Re: [Rdkit-discuss] Nuget C# Prerelease

y code. This seems relatively standard, but is a tad annoying. using GraphMolWrap; ... RDKit.Initialize(); Cheers, Brian On Mon, Jul 31, 2017 at 9:24 PM, Brian Kelley <fustiga...@gmail.com> wrote: > For the small percentage of you who use C# we finally have a NuGet release! > >

[Rdkit-discuss] Nuget C# Prerelease

For the small percentage of you who use C# we finally have a NuGet release! https://www.nuget.org/packages/RDKit2DotNet/2017.9.1-alpha Notes: 1. This is a prerelase, the number of C# tests is vanishingly small 2. x64 only for now, you'll need to change AnyCPU targets to specifically target

Re: [Rdkit-discuss] Delete several Atoms

Yes, go backwards through the index list. for index in sorted(indices, reverse=True): mol.RemoveAtom(index) Indices are only changed if they are higher than the removed index. Brian Kelley > On Jun 25, 2017, at 10:16 AM, Changge Ji <chicago...@gmail.com> wrote: >

Re: [Rdkit-discuss] Canonical order in SMILES

After canonicalization, do the following d = mol.GetPropsAsDict(True,True) In the dictionary there will be a key something like _smilesAtomOutputOrder which contains a vector of atom indices in output order. Brian Kelley > On Jun 17, 2017, at 1:42 PM, Jean-Marc Nuzillard <jm.

Re: [Rdkit-discuss] atom indexes and order of atoms in the input file

"_smilesAtomOutputOrder" We should probably make a helper function for this. ---- Brian Kelley > On Jun 15, 2017, at 6:27 PM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu> wrote: > >> On 06/15/2017 10:13 AM, Maciek Wójcikowski wrote: >> Hi, >> >> If you really want to r

Re: [Rdkit-discuss] AllChem.GetConformerRMSD: this is not RMSD between two conformers but an upper bound of it

Thanks for the documentation fix, I had read the same as Francois. Brian Kelley > On Jun 15, 2017, at 8:02 AM, Greg Landrum <greg.land...@gmail.com> wrote: > > > >> On Thu, Jun 15, 2017 at 6:30 AM, Francois BERENGER >> <beren...@bioreg.kyushu-u

Re: [Rdkit-discuss] AllChem.GetConformerRMSD: this is not RMSD between two conformers but an upper bound of it

The function you want is GetBestRMS, note that you can set the conformer idx for the probe and ref. http://www.rdkit.org/Python_Docs/rdkit.Chem.AllChem-module.html#GetBestRMS Brian Kelley > On Jun 15, 2017, at 5:30 AM, Francois BERENGER > <beren...@bioreg.kyushu-u.ac.

Re: [Rdkit-discuss] atom indexes and order of atoms in the input file

Yes, atoms are always added in file order. It would take a major change in rdkit to change/violate this. Brian Kelley > On Jun 15, 2017, at 7:52 AM, Francois BERENGER > <beren...@bioreg.kyushu-u.ac.jp> wrote: > > Hello, > > If I read a molecule from a .sdf fil

Re: [Rdkit-discuss] Conformational search not "converging" to low energy conformation

There shouldn't be any expectation that the MMFF energy should converge to 1kcal/mol. There *may* be a case to be made for the MMFF_energy - Global_minimum be < 1kcal/mol, however, in general, we don't know what the global minimum is. I suggest looking at this paper:

Re: [Rdkit-discuss] Memory issue when storing more than 300K mol in a list

What exactly are you doing? Is this 1000x500k substructure queries or something different? Brian Kelley > On Jun 9, 2017, at 9:12 AM, Alexis Parenty <alexis.parenty.h...@gmail.com> > wrote: > > Dear Greg and Brian, > Many thanks for your response. I was also think

Re: [Rdkit-discuss] Memory issue when storing more than 300K mol in a list

enhancement. Brian Kelley > On Jun 9, 2017, at 7:04 AM, Greg Landrum <greg.land...@gmail.com> wrote: > > Hi Alexis, > > I would approach this by loading the 1000 queries into a list of molecules > and then "stream" the others past that (so that you never attempt to

Re: [Rdkit-discuss] Does rdkit depend on pandas?

