.com

Re: [Rdkit-discuss] AllChem.ReplaceSubstructs

Greg, Is it available in c++? Also, just to make sure - the argument is a list of old positions for each new position? Thanks, Igor On Thu, Nov 7, 2013 at 8:41 AM, Greg Landrum greg.land...@gmail.com wrote: Dear Michal, On Thu, Nov 7, 2013 at 12:46 PM, Michal Krompiec

Re: [Rdkit-discuss] RDkit, OS X 10.9 and clang++

There is no g++ for OSX 10.9 at all? Would one of these work by any chance? http://sourceforge.net/projects/hpc/files/hpc/gcc/ Igor On Fri, Oct 25, 2013 at 12:43 PM, William G. Scott wgsc...@ucsc.edu wrote: Dear RDkit community: I’ve been maintaining a fink package for RDkit (primarily as a

Re: [Rdkit-discuss] Inconsistancy across elements in making Hs explicit

SMILES for carbon and other common organic elements already assume implicit hydrogens, implicitly. this is not RDKit thing, it's the definition of SMILES. I'm not sure there is such thing as implicit hydrogens for Silicone even though it's so similar to Carbon. HTH, Igor On Fri, Sep 27, 2013 at

Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

don't have administrator privileges on the server. Than also means I can't switch selinux. On Tue, Sep 10, 2013 at 7:59 PM, Igor Filippov igor.v.filip...@gmail.com wrote: Some kind of an answer seems to be already given at Stackoverflow. I would add two comments: 1) Unless there are some

Re: [Rdkit-discuss] Can't read SDF data lines when CTAB is in V3000 format

Greg, Does writing V3000 format work too? How do you trigger V3000 write-out instead of V2000? I never know RDKit can work with V3000! Thanks, Igor On Wed, Aug 21, 2013 at 7:43 AM, Greg Landrum greg.land...@gmail.comwrote: Hi Toby, On Wed, Aug 21, 2013 at 12:10 PM, Toby Wright

Re: [Rdkit-discuss] Can't read SDF data lines when CTAB is in V3000 format

sounds good! Thank you, Igor On Wed, Aug 21, 2013 at 7:56 AM, Greg Landrum greg.land...@gmail.comwrote: Hi Igor, On Wed, Aug 21, 2013 at 1:49 PM, Igor Filippov igor.v.filip...@gmail.comwrote: Does writing V3000 format work too? How do you trigger V3000 write-out instead of V2000? I

[Rdkit-discuss] chirality flag

I noticed that RDKit generated MDL MOL file without the chirality flag set on the top of the mol block (there are stereo atoms with wedge and hash bonds present in the molecule): RDKit 2D 796808 0 0 0 0 0 0 0 0999 V2000 Is there any way to tell MolToMolBlock() to set the

Re: [Rdkit-discuss] chirality flag

is parsed. -greg On Tue, Jul 9, 2013 at 5:08 AM, Greg Landrum greg.land...@gmail.comwrote: Hi Igor, On Tue, Jul 9, 2013 at 1:23 AM, Igor Filippov igor.v.filip...@gmail.comwrote: I noticed that RDKit generated MDL MOL file without the chirality flag set on the top of the mol block

Re: [Rdkit-discuss] chirality flag

Fantastic - this is the fastest feature implementation ever! Igor On Mon, Jul 8, 2013 at 11:45 PM, Greg Landrum greg.land...@gmail.comwrote: yeah. There you can/should set the flag using an unsigned int. On Tue, Jul 9, 2013 at 5:44 AM, Igor Filippov igor.v.filip...@gmail.comwrote

[Rdkit-discuss] aromatic nitrogens

Dear All, I think this question has been discussed before but now that I ran into this problem I can't seem to find a solution. Is there a SMILES string for Histidine that RDKit would be happy with? It seems does not matter what I try I can't use SmilesToMol() and sanitizeMol() without them

Re: [Rdkit-discuss] aromatic nitrogens

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 Filippov igor.v.filip...@gmail.com wrote: Histidine How about: N[C@@H

Re: [Rdkit-discuss] aromatic nitrogens

, 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 Filippov igor.v.filip

[Rdkit-discuss] publication using RDKit

Dear Greg et al., You might get this a lot - I hope you do! - but our work would not be possible without RDKit. Our modeling results obtained with RDKit got recently accepted for publication - many thanks to you and everyone else who contributed to the toolkit!

