Re: [Rdkit-discuss] Getting to grips with Open3DAlign

I just tried Tim’s example (or a version of it that Greg sent me, respectively). What is missing are the hydrogens for the torsion terms of ETKDG to work properly. Before generating the conformations AllChem.AddHs() should be called. Best, Sereina On 22 Jun 2016, at 06:48, Sereina

Re: [Rdkit-discuss] Getting to grips with Open3DAlign

Based on the code snippets, Paolo has not used the basic-knowledge terms whereas Tim did. When setting useExpTorsionAnglePrefs=True and useBasicKnowledge=True, a minimization is in principle not necessary anymore (unless there are aliphatic rings, because we currently don’t have torsion rules

Re: [Rdkit-discuss] Getting to grips with Open3DAlign

I don't have anything to add to the pieces about the alignment (Paolo is the expert there!), but one comment on the conformation generation: If you used the background knowledge terms in the embedding, I don't think you should be getting the really distorted aromatic rings. Since in this case that

Re: [Rdkit-discuss] Struggling with apache + rdkit + django

Dear Michał, I already went there and I'm really happy ChEMBL is using the same technologies as I do :-) (or the other way around :-) For sure I will consider the Beaker facility for inclusion in my project, but for now I'm too "old-school" minded, I want everything at home before querying

Re: [Rdkit-discuss] Struggling with apache + rdkit + django

Dear Paolon Le 21/06/2016 à 20:09, Paolo Tosco a écrit : > Dear Stéphane, > > I can run Python scripts import RDKit modules on CentOS 7 by putting > the following rdkit.conf file in /etc/ld.so.conf.d: > > $ cat /etc/ld.so.conf.d/rdkit.conf > /var/www/cgi-bin/rdkit/rdkit-Release_2016_03_1/lib >

Re: [Rdkit-discuss] Getting to grips with Open3DAlign

Dear Tim, the Align() method returns an RMSD value, which however is computed only on a limited number of atom pairs, namely those that the algorithm was able to match between the two molecules, so a low value is not particularly informative of the overall goodness of the alignment, as it

Re: [Rdkit-discuss] Struggling with apache + rdkit + django

Hi Stephane, Add some Python code to your uwsgi.py file that prints out the environment that the Python interpreter sees (maybe comment out everything else) when it is called by the Apache. It is very likely that the Apache calls another Python interpreter than you expect. What Paolo writes is

Re: [Rdkit-discuss] Struggling with apache + rdkit + django

Hi Stéphane, Just to let you know about two things: 1. ChEMBL web services are a Django application written using RDKit. We deploy it using gunicorn and Apache through Reverse Proxy and put on a Virtual Machine named myChEMBL that you can download. Here are some example configuration files:

Re: [Rdkit-discuss] Struggling with apache + rdkit + django

Dear Stéphane, I can run Python scripts import RDKit modules on CentOS 7 by putting the following rdkit.conf file in /etc/ld.so.conf.d: $ cat /etc/ld.so.conf.d/rdkit.conf /var/www/cgi-bin/rdkit/rdkit-Release_2016_03_1/lib and adding two SetEnv directives in the section of my Apache

Re: [Rdkit-discuss] Struggling with apache + rdkit + django

Le 21/06/2016 20:18, TJ O'Donnell a écrit : > I would suggest setting PYTHONPATH in > config or ini files for > Apache or Django or uwsgi > Not sure which is required. Dear all, This is already indicated using a WSGIprocessGroup : WSGIDaemonProcess manageLibrary

Re: [Rdkit-discuss] Struggling with apache + rdkit + django

I would suggest setting PYTHONPATH in config or ini files for Apache or Django or uwsgi Not sure which is required. On Tue, Jun 21, 2016 at 11:15 AM, Téletchéa Stéphane < stephane.teletc...@univ-nantes.fr> wrote: > Le 21/06/2016 20:05, Bennion, Brian a écrit : > > What is the actual problem that

Re: [Rdkit-discuss] Struggling with apache + rdkit + django

Le 21/06/2016 20:05, Bennion, Brian a écrit : > What is the actual problem that is occurring? You have listed what you have > tried to do to fix a problem. > > Brian Dear Brian, I get a 500 error meaning something is not working properly, but no trace in logs (either apache or django), so I

[Rdkit-discuss] Struggling with apache + rdkit + django

Dear all, I am willing to incorporate some rdkit functionalities using a django backend for an internal project (basically ligand annotation and comparison with docking studies) which will be published once ready. Using the "developper" mode of django and conda I can properly get all of them

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

On Jun 21, 2016, at 5:26 PM, Greg Landrum wrote: > Because chirality is represented relative to the ordering of the bonds around > an atom, it's pretty difficult to do this if you want to actually break and > add bonds on your own. This would probably be somewhat easier if there were > an

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

Boy is the list busy today. I love it! :-) Because chirality is represented relative to the ordering of the bonds around an atom, it's pretty difficult to do this if you want to actually break and add bonds on your own. This would probably be somewhat easier if there were an RWMol.ReplaceBond()

[Rdkit-discuss] Chirality conservation during atom replacement

Hi RDKitters, I am having trouble with chirality conservation during fragmentation of molecules. Is there a simple way of preserving chirality during splits on chiral atoms? Am I missing a simple function? Andrew has brought this topic has come up on the mailing list before, but so far there has

Re: [Rdkit-discuss] Counting H Atoms

Answering this may require a long explanation, or it could be really quick let's see where we end up. :-) If you replace "a.GetTotalNumHs()" with "a.GetTotalNumHs(includeNeighbors=True)", do the results then make sense to you? -greg On Tue, Jun 21, 2016 at 4:50 PM, David Cosgrove

[Rdkit-discuss] Counting H Atoms

Hi All, I'm a bit confused about counting hydrogen atoms. It's a perennial problem with cheminformatics toolkits in my experience, but this seems particularly perverse. If I run the code: from rdkit import Chem from rdkit.Chem import AllChem mol = Chem.MolFromSmiles( 'CCO' ) mol = Chem.AddHs(

[Rdkit-discuss] Getting to grips with Open3DAlign

Hi All, I'm trying to get to grips with using Open3D Align in RDKit, but hitting problems. My approach is to generate random conformers of the probe molecule and align it to the reference molecule. My example is cobbled together from the examples in the cookbook. from rdkit import Chem,

Re: [Rdkit-discuss] Transforming molecules into reduced graphs

Hi Jessica, On Tue, Jun 21, 2016 at 2:16 PM, Jessica Krause wrote: > > I am using RDKit for a while now. My focus is the transformation of molecules in simplified reduced forms. With the help of SMARTS I specify > molecular substructures and pattern to transform these

Re: [Rdkit-discuss] MCS on fused ring systems

You are absolutely correct. There's a typo in that function. I'll fix it. -greg On Mon, Jun 20, 2016 at 5:43 PM, Luca Fenu - Network < fenu_l...@network.lilly.com> wrote: > Thanks Greg, > > > > that works great. I’ve reconverted the isotopic smarts to smiles with the > function suggested in (