No. The main reason that the conda recipe includes pandas is for testing the pandas extension. We could probably remove it from the run-time dependency however and let the user install it in addition. In any case, feel free to remove pandas from the conda installation. Cheers, Brian On Tue,

Re: [Rdkit-discuss] RDKit on armv7h

Try cmake -DRDK_OPTIMIZE_NATIVE=off This should turn off popcnt which doesn't exist on arm7 Brian Kelley > On May 31, 2017, at 5:08 PM, Samo Turk <samo.t...@gmail.com> wrote: > > Dear RDKit community, > > I have trouble compiling RDKit on Arch Linux

Re: [Rdkit-discuss] canonical smiles for fragments with map numbers

Pavel, this isn't exactly trivial so I went ahead and made an example. The basics are that atomMaps are canonicalized, i.e. their value is used in the generation of smiles. To solve this problem: 1) backup the atom maps and remove them 2) canonicalize *without* atom maps but figure out the order

Re: [Rdkit-discuss] How to match any halogen of a structure with any halogen of a substructure?

Dear All, In case it helps, there is a wealth of functional groups already in RDKit available here: https://github.com/rdkit/rdkit/blob/master/Data/Functional_Group_Hierarchy.txt For instance, the functional group halogen pattern we use is a bit more complicated:

Re: [Rdkit-discuss] Check If Atom Is in Two Small Rings

ses less functions) than >> mine. (Although mine assumes that you want atoms that are part of >> _exactly_ two rings, not atoms that are part of _at least_ two rings as >> Brian's does. Probably Brian's solution is what you want but worth noting.) >> >> CF

Re: [Rdkit-discuss] Check If Atom Is in Two Small Rings

You are so close! >>> from rdkit import Chem >>> m = Chem.MolFromSmiles("C1CC12CCC2") >>> for atom in m.GetAtoms(): ... if atom.IsInRingSize(3) and atom.IsInRingSize(4): print atom.GetIdx() ... 2 >>> Cheers, Brian On Tue, Apr 11, 2017 at 1:38 PM, Jonathan Saboury

Re: [Rdkit-discuss] RDKit Reaction gives disconnected components

olToSmiles(prods[0][0]) 'CF.NI' However, it appears that you aren't mapping anything explicitly between [C:1] and [N:2] in some cases so the left hand side doesn't know what really to do. I'll have to dig into this a little more. Cheers, Brian On Thu, Mar 30, 2017 at 12:56 PM, Brian Kelley <fusti

Re: [Rdkit-discuss] RDKit Reaction gives disconnected components

I have a feeling you may need to make two reactions. Let's consider a dirt simple case: >>> rxn = AllChem.ReactionFromSmarts("[C:1][N:2]>>[C:1].[N:2]") >>> prods = rxn.RunReactants([Chem.MolFromSmiles("CN")]) >>> Chem.MolToSmiles(prods[0][0]) 'C' >>> Chem.MolToSmiles(prods[0][1]) 'N' >>>

Re: [Rdkit-discuss] aligning maximum common substructure of 2 molecules

I don't know the exact glide procedure, but I did write such a system for OpenEye (POSIT). The issue you are facing is that the RMSD portion is just a constraint used for docking, it isn't used as the "score", in fact, it can't tell if the conformation interpenetrates the active site or which

Re: [Rdkit-discuss] aligning maximum common substructure of 2 molecules

I believe (Greg can correct me) to align the bemis-murcko scaffold, you could (1) extract the original atom pairs and send them to the RMSD algorithm (2) take a bemis scaffold and convert it to a substructure query for use in the RMSD algorithm. In either case the RMSD is the rmsd of the

Re: [Rdkit-discuss] RDKit "cannot create mol from SMILE" error

That doesn't look like a valid SMILES to me, I don't think a think a smiles string can start with a parenthesis ( branch ). Brian Kelley > On Jan 18, 2017, at 6:18 PM, Larson Danes <lgda...@gmail.com> wrote: > > Hi all, > > I'm using the following query in postg

Re: [Rdkit-discuss] PMI API

6%2045> > MOBILE +41 (0)79 536 1039 <+41%2079%20536%2010%2039> > Firmenich SA > RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8 > > -- > *De :* Brian Kelley <fustiga...@gmail.com> > *Envoyé :* mardi 17 janvier 2017 13:4

