Re: [Rdkit-discuss] N-fmoc deprotection smarts error

Hi Fiorella, I don't believe your initial solution is actually wrong; I think it may just be the drawing of RDKit that is throwing you off. Whenever a red circle shows up in a mol image, that indicates the perfect overlap of two atoms. In this case, it is extra confusing because one of the atoms

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

Hi JP, Lots of good questions, and it is quite an involved topic. I'll let others who are more knowledgeable of the background answer questions on the history and relationship between the tools. One resource that may be helpful is the https://github.com/chembl/ChEMBL_Structure_Pipeline repo,

Re: [Rdkit-discuss] Problems with conda install on Google Colab

The conda-forge C++ compiler was updated recently, and this got used when building the latest 2020.09.3 release yesterday: https://github.com/conda-forge/rdkit-feedstock/pull/62/files It looks to me like the system libstdc++ is

[Rdkit-discuss] Issues with Java Compilation

Hi all, Compiling the latest version and I am having an issue I can't figure out with RDKit 2020_03. I can compile RDKit with python, without issue. But, when I throw the flag for the Java Swig wrappers I get this after everything is compiled: GraphMolJavaJAVA_wrap.cxx:227069:12: error:

Re: [Rdkit-discuss] anaconda and virtualenv

Hi Tom, If you are using Anaconda, I would recommend just using conda environments for this: https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html It is very tricky to get RDKit to work with virtualenv, but really easy with conda environments. Matt On Mar

Re: [Rdkit-discuss] [Question] Ok to switch to conda-forge for RDKit builds?

I think this demonstrates one drawback of conda-forge right now: it's best to go 'all in' on conda-forge for all packages or you run the risk of a broken environment. In this Mac example, I think the issue may just be due to minor discrepancies between the recipes on the conda-forge and rdkit

[Rdkit-discuss] Compilation Issues

Hi all, I've been fighting this again with the 2017_09_1 and the 2018_03_1 builds. Both fail to pass all of the tests and for neither does the python wrapper work at all (Java Wrappers work fine). Here is the 2017_09_1 test results: 99% tests passed, 1 tests failed out of 164 Total Test time

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

I’d be happy to help with a MolVS-inspired standardization project. Another possible starting point is the mysterious StructChecker already within RDKit... Matt On 16 January 2018 at 18:04:24, George Papadatos (gpapada...@gmail.com) wrote: Same here. I would also add the standardisation work

Re: [Rdkit-discuss] RDKit Compile Issue

% tests passed, 1 tests failed out of 1 Total Test time (real) = 2.53 sec The following tests FAILED: 5 - testMultiFPB (OTHER_FAULT) Matt On Wed, Jun 21, 2017 at 11:33 AM, Paolo Tosco <paolo.to...@unito.it> wrote: > Hi Matthew, > > try running a couple of the failing t

[Rdkit-discuss] RDKit Compile Issue

Hi all, I'm trying to get a new build for any version of RDKit from 2016_4 to the most reccent release. Everything builds correctly, but when I perform the tests each version fails at the same place: Start 5: testMultiFPB 5/116 Test #5: testMultiFPB

Re: [Rdkit-discuss] numpy array to bit vector

I don't think you even need to cast them to numpy arrays if you use scipy. It should be able to take bit arrays. Also, jaccard distance is another name for tanimoto distance. This simplifies the code above: *from __future__ import print_function from rdkit import Chem* *from rdkit.Chem import

[Rdkit-discuss] Re: conda / Windows update to 2016.09 release gives error

I've also encountered this problem with the 2016.09.2 windows packages on the rdkit conda channel. It looks like somehow the RDConfig patch in the conda recipe hasn't been applied properly in the published packages. The original lines in the rdkit are:     condaDir += ['share', 'RDKit']    

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

Sorry Steve, there was a bug in MolVS that you encountered. Should now be fixed. "pip install -U molvs" to get the update (v0.0.7). Matt > On 1 Dec 2016, at 15:52, Stephen O'hagan wrote: > > Thanks for the interesting links. > > MolVS looks good, but failed on

Re: [Rdkit-discuss] RDKit build issues

Passed1.99 sec > > The following tests passed: > JavaAromaticTests > > 100% tests passed, 0 tests failed out of 1 > > Total Test time (real) = 2.00 sec > glandrum@Otter:/scratch/RDKit_git/build$ > > > I do not have CLASSPATH set and I don't think it's

