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
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
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 Perfor
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 to
> do better. I'm trying t
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 :
>
> Yo RDKitters,
>
> I am stuck on something so basic, it
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 nic
Hi all
I have a problem with generating molecule from smiles.
from rdkit import Chem
template = Chem.MolFromSmiles('F[P-](F)(F)(F)(F)F.CN(C)C(F)=[N+](C)C')
I got an error:
Explicit valence for atom # 1 P, 7, is greater than permitted
But the SMILES for this structure should be valid.
I checked
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 :
> Ah, what timing.
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 :
> Hi all,
>
>
you can allways visualise yours SMARTS by using http://www.smartsview.de/
pozdrawiam
Adrian
2014-03-27 17:44 GMT+01:00 Jameed Hussain :
> Try this:
>
> [*!H0;!$(*~[#0])]
>
>
>
> I don't think you can do what you want without a recursive SMARTS. It's
> well worth doing the Daylight exercises to
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 :
> Hi Hari,
>
> You can use "mol_from_pkl()". Here's a quick demo:
> In [20]: m = Chem.MolFromSmiles('c1cnccc1')
>
> In [21]: pkl = buffer(m.To
t=True,
>> bool clearConfs=True, boost::python::dict {lvalue} coordMap={}, unsigned
>> int nFlipsPerSample=0, unsigned int nSample=0, int sampleSeed=0, bool
>> permuteDeg4Nodes=False, double bondLength=-1.0)
>>
>>
>> Actually, "ccc[nH]c" is a fragm
t.Chem import Draw>>> Draw.MolToFile(ms[0],'images/cdk2_mol1.png')>>>
>>> Draw.MolToFile(ms[1],'images/cdk2_mol2.png')
for this example with you pasted you can just write mol to file:
>>> from rdkit.Chem import AllChem
>>> from rdkit import Chem
&g
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
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
> Yes it does; many thanks!
> I've just found the notebook I mentioned:
> http://nbviewer.
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/
http://opsin.ch.cam.ac.u
http://opsin.ch.cam.ac.uk/
I found that something like this is added to Rubidium, some
chemical-informatics tool written in Ruby
http://depth-first.com/articles/2007/10/19/easily-convert-iupac-nomenclature-to-smiles-inchi-or-molfile-with-rubidium/
regards
Adrian Jas
Hi all,
Greg thanks for new release.
By the way I have the question:
How can I change font size on image?
When I create small images the font is too big and on some big size
images it is too small.
Regards
Adrian
--
Liv
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.
2012/
> An update on this thread:
>
> On Tue, Jun 19, 2012 at 9:19 AM, Adrian Jasiński
> wrote:
>>
>> There is some example code:
>>
>> from rdkit import Chem
>> from rdkit.Chem import Draw
>> mol = Chem.MolFromSmiles('CC(=O)Nc1c1C(=O)C11C1CCC
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 :
> Dear Adrian,
>
> On Tue, Jun 19, 2012 at 9:19 AM, Adrian Jasiński
> wrote:
>&
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 = Chem.MolFromSmiles('CC(=O)Nc1c1
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