Re: [Rdkit-discuss] PMI API

he atoms in a non-linear molecule, which would be a > requirement for the corresponding moment of inertia to be zero. > > Chris > > On 17 January 2017 at 12:29, Brian Kelley <fustiga...@gmail.com> wrote: > >> Looks like I'm late to the game. I don't know about the PMI desc

Re: [Rdkit-discuss] PMI API

Looks like I'm late to the game. I don't know about the PMI descriptors per-se, but if a planar molecule is in it's inertial frame, one of the axes should be zero (whether it is x, y or z) which means that the one of the M1x, M1y or M1z should be zero. We had some good experimentation with

Re: [Rdkit-discuss] Missing Properties for Mol in Multiprocessing Pool

By default, normal molecules don't pickle properties. The pickling is used to transfer mols in Python multiprocessing. Wrapping them in a PropertyMol should solve the issue: http://www.rdkit.org/Python_Docs/rdkit.Chem.PropertyMol.PropertyMol-class.html Brian Kelley > On Jan 13, 2

Re: [Rdkit-discuss] UpdatePropertyCache() after RunReactants

non sensical molecules so you may want to draw with sanitizaton turned off so you can see the reaction output. Brian Kelley > On Jan 11, 2017, at 9:11 PM, Curt Fischer <curt.r.fisc...@gmail.com> wrote: > > Hi all, > > I recently wanted to use RDKit to model the fa

Re: [Rdkit-discuss] SubstructureMatch

substructure search you will find plenty of benchmarks Brian Kelley > On Jan 9, 2017, at 4:49 AM, Axel Rudling <axru6...@gmail.com> wrote: > > Hello, > > I've been benchmarking different softwares for substructure searching of > molecules. From what I can tell, RDKits substru

Re: [Rdkit-discuss] PMI API

that was postponed that we should probably resurrect. Basically it is an rdkit.h header file that has these flags built in so you won't have to include them yourself. Brian Kelley > On Jan 8, 2017, at 11:31 AM, Greg Landrum <greg.land...@gmail.com> wrote: > > Hi Chris, >

Re: [Rdkit-discuss] It's not possible to build the RDKit with Visual Studio 2015 Update 3

latile BisectLine* p) { return p; } } Ug. Perhaps this can be automated... Brian Kelley > On Jan 4, 2017, at 2:53 AM, Greg Landrum <greg.land...@gmail.com> wrote: > > I'm not sure how many of you this will be relevant to, but it's important to > know that Update

Re: [Rdkit-discuss] drawing code take 3

Perhaps we could train a ML algorithm to know which algorithm to use when :) Cheers, Brian On Thu, Dec 29, 2016 at 8:19 AM, John M wrote: > Hi Peter, > > I uploaded the benchmark set here: https://github.com/ > johnmay/layout-benchmark and have tested on their web

Re: [Rdkit-discuss] Bug in AllChem.EmbedMultipleConfs pruning?

Missed the swap == swap with same type. There probably is some moment based heuristic you use to check for bad outliers. Brian Kelley > On Dec 22, 2016, at 11:49 AM, Greg Landrum <greg.land...@gmail.com> wrote: > > >> On Thu, Dec 22, 2016 at 5:37 PM, Brian Cole <

Re: [Rdkit-discuss] MolToSmiles

I would vote for make a more obvious way to get to these values. I have had the need to do this when working with external depictors (i.e. mol -> smiles -> depict with atom highlighting is one use case) I just couldn't think of a valid API way of doing this. Attaching these values to the

Re: [Rdkit-discuss] MolToSmiles

Jean-Marc, This is very non-obvious, but here is how you can do it from python: >>> from rdkit import Chem >>> m = Chem.MolFromSmiles("NCCC") >>> Chem.MolToSmiles(m) 'CCCN' >>> m.GetProp("_smilesAtomOutputOrder") '[3,2,1,0,]' Note that this returns the list as a string which is

Re: [Rdkit-discuss] Incorrect results for substructure search obtained with Tversky similarity.