Re: [Rdkit-discuss] RDKit build issues

f. > > Here is what I normally use for testing ( note I usually build into an > rdkit_build directory via: -DCMAKE_INSTALL_PREFIX= > ) > > > RDBASE=`pwd`/../../rdkit LD_LIBRARY_PATH=`pwd`/rdkit_build/lib > PYTHONPATH=`pwd`/rdkit_build/lib/python2.7/site-packages ctest >

Re: [Rdkit-discuss] RDKit build issues

in thread "main" java.lang.NoClassDefFoundError: org/hamcrest/SelfDescribing Is my CLASSPATH wrong? Did I forget a SO in my LD_LIBRARY_PATH? Thanks in advance! Matt On Mon, Apr 18, 2016 at 9:56 AM, Matthew Lardy <mla...@gmail.com> wrote: > My thoughts exactly. I've forg

Re: [Rdkit-discuss] RDKit build issues

THS=ON >> >> When running cmake, otherwise cmake can get very confused. >> >> >> >> Brian Kelley >> >> On Apr 15, 2016, at 6:26 PM, Matthew Lardy <mla...@gmail.com> wrote: >> >> I'll add, that remembering that cmake and ccmake ca

Re: [Rdkit-discuss] RDKit build issues

/rdkit/blob/master/.travis.yml > > Note the > > -D Boost_NO_SYSTEM_PATHS=ON > > When running cmake, otherwise cmake can get very confused. > > > > Brian Kelley > > On Apr 15, 2016, at 6:26 PM, Matthew Lardy <mla...@gmail.com> wrote: > > I'll add, that remem

Re: [Rdkit-discuss] RDKit build issues

in ccmake) are called, I'd love to know. Thanks in advance! Matthew On Fri, Apr 15, 2016 at 2:58 PM, Matthew Lardy <mla...@gmail.com> wrote: > Hi all, > > If someone has an insight I would love to hear it about how best to build > RDKit from scratch. > > I am using the follow

[Rdkit-discuss] RDKit build issues

ideas are welcome! Thanks, Matthew The following tests FAILED: 2 - testDataStructs (OTHER_FAULT) 3 - pyBV (Failed) 4 - pyDiscreteValueVect (Failed) 5 - pySparseIntVect (Failed) 7 - testGrid (OTHER_FAULT) 8 - testPyGeometry (Failed

Re: [Rdkit-discuss] RDKit 2016.03 Installation

, so I'm on the right track! Thanks! Matthew On Thu, Apr 14, 2016 at 10:37 PM, Greg Landrum <greg.land...@gmail.com> wrote: > Hi Matt, > > 2016.03 isn't quite there (we're still working out some compatibility > things with older operating systems), but it should sup

[Rdkit-discuss] RDKit 2016.03 Installation

Hi all, Does someone know which version of boost, cmake, and swig seems to work best for the current release? Thanks in advance! Matt -- Find and fix application performance issues faster with Applications Manager

Re: [Rdkit-discuss] Reaction Question

'),)) > > In [20]: Chem.MolToSmiles(ps[0][0]) > Out[20]: 'CCc1c1F' > > > I hope that helps, > -greg > > > > On Mon, Sep 21, 2015 at 4:41 PM, Matthew Lardy <mla...@gmail.com> wrote: > >> I've repeated the previously seen behavior in Python in case

Re: [Rdkit-discuss] Reaction Question

r x in ps]) print Chem.MolToSmiles(ps[0][0]) #for p in uniq: #print Chem.MolToSmiles(p) #for prod in uniq: # writer.write(prod) else: writer.write(m) writer.close() gz.close() On Mon, Sep 21, 2015 at 12:39 PM, Matthew Lardy <mla...@gmai

[Rdkit-discuss] Reaction Question

Hi all, I am attempting to transform a functional group in a series of molecules. The reaction is pretty simple (a re-aromatization): C=C1CC=CC=C1>>Cc1c1 The code which generates this runs without error (and it was written in Java). What I don't understand is that the products of the

