Re: [Rdkit-discuss] Hello questions about the Synthetic Accessibility score

The paper is pretty vague on implementation details. However, note that the code is copyright Novartis Institutes for BioMedical Research Inc. It was released in the public domain and at that point (2013) it was the implementation that was used internally at Novartis. You can therefore use the

Re: [Rdkit-discuss] Programatic access to the mol sanitation process results

Hello Lukas, The file rdkit/TestRunner.py contains a class/context manager called OutputRedirectC. If I remember correctly, this allowed capturing these messages. It's not used anywhere in the RDkit code base, so it not work anymore. Anyway, give it a try and if it works, you can modify it to

Re: [Rdkit-discuss] mmpdb installation on windows using mingw

Here is a relevant stackoverflow question. https://stackoverflow.com/questions/1948862/is-the-python-3-x-signal-library-for-windows-incomplete What happens if you comment out the code if you run on windows? Best Peter On Fri, Sep 22, 2017 at 7:25 AM Markus Metz wrote: >

Re: [Rdkit-discuss] FindAtomEnvironmentOfRadiusN

Hello, The atom numbers start with 0. From the middle atom, there are no environments with radius 2. You will get a result if you use the first (=0) or the last (=2) atom. Try this: m = Chem.MolFromSmiles("NCO") i = Chem.FindAtomEnvironmentOfRadiusN(m, 1, 0) Chem.MolToSmiles(Chem.PathToSubmol(m,

Re: [Rdkit-discuss] Drawing structure with generic labels

Hello Alexis, I had a look at the python and the C++ code for drawing of molecules. Neither supports your requirement. It would be useful to implement it. I can have a look at it in more detail and see if I could implement a quick fix, e.g. Drawing a custom label based on an atom property. Best

Re: [Rdkit-discuss] PMI API

According to this: https://en.wikipedia.org/wiki/List_of_moments_of_inertia The moments of inertia of a disk (something like benzene) are: Iz = mr^2/2 Ix = Iy = mr^2/4 None of them is zero. The smallest moment of inertia of a rod-like molecule (e.g. C#C) is zero. Best, Peter On Sun, Jan 15,

Re: [Rdkit-discuss] SetAtomAlias

ill...@univ-reims.fr> wrote: > Dear Peter, > > I got: > > AttributeError: 'module' object has no attribute 'SetAtomAlias' > > with your example code, below. > > Best regards, > > Jean-Marc > > > Le 17/12/2016 à 00:44, Peter Gedeck a écrit : > > Hello

Re: [Rdkit-discuss] SetAtomAlias

Hello, SetMolAlias is available in Python as a function and not as an Atom method: from rdkit import Chem import sys m = Chem.MolFromSmiles('CCC') for i, atom in enumerate(m.GetAtoms()): Chem.SetAtomAlias(atom, 'C' + str(i + 1)) w = Chem.SDWriter(sys.stdout) w.write(m) w.close() Best,

Re: [Rdkit-discuss] Extracting SMILES from text

Hello Alexis, Depending on the size of your document, you could consider limit storing the already tested strings by word length and only memoize shorter words. SMILES tend to be longer, so everything above a given number of characters has a higher probability of being a SMILES. Large words

Re: [Rdkit-discuss] Pandas

Is it possible to use the bulk similarity searching functionality for better performance instead of the list comprehension? Best, Peter On Wed, Nov 23, 2016 at 9:11 AM Greg Landrum wrote: No worries. This, and Anna's question about similarity searching and clustering

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

One of the tests says: > ImportError: libInfoTheory.so.1: cannot open shared object file: No such file or directory Did you "make install" and does LD_LIBRARY_PATH contain $RDBASE/lib? Best, Peter On Tue, Oct 4, 2016 at 11:18 AM Philip Adler wrote: > Unfortunately

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

You can also check the CMakeCache.txt file in the build directory. When I last compiled for 3.5 on the Mac, I had to correct the PYTHON_INCLUDE_DIR. Greg, PYTHON_INCLUDE_DIR was incorrectly set after "cmake ..". Executable and library correctly found. //Path to a program.