/sec in real world searches. I'm happy to provide an example of this if you need it. I hope this helps. Brian Kelley > On Dec 12, 2016, at 11:29 AM, Axel Rudling <axru6...@gmail.com> wrote: > > Hello all, > > Currently I'm doing a project with Tversky searching

Re: [Rdkit-discuss] Generating all stereochem possibilities from smile

bond.GetStereo >>> from rdkit import Chem >>> m = Chem.MolFromSmiles("F/C=C/F") >>> for bond in m.GetBonds(): ...print bond.GetStereo() ... STEREONONE STEREOE STEREONONE However, setting bond stereo doesn't appear to be exposed. I suppose you could permute the smiles strings \ => /

Re: [Rdkit-discuss] Extracting SMILES from text

Note: I turned logging off, otherwise a lot of time was spent spewing to stderr: from rdkit import Chem, rdBase rdBase.DisableLog("rdApp.*") On Sat, Dec 3, 2016 at 9:02 AM, Brian Kelley <fustiga...@gmail.com> wrote: > Here are some number from my laptop for parsing: >

Re: [Rdkit-discuss] Extracting SMILES from text

just use the normal MolFromSmiles, if you don't expect many actual smiles strings in your corpus, it's plenty fast. Cheers, Brian On Fri, Dec 2, 2016 at 5:08 PM, Andrew Dalke <da...@dalkescientific.com> wrote: > On Dec 2, 2016, at 10:05 PM, Brian Kelley wrote: > > Here is a v

Re: [Rdkit-discuss] Extracting SMILES from text

be fun to resurrect use it in some form. Brian Kelley > On Dec 2, 2016, at 2:36 PM, Andrew Dalke <da...@dalkescientific.com> wrote: > >> On Dec 2, 2016, at 11:11 AM, Greg Landrum wrote: >> An initial start on some regexps that match SMILES is here: >> https://

Re: [Rdkit-discuss] Extracting SMILES from text

handy. I expect it to be even faster with failing non smiles. This should be sufficient for document scanning I think. Brian Kelley > On Dec 2, 2016, at 1:28 PM, George Papadatos <gpapada...@gmail.com> wrote: > > I think Alexis was referring to converting actual SMILE

Re: [Rdkit-discuss] Extracting SMILES from text

This was why they started using the dictionary lookup as I recall :). The iupac system they ended up using was Roger's when at OpenEye. Brian Kelley > On Dec 2, 2016, at 12:33 PM, Igor Filippov <igor.v.filip...@gmail.com> wrote: > > I could be wrong but I believe

Re: [Rdkit-discuss] Extracting SMILES from text

I hacked a version of RDKit's smiles parser to compute heavy atom count, perhaps some version of this could be used to check smiles validity without making the actual molecule. >From a fun historical perspective: IBM had an expert system to find IUPAC names in documents. They ended up finding

Re: [Rdkit-discuss] errors with windows10 RDKit installation using conda

Another point: I had the same path length issues and eventually installed anacond3 into C:\a3 For building packages and they magically went away. Super annoying. Brian Kelley > On Nov 29, 2016, at 8:11 AM, Mike Mazanetz <mi...@novadatasolutions.co.uk> > wrote: > >

Re: [Rdkit-discuss] errors with windows10 RDKit installation using conda

I'm very close to having stable c# wrappers again. The painful bit is writing all the tests, but if you would like to help out, I can send you the current builds. Brian Kelley > On Nov 29, 2016, at 3:06 PM, Michal Krompiec <michal.kromp...@gmail.com> > wrote: > > &g

Re: [Rdkit-discuss] Pandas

Peter, If you have chemfp and can make a chemfp arena, RDKit now supports these structures for reading and searching. This, by far, is the fastest way I know of similarity searching. I believe that Greg's implementation is compatible with chemfp 1.0 which is available on pypi:

Re: [Rdkit-discuss] Find out if a molecuole object was generated from smiles or smarts

I would try checking: atom.HasQuery() I expect the smarts molecules have this property by default and smiles don't. Greg can confirm, and I can double check later today. Brian Kelley > On Nov 7, 2016, at 7:57 AM, Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote: > >> O

Re: [Rdkit-discuss] Is there a way to init the conformations of smiles supplier to improve the performance for substructure matching.

and not from a supplier. If they are being read from a supplier, you can easily keep them all in memory with: queries = list(query_supplier) Note that for large files, this can take up a lot of memory. Thanks for the clarification Greg. Brian Kelley > On Nov 1, 2016, at 4:22 AM,

Re: [Rdkit-discuss] Is there a way to init the conformations of smiles supplier to improve the performance for substructure matching.