Re: [Rdkit-discuss] Memory Issue

think calling rdmol.delete() at the end of each iteration (this frees the underlying C++ object) should help. -greg On Tuesday, July 14, 2015, Matthew Lardy mla...@gmail.com wrote: Hi all, I have had a strange issue that I can't seem to find a way around. The following code block

Re: [Rdkit-discuss] Memory Issue

Just to add, I can confirm that re-writing this in Python did indeed bounce the memory issue I've been having. Total consumption never crossed 0.1% of my system memory. :) Way less than the 89% I was seeing with the Java version of the same application! On Wed, Jul 15, 2015 at 2:05 PM, Matthew

[Rdkit-discuss] Memory Issue

Hi all, I have had a strange issue that I can't seem to find a way around. The following code block consumes a ton of memory, which is strange as just using the SD File reader I have no memory issues. I think that the issue is related to the java garbage collection not being picked up, even

[Rdkit-discuss] Java and sdf.gz files

Hi all, I am trying to open and write compressed sd files with the Java wrappers. I know, and have, been able to do this in Python but has anyone cracked how to read and write sdf.gz files in Java? Thanks in advance! Matthew

Re: [Rdkit-discuss] RDKit SDMolSupplier

hours I burned until I realized that was the problem. Thanks for the quick response! Matthew On Thu, Mar 12, 2015 at 8:46 AM, Christos Kannas chriskan...@gmail.com wrote: Hi Mathew, In order to store the tags and the data associated with them prior to writing the molecule to SDF/SMILES file

[Rdkit-discuss] RDKit SDMolSupplier

over it the tags are missing again. Is this the expected behaviour, or I am doing something wrong? Thanks in advance! Matthew -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel

Re: [Rdkit-discuss] SimilarityMaps

Hi Serenia, Yep that fixed it! Thanks! Matthew On Fri, Feb 20, 2015 at 10:59 PM, Sereina sereina.rini...@gmail.com wrote: Hi Matthew, I think this is related to a previous mailing list item ( https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg03528.html ). It has

[Rdkit-discuss] SimilarityMaps

Hi, I am having an issue with the python similaritymaps. I am only seeing a fraction of the molecule. Anyone else have this issue? Thanks in advance! Matthew -- Download BIRT iHub F-Type - The Free Enterprise-Grade

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

Greg! Matthew On Thu, Feb 19, 2015 at 10:29 PM, Greg Landrum greg.land...@gmail.com wrote: On Thu, Feb 19, 2015 at 11:59 PM, Matthew Lardy mla...@gmail.com wrote: I have been able to build models via scikit-learn with the RDKit python wrappers. That all works beautifully! It's a nice

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

Hi Maciek, Thanks! My brain was stuck on this for a while, as it has been ages since I have written any Python. BTW- I also took a look at your ODDT, and it reminded me that I need to get the OB python wrappers re-compiled. :) Thanks, Matthew On Fri, Feb 20, 2015 at 1:06 AM, Maciek

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

looking for example code doing exactly this.) Thanks! Matthew -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity

Re: [Rdkit-discuss] Replacing H's with F's

for the walkthrough Greg! It was very helpful! Thanks again! Matthew On Sat, Jan 31, 2015 at 1:58 AM, Greg Landrum greg.land...@gmail.com wrote: For anyone interested in this topic, I just did an RDKit blog post that has a somewhat expanded version of this answer: http://rdkit.blogspot.com/2015/01

[Rdkit-discuss] Replacing H's with F's

, that the molecule that I read (and the molecule for HF) were both loaded without issue. Anyone else try to do something like this? Matthew -- Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel

Re: [Rdkit-discuss] Using ChemicalReactions to set double bond (E/Z)

to find a path through this as well. Thanks, as always, for responding so quickly! I'll share the logs once I locate them! Matthew On Tue, Nov 11, 2014 at 8:46 PM, Greg Landrum greg.land...@gmail.com wrote: Hi Matthew, On Wed, Nov 12, 2014 at 12:24 AM, Matthew Lardy mla...@gmail.com wrote

[Rdkit-discuss] Using ChemicalReactions to set double bond (E/Z)

) at org.RDKit.ChemicalReaction.runReactants(ChemicalReaction.java:129) Has anyone else seen this? Or, have I just entered a semi-valid SMARTS transformation? Thanks in advance! Matthew -- Comprehensive Server Monitoring

