Hi Ling,
Maybe you should switch to conda-forge channel. Replace "-c rdkit" with "-c
conda-forge".
At least that's what I'm using personally and I have no problems so far.
The latest version of rdkit there is 2020.03.6.
Best,
Christos
Christos Kannas
ty set to True, the process hangs.
Here is a notebook showing the issue
https://nbviewer.jupyter.org/gist/CKannas/d54bb5ab0fa3c964086c75f18250ddac
Is there any workaround for this?
Looking for a solution to stop the computation in a graceful manner.
Thanks,
Christos
Christos Kannas
Research Sof
Thanks a lot Paolo.
Christos
Christos Kannas
Research Software Engineer (Cheminformatics)
[image: View Christos Kannas's profile on LinkedIn]
<http://cy.linkedin.com/in/christoskannas>
On Fri, 26 Mar 2021 at 16:01, Paolo Tosco
wrote:
> Hi Christos,
>
> this is a poss
Hi Andres,
Maybe Spyder runs on the base conda environment.
Do you run Spyder from your activated environment?
Kind regards,
Christos
On Wed, Apr 14, 2021, 17:52 Andrés Sánchez Ruiz <
andressanchezrui...@gmail.com> wrote:
> Dear Greg,
>
> It works! It seems I can call functions of RDKit from t
Hi Steve,
I think it would be better to use a similarity metric based on fingerprints.
Regards,
Christos
Christos Kannas
Researcher
Ph.D Student
[image: View Christos Kannas's profile on LinkedIn]
<http://cy.linkedin.com/in/christoskannas>
On 28 November 2016 at 18:25, Step
correct.*
Best,
Christos
Christos Kannas
Researcher
Ph.D Student
[image: View Christos Kannas's profile on LinkedIn]
<http://cy.linkedin.com/in/christoskannas>
On 19 May 2017 at 12:52, Alexis Parenty
wrote:
> Hi everyone,
>
>
> I need a function that could gener
lution for a script I think is the best approach for
having different Python environments activated along with additional
instances of PyCharm.
Regards,
Christos
Christos Kannas
Researcher
Ph.D Student
[image: View Christos Kannas's profile on LinkedIn]
<http://cy.linkedin.com/in/chri
, i.e. [OH-].C>>COH, and use RDKit's reaction functionality
to perform the reaction on your molecules.
Hope this was a bit helpful.
Regards,
Christos
Christos Kannas
Chem[o]informatics Researcher & Software Developer
[image: View Christos Kannas's profile on LinkedIn
ve to filter out the molecules that are not valid.
See this Jupyter Notebook
<https://gist.github.com/CKannas/11bb9bcaa9435dd18a0bb969501219b2> at cell
5 the 1st line in the while loop.
Best,
Christos
Christos Kannas
Chem[o]informatics Researcher & Software Developer
[image: View Christo
omSmiles('C=C')))>>> Chem.MolToSmiles(ps[0][0])'C1=CC=CC=C1'>>>
>>> p0 = ps[0][0]>>>
>>> Chem.SanitizeMol(p0)rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE>>>
>>> Chem.MolToSmiles(p0)'c1c1'
Hi Patrick,
I had a similar problem with RDKit 2017.09.03 on MacOS, using rdkit channel
in anaconda.
Using the conda-forge channel with python 3.5.5 and ipython 6.2 works fine.
I can post my env tomorrow from work.
Best,
Christos
Christos Kannas
Chem[o]informatics Researcher & Soft
Hi RDKiters,
Is it possible to install RDKit PostgreSQL cartridge via Anaconda on MacOS?
Or would be better to try with a Linux VM?
Best,
Christos
Christos Kannas
Chem[o]informatics Researcher & Software Developer
Mob (UK): +44 (0) 7447700937
Mob (Cyprus): +357 99530608
[image:
conda environment. If
I need to connect it to an existing PostgreSQL installation I will have to
build RDKit and the cartridge from source don't I?
2. Will the cartridge work in the latest RDKit 2018 version, if I build
it from the source?
Best,
Christos
Christos Kannas
Chem[o]i
dge?
Best,
Christos
Christos Kannas
Chem[o]informatics Researcher & Software Developer
Mob (UK): +44 (0) 7447700937
Mob (Cyprus): +357 99530608
[image: View Christos Kannas's profile on LinkedIn]
<http://cy.linkedin.com/in/christoskannas>
On Thu, 3 May 2018 at 09:47, Paolo Tos
9552d7c8899cfaff030
Best,
Christos
Christos Kannas
Chem[o]informatics Researcher & Software Developer
[image: View Christos Kannas's profile on LinkedIn]
<http://cy.linkedin.com/in/christoskannas>
On Thu, 23 Aug 2018 at 12:36, Paolo Tosco
wrote:
> Dear Kovas,
>
> It loo
4-7+*/t17-,19-/m1/s1
m2 ->
InChI=1S/C20H26O4/c1-12(2)17-11-18(22)14(4)7-5-6-13(3)8-16(21)9-15-10-19(17)24-20(15)23/h6-7,10,12,17,19H,5,8-9,11H2,1-4H3/*b13-6-,14-7-*/t17-,19-/m1/s1
Not sure why it happens, but I've seen it multiple times...