A supplier is random access, so your call to supp[I] here is probably quite expensive: suppl = AllChem.SmilesMolSupplier('allmoleculenew.smi',delimiter='\t') l = len(suppl) for j in range(ll): # I have to make substructures in the first loop. for i in range(l):

Re: [Rdkit-discuss] reading multiple conformers from file

Rdkit already has a way to serialize conformers, the binary pickle format! Perhaps we should make a file extension for multiple molecules. Say ".rdk" and call it a day. Like inchi the source code is the reference :) ---- Brian Kelley > On Oct 27, 2016, at 2:05 AM, Greg Landr

Re: [Rdkit-discuss] property of name in smilesMolSupplier

Paolo, _Name might be considered a private property, you might need to use GetPropNames(True,True) or something like that. Brian Kelley > On Oct 13, 2016, at 6:56 AM, Paolo Tosco <paolo.to...@unito.it> wrote: > > Hi Hongbin, > > suppl[0].GetPropNames() is an interab

Re: [Rdkit-discuss] property of name in smilesMolSupplier

believe will list them all. Brian Kelley > On Oct 13, 2016, at 6:31 AM, 杨弘宾 <yanyangh...@163.com> wrote: > > Hi， > I spent a lot of time to explorer "How to get the property of name when > using SmilesMolSupplier" > > I had a smiles

Re: [Rdkit-discuss] Implementation details bitvectors from morgan/circular fingerprints

It should be noted that hashing to bits always looses information, there is simply no way around this. While this is a partial answer to your question, you can at least find the atoms that set a bit. Look for "Explaining bits from Morgan Fingerprints"

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

Phillip, if you run ctest --debug This may help us diagnose the issue with paths and such. Note that you will get a LOT of output. Brian Kelley > On Oct 3, 2016, at 4:05 PM, Philip Adler <padl...@haverford.edu> wrote: > > it does not seem that I am missing a

Re: [Rdkit-discuss] MolFromMolBlock does not read properties

() A minor optimization which isn't as easily possible with the StringIO implementation. Brian Kelley > On Oct 3, 2016, at 9:04 AM, Greg Landrum <greg.land...@gmail.com> wrote: > > > >> On Mon, Oct 3, 2016 at 2:53 PM, Brian Kelley <fustiga...@gmail.com> wrote: >

Re: [Rdkit-discuss] MolFromMolBlock does not read properties

No, you have the correct method. The general idea, I believe, is that if the format can result in multiple molecules a supplier should be used. Brian Kelley > On Oct 2, 2016, at 4:48 PM, Maciek Wójcikowski <mac...@wojcikowski.pl> wrote: > > Yes I get it

Re: [Rdkit-discuss] MolFromMolBlock does not read properties

le If you see the dollar signs in your text block, it is indeed an sd record not just a mol block. ---- Brian Kelley > On Oct 2, 2016, at 3:46 PM, Maciek Wójcikowski <mac...@wojcikowski.pl> wrote: > > Hi RDKitters, > > Is it a bug or a feature? When using Chem.MolFromMol

Re: [Rdkit-discuss] Getting started with C++

I think this is a fantastic idea. I'll even contribute and include the examples in standard dist as cmake targets to boot. This will both help people start projects but also validate the docs. Nothing worse than examples that don't compile :) Brian Kelley > On Sep 24, 2016, at 11

Re: [Rdkit-discuss] The RDKit and modern C++

I whole heartedly agree. One thing that may help RHEL6 is that anaconda actually can install/build gcc4.8 in user space: https://anaconda.org/anaconda/gcc/. Note: it does require root to install some dependencies, but doesn't override the system gcc. While this is not a complete solution for

Re: [Rdkit-discuss] RDKit Meetup in Cambridge October 19

udgeon...@gmail.com> > wrote: > >> Which Cambridge? Assume this is Cambridge MA not Cambridge UK? >> >> On 15/09/2016 19:29, Brian Kelley wrote: >> >> Novartis is kindly hosting an RDKit Meetup October 19th starting at >> 4:30pm >> >> The first 45 m

Re: [Rdkit-discuss] highlightColor in Draw.MolsToGridImage()

I'll need to test to seen it works, but the ids should be generated from the atom and bond indices in a deterministic fashion. Brian Kelley > On Jul 18, 2016, at 4:35 AM, Dmitri Maziuk <dmaz...@bmrb.wisc.edu> wrote: > >> On 7/17/2016 8:17 AM, Brian Kelley wrote: &

Re: [Rdkit-discuss] highlightColor in Draw.MolsToGridImage()

options for rendering is always a good thing. Brian Kelley > On Jul 17, 2016, at 7:21 AM, Dmitri Maziuk <dmaz...@bmrb.wisc.edu> wrote: > >> On 7/17/2016 5:29 AM, Greg Landrum wrote: >> >> >> On Sat, Jul 16, 2016 at 9:37 PM, DmitriR <xzf...@gmail.

