Re: [Rdkit-discuss] Polar surface areas

Hi Josh You have TPSA (Topological Polar Surface Area) in Rdkit Descriptors http://www.rdkit.org/Python_Docs/rdkit.Chem.Descriptors-module.html Check the list of all descriptors http://www.rdkit.org/docs/GettingStartedInPython.html#list-of-available-descriptors regards Adrian Jasiński 2016

[Rdkit-discuss] PgSQL / cartridge installation problem

I'm using Ubuntu 16.04 LTS, I successfully installed latest rdkit version 2016_03_03 from source, but when I tried to install Cartridge I found difficulties. Theres no good instruction in RDKit documentation how to install it. Only info is in README file but it is not valid. Possibly there should

[Rdkit-discuss] next RDKit UGM?

Are there any plans for next RDKit UGM in 2016? I planning my conferences calendar for this year, for this reason it will be good to know. regards Adrian -- Site24x7 APM Insight: Get Deep Visibility into Application

Re: [Rdkit-discuss] Latest version

The release and binary files are on the github release page: https://github.com/rdkit/rdkit/releases/tag/Release_2015_09_2 regards Adrian 2015-12-10 11:12 GMT+01:00 David Cosgrove : > Hi All, > > I'm sorry to trouble you all with this one, as I feel I should be able

Re: [Rdkit-discuss] Ridiculously easy problem - capture RDKit's error messages

see: https://docs.python.org/2/tutorial/errors.html import rdkit from rdkit import Chem try: Chem.MolFromSmiles('XXX') except Exception as msg: (do something here e.g. pring msg) pozdrawiam Adrian 2015-01-23 14:58 GMT+01:00 JP jeanpaul.ebe...@inhibox.com: Yo RDKitters, I am stuck

[Rdkit-discuss] logD

Hi, Is there a way to calculate *distribution-coefficient* *(logD)* for a compound? I'm interested in calculation at PH 7.4 for some compounds. I haven't found it in the list of descriptors: http://www.rdkit.org/docs/GettingStartedInPython.html#list-of-available-descriptors If not it will be

Re: [Rdkit-discuss] 2D Drawing in C++

If I can start a list of wishes for new function it will be nice to add a possibility for drawing the series of molecules with the same core in the same orientation (based on some alignment or something like that). pozdrawiam Adrian 2014-07-02 14:04 GMT+02:00 Greg Landrum

Re: [Rdkit-discuss] Chemical formula

http://www.rdkit.org/Python_Docs/rdkit.Chem.rdMolDescriptors-module.html#CalcMolFormula from rdkit.Chem.rdMolDescriptors import CalcMolFormula formula = CalcMolFormula(Chem.MolFromSmiles(CCCOC)) pozdrawiam Adrian 2014-06-13 10:20 GMT+02:00 Alexey Chernobrovkin

Re: [Rdkit-discuss] SMARTS behaviour

you can allways visualise yours SMARTS by using http://www.smartsview.de/ pozdrawiam Adrian 2014-03-27 17:44 GMT+01:00 Jameed Hussain jameed.x.huss...@gsk.com: Try this: [*!H0;!$(*~[#0])] I don't think you can do what you want without a recursive SMARTS. It's well worth doing the

Re: [Rdkit-discuss] Insert mol objects directly into postgres rdkit cartridge column?

you can try use razi: http://razi.readthedocs.org/en/latest/database_creation_tutorial.html pozdrawiam Adrian 2014-02-26 18:34 GMT+01:00 Greg Landrum greg.land...@gmail.com: Hi Hari, You can use mol_from_pkl(). Here's a quick demo: In [20]: m = Chem.MolFromSmiles('c1cnccc1') In [21]:

Re: [Rdkit-discuss] generate 2D figure

') pozdrawiam Adrian Jasiński 2014-02-17 18:34 GMT+01:00 Yingfeng Wang ywang...@gmail.com: I want to draw a 2D figure of a compound. And I follow the example given at the following link, http://www.rdkit.org/docs/GettingStartedInPython.html My code is given as follows, from rdkit.Chem

Re: [Rdkit-discuss] SDMolSupplier doesn't support file handlers?

Example from tutorial: import gzip inf = gzip.open('data/actives_5ht3.sdf.gz') gzsuppl = Chem.ForwardSDMolSupplier(inf) ms = [x for x in gzsuppl if x is not None] len(ms)180 pozdrawiam Adrian Jasiński 2014-01-31 Michał Nowotka mmm...@gmail.com: Hi, I need to process large

Re: [Rdkit-discuss] rdkit mol objects from sql

One of the solutions is razi but it's for sqlalchemy https://razi.readthedocs.org/en/latest/database_creation_tutorial.html pozdrawiam Adrian Jasiński 2013/10/23 George Papadatos gpapada...@gmail.com Yes it does; many thanks! I've just found the notebook I mentioned: http

[Rdkit-discuss] IUPAC nomenclature

Is there a way to converting IUPAC nomenclature into SMILES, InChI, or Molfile formats? I didn't found any clues in RDKit Documentation. it would be nice if you can add such functionality. Fast way for that can be using OPSIN library: https://bitbucket.org/dan2097/opsin/

Re: [Rdkit-discuss] Announcement: 1st RDKit User Group Meeting scheduled

I have the question connected with the topic, Is there any temporary plan of the meeting or topics which will be discussed during this event? If yes where I can find it? If no will it be announced and when? I suggest to publish such a list of topics and to vote for most interesting of them.

Re: [Rdkit-discuss] problem with overlap in drawing.

...@gmail.com: An update on this thread: On Tue, Jun 19, 2012 at 9:19 AM, Adrian Jasiński jasinski.adr...@gmail.com wrote: There is some example code: from rdkit import Chem from rdkit.Chem import Draw mol = Chem.MolFromSmiles('CC(=O)Nc1c1C(=O)C11C1C1') Draw.MolToFile(mol

Re: [Rdkit-discuss] problem with overlap in drawing.

I have many others examples where I have found overlapping. Even rings overlap in some of them. It will be nice if it will be fixed for next realize. Best Regards Adrian 2012/6/20 Greg Landrum greg.land...@gmail.com: Dear Adrian, On Tue, Jun 19, 2012 at 9:19 AM, Adrian Jasiński jasinski.adr

[Rdkit-discuss] problem with overlap in drawing.

Hi All I have some problem with drawing. When I draw molecules using RDkit sometimes I have some structure overlap. But when I draw it using for example marvin it's look fine. There is some example code: from rdkit import Chem from rdkit.Chem import Draw mol =