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

Hello Python failures are usually an indication of problems with the boost library. You might pickup libraries for the wrong Python version. Best Peter On Mon, Oct 3, 2016 at 11:06 AM Philip Adler wrote: > Dear All, > > I am trying to compile rdkit to run with Python3.4

Re: [Rdkit-discuss] Angstroms Hydrogen bonding

Hello Here are a few suggestion you can try that may speed up your code. Instead of GetSubstructMatches, you can use the list of neighbours of each atom. Here is something that may work, it creates an iterator that will return all the atoms for bond angles. I did not test it, however it may give

Re: [Rdkit-discuss] Querying when using CTabs

My solution for the problem was the following: qmol = Chem.MolFromMolBlock(molblock) for atom in qmol.GetAtoms(): if atom.HasQuery(): continue atom.SetNumExplicitHs(atom.GetTotalNumHs()) This gives a SMARTS like this: [#7]1(-[#6](-[#6H2]-[#6,#8]-[#6H](-[#6H2]-1)-[*])=[#8])-[*] This may

Re: [Rdkit-discuss] OCN = NCO, and I don't want that.

Hello This is the expected behaviour. The path of length 2 creates one fragment OCN. That fragment is the same if you start from oxygen or from the nitrogen. You will get a differentiation of the O and the N if you include paths of different length. It could also be that substitution can modify

Re: [Rdkit-discuss] Stereochemistry Perception

Hello Rob The compound is not chiral. There is a mirror plane that contains the 5-ring and the C-NH3 bond. There is a cis / trans stereoisomers here like in 1,4-dichloro-cyclohexane. That cannot be defined using the @symbols. However I cannot tell you how to do this for cases like this in SMILES.

Re: [Rdkit-discuss] SetProp behavior

Hello To change properties of a molecule, it is not necessary to convert to a RWMol. This is required only if you want to modify the structure. molsin2[0].GetProp('PUBCHEM_ATOM_DEF_STEREO_COUNT') molsin2[0].SetProp('PUBCHEM_ATOM_DEF_STEREO_COUNT', str(5))

Re: [Rdkit-discuss] trouble with SMARTs interpretation of 'not hydrogen'

Hello This may be just an example that you picked out of many, however why don't you just make this atom an 'any atom'? It's in a ring and normally hydrogen don't come up in rings. Best Peter On Thu, 17 Sep 2015 at 6:24 am, Andrew Dalke wrote: > On Sep 16, 2015, at

Re: [Rdkit-discuss] Errors while running CTest

Hello, Running the tests creates the directory Testing/Temporary which contains a file LastTest.log. This file is the actual output from the tests and may help you identify the reason why your tests failed. Best, Peter On 24 September 2014 17:22, Shantheya Balasupramaniam

Re: [Rdkit-discuss] MMFFGetMoleculeProperties()

Hello, I searched through the source code for MMFFGetMoleculeProperties and found a few test files. The method MMFFGetMoleculeProperties is part of the ChemicalForceFields module: from rdkit.Chem import ChemicalForceFields def testMMFFAngleConstraints(self) : m =

Re: [Rdkit-discuss] Problem reading a specific smiles with the cartridge

Hi If we had known that the helpdesk advice would work here, ... ;-) Best, Peter On 24 March 2014 19:05, Gerebtzoff, Gregori gregori.gerebtz...@roche.comwrote: Hi guys, Many thanks for your help and suggestions! Don't ask me why but restarting PostgreSQL did the trick, now my

Re: [Rdkit-discuss] Problem reading a specific smiles with the cartridge

Hello Can you construct similar SMILES like  C12(C1)C2  N12CCC(C1)C2 C1(CCC2)CCC12 Are other smiles in your dataset  bicyclic systems?  Does it work with the rewritten smiles C1C2CC1C2? Best Peter On Sat, Mar 22, 2014 at 7:42 pm, Gerebtzoff, Gregori

[Rdkit-discuss] One flavour of mcss

Hello given a data set of let's say 2000 compounds, how do I extract the most common substructures rather than the maximum common substructures? In addition, I would like to output the frequency of the found One approach would be to take a brics decomposition where you keep the full