Re: [Rdkit-discuss] m.GetProp('property'): KeyError: 'property'

Markus, In newer versions of RDKit there is a handy method: d = mol.GetPropsAsDict() which returns a python dictionary of all the sd data by default. It also has a nice feature that it converts numeric values to proper python numbers. This can be used as a python dictionary: for prop,value

Re: [Rdkit-discuss] SMILES string from SureChEMBL iPython Notebook Tutorial

10.11.5, jupyter 4.1.0, > Firefox > > Thanks. > Dmitri > > > > On Jun 29, 2016, at 9:07 AM, Brian Kelley <fustiga...@gmail.com> wrote: > > > > Dmitri, > > Could you send me the notebook that displays these issues? I can't > reproduce them. > &g

Re: [Rdkit-discuss] SMILES string from SureChEMBL iPython Notebook Tutorial

Dmitri, Could you send me the notebook that displays these issues? I can't reproduce them. Thanks, Brian On Tue, Jun 28, 2016 at 6:25 PM, Brian Kelley <fustiga...@gmail.com> wrote: > It looks like there may be an issue calling WrapLogs twice. If you see > the er

Re: [Rdkit-discuss] Error compiling RDKit with MinGW on Windows

mingw installed. Brian Kelley > On Jun 23, 2016, at 1:47 PM, Paolo Tosco <paolo.to...@unito.it> wrote: > > Dear Anne, > > tonight I'll be working on getting a working RDKit build using MinGW > compilers; I'll update you as soon as I have finished. > > Best, >

Re: [Rdkit-discuss] Chirality conservation during atom replacement

Christian, I believe this was a bug fix where smarts chirality wasn't respected with dummy atoms. We fixed this during an investigation about r-group decomposition, basically stereo cores were behaving oddly. Brian Kelley > On Jun 22, 2016, at 10:30 AM, Kramer, Christian <christi

Re: [Rdkit-discuss] Querying when using CTabs

I also like the term "FuzzyBonds" better than vague bonds if we get to rename it :) Cheers, Brian On Tue, Jun 7, 2016 at 3:21 PM, Brian Kelley <fustiga...@gmail.com> wrote: > I was also thinking that instead of protonating, we could just "and" with > a heavy de

Re: [Rdkit-discuss] Querying when using CTabs

keeping somewhere in mind that the core of the RDKit is >> really using a more "Daylight-like" model and that there is almost >> certainly going to be some mismatch with the MDL model... but we'll worry >> about that when we get there. >> >> >> >&

[Rdkit-discuss] Querying when using CTabs

An interesting conversation came up at work a few days ago regarding MolBlocks/CTABs with queries that behave in an unexpected manner. I'm tackling some of these issues when it comes to reaction processing .rxn based files and plan on contributing it relatively soon. However, I hadn't considered

Re: [Rdkit-discuss] two versions of RDKit in one python program - static compilation?

/questions/1879971/what-is-the-current-choice-for-doing-rpc-in-python Brian Kelley > On Apr 28, 2016, at 7:13 PM, Rafal Roszak <rmrmg.c...@gmail.com> wrote: > > Hello, > > I have python program which uses RDKit and: some functions in the > program require old version of

Re: [Rdkit-discuss] Ubuntu 14.04 LTS Build Post Commit 7478e3fd3bee0c20291c2b99776c40a0c7d8a955

/762 Brian Kelley > On Apr 17, 2016, at 8:28 AM, Tim Dudgeon <tdudgeon...@gmail.com> wrote: > > I've hit the same issue. Any thoughts on what the underlying issue is > (without reverting to using anaconda)? > An example that illustrates this is here: > https://githu

Re: [Rdkit-discuss] RDKit build issues

. 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 can produce different > outcomes I've gone back to trying cmake. But I can't overwrite the variables > in cmake. Here are th