Re: [Rdkit-discuss] java wrapper problem on CentOS 6.5

! Matthew On Tue, Sep 9, 2014 at 3:13 PM, Whitmore, Mattie [USA] whitmore_mat...@bah.com wrote: Dear All, I am building RDKit with java wrappers using the following code: cmake -D BOOST_ROOT=/usr/local -D PYTHON_LIBRARY=/usr/local/lib/python2.7/config/libpython2.7.a -D

Re: [Rdkit-discuss] MaxMin Picker and Python

. If this is the code you are using for the distance matrix: On Thu, Jul 17, 2014 at 12:18 AM, Matthew Lardy mla...@gmail.com wrote: dm=[] for i,fp in enumerate(zims_fps[:26000]): # only 1000 in the demo (in the interest of time) dm.extend(DataStructs.BulkTanimotoSimilarity(fp,zims_fps[1+1:26000

Re: [Rdkit-discuss] MaxMin Picker and Python

selected to avoid the pathological case he describes. Dave On Thu, Jul 17, 2014 at 5:19 AM, Greg Landrum greg.land...@gmail.com wrote: one other short thing. If this is the code you are using for the distance matrix: On Thu, Jul 17, 2014 at 12:18 AM, Matthew Lardy mla...@gmail.com wrote

[Rdkit-discuss] MaxMin Picker and Python

Hi all, I have been playing with the diversity selection in RDKit. I am running through a set of ~26,000 molecules to pick a set of 200 diverse molecules. I saw some examples of how to do this in Python (my variant of their script below), but the memory consumption is massive. I burned through

Re: [Rdkit-discuss] MaxMin Picker and Python

for the info! Matt On Wed, Jul 16, 2014 at 3:31 PM, Igor Filippov igor.v.filip...@gmail.com wrote: 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

Re: [Rdkit-discuss] MaxMin Picker and Python

) for x in Chem.ForwardSDMolSupplier(gzip.open('a.sdf.gz')) if x is not None] because zims keeps the whole file in memory for no good reason :-) (is that sdf.gz big?) Markus On Thu, Jul 17, 2014 at 12:43 AM, Matthew Lardy mla...@gmail.com wrote: Hi Igor, Thanks! Maybe I am a throwback

Re: [Rdkit-discuss] installation problem

Hi Sergio, What version of Swig, Boost and Cmake are you using? I found that switching to Swig (v2.0.10), Boost (v1.55), and Cmake (v 2.8.10.2) resolved those types of errors when I was having them. At least that worked on CentOS 6.x. :) Matt On Thu, Jun 5, 2014 at 1:09 PM, Wong, Sergio E.

Re: [Rdkit-discuss] Molecule reading issues

:03, Matthew Lardy mla...@gmail.com wrote: Hi all, I am having this issue with the Java wrapper while trying to create a smiles string from a RWMol class object. I don't care about trying to figure out what is going wrong, I just want to bypass this record without my application closing. Any

Re: [Rdkit-discuss] Molecule reading issues

, Matthew Lardy wrote: Hi all, Thanks all! I should have been a bit more explicit. This is the context of the offending line: try { smi = rdmol.MolToSmiles(); } catch (org.RDKit.MolSanitizeException e) { System.err.println(Bad Mol Found: + smi); } I thought after reading the comments

Re: [Rdkit-discuss] Molecule reading issues

! Matt On Mon, Jun 2, 2014 at 1:27 PM, Matthew Lardy mla...@gmail.com wrote: Hi Jan, The exception should be a org.RDKit.MolSanitizeException, but the following code fails too: String smi = ; try { smi = rdmol.MolToSmiles(); } catch (Exception e) { System.err.println(Bad Mol Found

Re: [Rdkit-discuss] RDKit, Java, and Memory

...@gmail.com wrote: The code distribution on source forge hasn't been updated in over a year. Please use github instead On Thursday, May 29, 2014, Matthew Lardy mla...@gmail.com wrote: Hi Greg, So I took a development copy from sourceforge, but I am now unable to compile the C++ code. Is anyone