Re: [Rdkit-discuss] implementation of tautomer enumeration/canonicalization

Note: another method for tautomer canonicalization (but not enumeration) is to convert to inchi and back. This is similar to Noel's canonical smiles using inchi idea. The approach may be somewhat fragile (I'm not convinced that the RDKit's inchi-molecule implementation is the best), but is

Re: [Rdkit-discuss] retrosynthesis

feature request Indeed, several people have approached me (through Open Babel) with a similar request. As Greg said, there is no existing open database of reactions. I've tried to catalyze the issue by asking Igor Filippov (of OSRA) to do reaction recognition (now in beta) and we've added

Re: [Rdkit-discuss] building models using descriptors

Thank you, Greg! As always, right on the mark! If I may bother you just a bit more :) Here's the example output: *** Vote Results *** misclassified: 93/242 (%38.43) 93/242 (%38.43) Why the same set of numbers is printed twice? average correct confidence:0.8520 average

[Rdkit-discuss] building models using descriptors

Dear Colleagues, I am following the tutorials at http://code.google.com/p/rdkit/wiki/BuildingModelsUsingDescriptors1 and http://code.google.com/p/rdkit/wiki/BuildingModelsUsingFingerprints1 to use RDKit to build a random forest model with floating point type descriptors. Perhaps someone can

Re: [Rdkit-discuss] help prioritize feature additions to the RDKit

Things like new feature proposals are not going to happen overnight, I would suggest keeping the ideatorrent (or a different feature request system) running continuously. As a matter of fact I just thought of something that is nagging me every time I compile RDKit so I put together a feature

Re: [Rdkit-discuss] maximum common substructure

I sent c++ code for MCES and MCIS for submission for OpenBabel, it should be possible in principle to modify it to work with RDKit as well. Igor On Sun, 2011-08-14 at 23:03 -0400, Greg Landrum wrote: Dear TJ, On Mon, Aug 15, 2011 at 1:03 AM, TJ O'Donnell t...@acm.org wrote: Is there a

Re: [Rdkit-discuss] depict R-group property

I don't know about reading but openbabel can certainly write out SD files with R-groups as atomic aliases. Those SD files are then displayed correctly in most molecular editors I've tested (Symyx Draw, MolSketch, ChemDraw). Igor On Tue, 2011-06-14 at 16:22 -0400, Donald Keidel wrote: Greg,

Re: [Rdkit-discuss] Antwort: Re: random forest in RDKit - ctd.

Paul, nPossible = [0]+[2]*ndescrs+[3] Then it should work. Where does ndescrs come from? Using the MorganFingerprint example from the Wiki: # build fingerprints: fps = [AllChem.GetMorganFingerprintAsBitVect(x,2,2048) for x in ms] nPossible = [0]+[2]*fps+[3] I'm new to this

Re: [Rdkit-discuss] random forest in RDKit

Igor, On Mon, May 2, 2011 at 9:52 PM, Igor Filippov igor.v.filip...@gmail.com wrote: Yes, actually for this project I'm interested in Python specifically! Time to learn me some new tricks :) Sad... I was kind of hoping to get the response: oh? only in python? never mind! because

[Rdkit-discuss] random forest in RDKit

Greg et al, Can anybody point me in the right direction (some simple code snippets would be best) how to use machine learning methods in RDkit? I am especially interested in RandomForest implementation. Thank you in advance, Igor

Re: [Rdkit-discuss] random forest in RDKit

:08 PM, Igor Filippov igor.v.filip...@gmail.com wrote: Can anybody point me in the right direction (some simple code snippets would be best) how to use machine learning methods in RDkit? I am especially interested in RandomForest implementation. The machine learning code is mostly

Re: [Rdkit-discuss] RDKit on CentOs 5

, 2011 10:11am, Igor Filippov [Contr] ig...@helix.nih.gov wrote: Dear Kirk, Thank you so much! I'm in the process of compiling gcc-4.5.1 right now, having got gmp, mpc, and mpfr built with the older version of gcc. Your instructions have to be preserved for the others, I can't

[Rdkit-discuss] RDKit on CentOs 5

Dear All, Has anyone successfully compiled RDKit on CentOs 5? I'm running into the following error message: [ 15%] Building CXX object Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o