Re: [Rdkit-discuss] RDKit build issues

This looks suspiciously like you haven't set RDBASE to point to the source directory when running the tests. The tests need to find the data directory with the test data. Brian Kelley > On Apr 15, 2016, at 6:26 PM, Matthew Lardy <mla...@gmail.com> wrote: > > I'll add, t

Re: [Rdkit-discuss] ring bond query

Not sure if it will help, but the python version of IsInRing checks to see if the sssr is initialized. Here is the C++ code that is used, you may be able to adapt it to your needs: bool BondIsInRing(const Bond *bond) { if (!bond->getOwningMol().getRingInfo()->isInitialized()) {

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

In C++ you don't have to, RWMol can be sent to any function that takes an ROMol. Actually, this is true now in Python as well. In C++ if you really need to copy the molecule: ROMol mol = new ROMol( *rwmol ); But you really don't have to. Brian Kelley > On Apr 10, 2016, at 6:27

Re: [Rdkit-discuss] compiling error with C++ on maverick

One thing we could fairly easily set up is a "companion" CMakeLists.txt for a sample C++ project that builds a test project against a built distribution. It could prove useful as a basis for building C++ extensions. Basically we would hedge our bets and just link against everything :) Cheers,

Re: [Rdkit-discuss] Molecular properties + pickling

one ( with the same loss of properties ). Brian Kelley > On Mar 18, 2016, at 1:04 PM, Maciek Wójcikowski <mac...@wojcikowski.pl> wrote: > > Thanks. Is there a reason that this is not in the main Mol class? > > > Pozdrawiam, | Best regards, > Maciek Wójcikow

Re: [Rdkit-discuss] canonical atom indexing

No, prochiral atoms have the same rank. Your question got me thinking to how we could detect prochiral atoms, here is the stupidest/simplest solution I could come up with, it changes isotopes on every atom until a new chiral center is added, this atom is considered prochiral: def

Re: [Rdkit-discuss] canonical atom indexing

being discussed. And as a bonus: mol_ordered = Chem.RenumberAtoms(m, list(order)) Will make a copy in canonical atom order, but not canonical smiles output order. Brian Kelley > On Mar 10, 2016, at 7:36 AM, Maciek Wójcikowski <mac...@wojcikowski.pl> wrote: > > Hi, > >

Re: [Rdkit-discuss] canonical atom indexing

The canonicalizer doesn't treat hydrogens any differently than any other atom, but they have to be in the graph. If you are starting from smiles, simply add explicit hydrogens, python example below: >>> from rdkit import Chem >>> m = Chem.MolFromSmiles("CC") >>> mh = Chem.AddHs(m) >>>

Re: [Rdkit-discuss] Peptides and proteins in RDkit with Pseudo atoms support

. Nice work! Brian Kelley > On Mar 1, 2016, at 7:38 AM, Greg Landrum <greg.land...@gmail.com> wrote: > > Thanks for sharing that! > > -greg > > >> On Mon, Feb 29, 2016 at 9:21 AM, Esben Jannik Bjerrum >> <esbenjan...@rocketmail.com> wrote: >

Re: [Rdkit-discuss] Atoms with strange positions/bonds when drawer makes PNG

I have a fix for this in the conda recipes I can submit, it boils down to something like the following ( setting the CXXFLAGS for c++11 ) if otool -L "$PYROOT/lib/libboost_python.dylib" | grep libc++ ; then FLAGS="-std=c++11 -stdlib=libc++" else FLAGS="-stdlib=libstdc++" fi

Re: [Rdkit-discuss] Molecule losing properties

Joos, I'm glad you found the issue. Perhaps GetMolFrags should retain or have an option to retain public properties such as sd data. Brian Kelley > On Jan 21, 2016, at 8:14 AM, Joos Kiener <joos.kie...@gmail.com> wrote: > > Hi Brian, > > thanks for your rep

Re: [Rdkit-discuss] Molecule losing properties

Joos, In your second loop, could you "print repr(prop)"as opposed to "print prop" It could be that the name actually has a space in it which the sd format supports and can drive one to distraction. Brian Kelley > On Jan 21, 2016, at 2:11 AM, Joos Kiener <jo

Re: [Rdkit-discuss] Substructure subtraction in RDKit

e side chains added by the reaction. The output is a molecule with attached wildcards indicating where the product was attached. The isotope of the dummy atom is the reaction map number of the product's atom (if available). If this would be useful, let us know, I would be happy to have a te