Re: [Rdkit-discuss] No head on brew install

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 existing pack

Re: [Rdkit-discuss] RDKit, Java, and Memory

, 2014 at 9:17 PM, Greg Landrum greg.land...@gmail.comwrote: Hi Matt, On Fri, May 23, 2014 at 6:01 PM, Matthew Lardy mla...@gmail.com wrote: Hi all, I am loving the Swig based wrappers for RDKit, Great to hear! but I keep running across one issue. Memory use. Using the SDMolSupplier I

[Rdkit-discuss] RDKit, Java, and Memory

Hi all, I am loving the Swig based wrappers for RDKit, but I keep running across one issue. Memory use. Using the SDMolSupplier I typically eat 2-3GBs of memory to process 10-20K molecules. Is anyone else having this issue and, if so, has anyone solved it? Thanks in advance! Matt

[Rdkit-discuss] MolToPDBFile

Hi all, Hopefully this is easy, but I have an ROMol object that I want to convert into a PDB file. It seems to me that the MolToPDBFile is exactly what I should be using, but I am missing the protons in the resulting file. What's weird is that the input file has protons, and I have added a step

Re: [Rdkit-discuss] MolToPDBFile

check to ensure that it is indeed seeing the protons, and get back to you. Thanks! Matt On Thu, May 1, 2014 at 8:44 PM, Greg Landrum greg.land...@gmail.com wrote: Hi Matt, On Thu, May 1, 2014 at 11:19 PM, Matthew Lardy mla...@gmail.com wrote: Hopefully this is easy, but I have an ROMol

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

Hi, I made a start on some tautomer enumeration and canonicalization code using RDKit in python a few months ago but got distracted before it was fully complete. Here's what I have: https://gist.github.com/mcs07/9956421 It's a bit of a mess, but seems to work and might be useful if someone

Re: [Rdkit-discuss] rdkit homebrew recipe moved to the rdkit organization

Hi, I've submitted some changes to the homebrew formula here: https://github.com/rdkit/homebrew-rdkit/pull/6 Also, to avoid having worry about the redirection working correctly, those using the formula may want to just point homebrew towards the new location: brew untap edc/rdkit brew

[Rdkit-discuss] SD Tag Reording

Hi all, I've noticed that I am unable to reorder SD tags in RDKit. It appears that no matter what I try, they get reordered in alphabetical order. Is anyone else experiencing this behaviour? Thanks! Matt -- Flow-based

Re: [Rdkit-discuss] Aromatic Boron SMARTS

Hi, I don't really know what's going on here, but you could try [#5!B] for you SMARTS. #5 to match any boron, and !B to disallow non-aromatic. Matt On 18 Feb 2014, at 16:05, Elizabeth Wylie ewyli...@gmail.com wrote: Hello All, I have a series of 'aromatic' compounds in SMILES provided

[Rdkit-discuss] Stop reaction opening ring

Hi, If any atoms specified in a reaction happen to form a ring, RDKit will break it open: rxn = AllChem.ReactionFromSmarts('[C:1][C:2][O:3][C:4][C:5][C:1][C:2][C:3][C:4][C:5]') mol = Chem.MolFromSmiles('C1CCOC1') prod = rxn.RunReactants((mol,))[0][0] Chem.MolToSmiles(prod)

Re: [Rdkit-discuss] RDKit Java/Swig Boost

Thanks Oriol and Greg! I wasn't aware of needing to do that, but I will give it a whirl. :) Thanks so much for your help! Matt On Tue, Jan 14, 2014 at 2:34 AM, Greg Landrum greg.land...@gmail.comwrote: On Tue, Jan 14, 2014 at 3:37 AM, Oriol López Massaguer olo...@imim.eswrote: I use

[Rdkit-discuss] RDKit Java/Swig Boost

Hi all, First Swig and Java: While I was able to build the Java wrappers (2013-09-01-beta), and the resulting jars passed the tests (at least the Java wrappers did) I am being frustrated by the following error: Exception in thread main java.lang.UnsatisfiedLinkError:

Re: [Rdkit-discuss] install RDKit on CentOS

Hi Yingfeng, Forgive me if I am jumping in without knowing all that you have tried, but did you try pulling boost with Yum? I was able to get RDKit, and the Java wrappers, to cleanly compile on CentOS 6.4 with that flavor of boost. Matt On Mon, Jul 15, 2013 at 9:39 PM, Greg Landrum