Re: [Rdkit-discuss] RPM packages for Fedora

This is very nice work! Can I have a fedora 13 64-bit package? Best regards, Igor On Fri, 2010-11-19 at 16:57 -0500, gia...@gmail.com wrote: For those of you running Fedora I am happy to announce the availability of RPM packages so you can use rdkit without compiling stuff on your own. For

Re: [Rdkit-discuss] BEGINWEDGE and BEGINDASH

journal issue could serve as an example - http://pubs.acs.org/toc/orlef7/11/1 Igor -- Igor Filippov [Contr] ig...@helix.nih.gov

Re: [Rdkit-discuss] BEGINWEDGE and BEGINDASH

Igor, as you said, you spend a lot of time thinking about this stuff: what would you say the general rule is? -greg Oh, I'm certainly not getting into a flame war about the correct way to depict stereochemistry!!! :) I've seen people far more knowledgeable than me having arguments about

Re: [Rdkit-discuss] GUI

George, I believe the comment from Greg was that the GUI part is badly outdated and was of limited usability even in its heyday. Best, Igor On Tue, 2009-05-19 at 15:25 +, George Oakman wrote: Dear all, I was wondering if there is a GUI part of the RDKit. From the various documents it

Re: [Rdkit-discuss] Compiling on Red Hat linux

I don't think it's a question of upgrade, it's a question of actually installing lapack libs. Simply running yum install lapack lapack-devel blas blas-devel should take care of things. I have compiled RDKit on Centos 4, CentOs 5 and Fedora 8 and 9. Cheers, Igor On Fri, 2009-03-27 at 17:52

Re: [Rdkit-discuss] Structure Search Engine for All Major RDBMSs

Interesting, but 90,000 structures is a tiny database by today's standards. For CSLS - http://cactus.nci.nih.gov/cgi-bin/lookup/search we have to deal with 46 million unique structures so in-memory fingerprints might run out of memory and into problems. Another point worth mentioning is that

Re: [Rdkit-discuss] Developing on Visual C++

@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss __ Share your photos with Windows Live Photos – Free Find out more! -- Igor Filippov [Contr] ig...@helix.nih.gov

Re: [Rdkit-discuss] Developing on Visual C++

George, I compiled your example with gcc, everything works fine there. Igor On Fri, 2009-02-20 at 16:25 +, George Oakman wrote: Hi all, I am trying to write a piece of C++ code with the RDKit C++ library (I'm using Visual C++ Express edition as the development environment). Thank

Re: [Rdkit-discuss] ring stereochemistry changes

://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Igor Filippov [Contr] ig...@helix.nih.gov

Re: [Rdkit-discuss] New stuff in subversion

I tried that, also with adding --prefix=/home... to both boost and RDKit bjam run options but it's still the same error. I wonder where does it get c:/ prefix... Igor On Wed, 2008-11-26 at 20:37 +0100, Greg Landrum wrote: On Wed, Nov 26, 2008 at 8:11 PM, Igor Filippov [Contr] ig

[Rdkit-discuss] RDKit and MinGW

Dear all, Has anyone reported a successful build in MinGW environment? I'm getting some obscure error messages, the log file is attached. Igor

[Rdkit-discuss] RDKit and MinGW

And now the log file is really attached. Igor C:/msys/1.0/home/Administrator/boost_1_37_0/tools/build/v2/build\property.jam:613: in find-replace from module object(property-map)@1 error: Ambiguous key C:/msys/1.0/home/Administrator/boost_1_37_0/tools/build/v2/build\property.jam:590: in

[Rdkit-discuss] NO2 bug/feature?

or RDKit as a molecular back-end. Best regards, Igor -- Igor Filippov [Contr] ig...@helix.nih.gov

Re: [Rdkit-discuss] c++ example

patterns? Sincerely, Igor On Fri, 2008-04-04 at 16:19 +0200, Greg Landrum wrote: Dear Igor, On Fri, Apr 4, 2008 at 1:41 PM, Igor Filippov [Contr] ig...@helix.nih.gov wrote: Did you have a chance to take a look at compiling RDkit on 64-bit Linux? Unfortunately OSRA has dependencies

Re: [Rdkit-discuss] c++ example

, On Wed, Mar 26, 2008 at 4:54 AM, Igor Filippov [Contr] ig...@helix.nih.gov wrote: Thank you, very fast response and exactly the code snippet I was looking for! Glad to hear it. I'm trying to compile it now and it looks like it cannot find libblas ~/boost-jam-3.1.16-1-linuxx86/bjam