Best,
Christos
Christos Kannas
Chem[o]
ochemistry.
I guess that's why there are inconsistencies [sometimes] when the molecule
has been generated from a SMILES instead from a MOL block with 2D or 3D
coordinates...
Christos
Christos Kannas
Chem[o]informatics Researcher & Software Developer
[image: View Christos Kannas's
the data to be
picklable.
Best,
Christos
Christos Kannas
Cheminformatics Researcher & Software Developer
[image: View Christos Kannas's profile on LinkedIn]
<http://cy.linkedin.com/in/christoskannas>
On Wed, 20 Feb 2019 at 11:28, Stamatia Zavitsanou <
stamatia.zavitsa...@ori
ecule"] = mols
Best,
Christos
Christos Kannas
Scientific Software Developer (Cheminformatics)
On Thu, 25 Jul 2019 at 15:45, Gianluca Sforna wrote:
> Hi all,
> is it possible to manually add molecules to a pandas dataframe? I am
> reading a bunch of mol2 files, adding some propert
com/a/EnYoHWG
Best,
Christos
Christos Kannas
Scientific Software Developer (Cheminformatics)
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:string const&, std::vector>>>> std::allocator >, std::allocator
>>>>> > > >&) const in FindRings.cpp.o
>>>>> "std::vector >
>>>>> RDKit::Dict::fromany
>>>>> >
>>>
Hi Michal,
I don't think it will work, at least with Python since it requires the
RDKit directory in PYTHONPATH and RDKit/lib is required in LD_LIBRARY_PATH
in order that Python can find the library files created when building
RDKit.
Regards,
Christos Kannas
Sent from my Galaxy Note!
On
Hi,
I'm also using Mercurial (Hg) & BitBucket for private projects and also
follow some public ones.
Git & Hg are similar, they are both dvcs and they are highly adopted by
the open source community.
My vote though goes to Bitbucket and Hg.
Regards,
Christos
Sent from my Galaxy Note!
On Feb 1
slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
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> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourcef
nd regards,
Christos
--
Christos Kannas
Sent from my Galaxy Note!
On Mar 19, 2013 3:42 PM, wrote:
> Dear RDKitters,
>
> anyone worked with RDKit (data processing & descriptor calculation) &
> scikit-learn (train Random Forests) and could share some experiences with
> setting up/d
t as a new
descriptor, clogSw (like clogP), within the RDKit distribution?
Kind Regards,
Christos
--
Christos Kannas
Researcher
Ph.D Student
e-Health Laboratory <http://www.medinfo.cs.ucy.ac.cy/>
kannas.chris...@ucy.ac.cy
kannas.chris...@cs.ucy.ac.cy
chriskan...@gmai
from
> the latest Intel processors and coprocessors. See abstracts and register >
> http://pubads.g.doubleclick.net/gampad/clk?id=60135991&iu=/4140/ostg.clktrk
> _______
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
&g
stand I've created this small IPython Notebook
http://nbviewer.ipython.org/gist/CKannas/9089271
Can you give me the reasons why this happens?
Best,
Christos
--
Christos Kannas
Researcher
Ph.D Student
Mob (UK): +44 (0) 7447700937
Mob (Cyprus): +357 99530608
[image: View Christos Kannas&#x
True
> >>> m3.HasSubstructMatch(m2)
> True
> >>> m3H.HasSubstructMatch(m2)
> True
>
> Hope that helps.
>
> Yours,
>
> Toby Wright
>
> --
> InhibOx Ltd, Oxford
>
>
>
> On 19 February 2014 10:25, Christos Kannas wrote:
>
>> Hi
t; Customize your own dashboards, set traffic alerts and generate reports.
> Network behavioral analysis & security monitoring. All-in-one tool.
>
> http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
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> Rdkit-discu
3.HasSubstructMatch(patt)
Out[13]: True
Shouldn't be that z2 and z3 have the same information?
Thanks,
Christos
Christos Kannas
Researcher
Ph.D Student
Mob (UK): +44 (0) 7447700937
Mob (Cyprus): +357 99530608
[image: View Christos Kannas's profile on
LinkedIn]<htt
Hi Greg,
Thanks a lot for the explanation.
It makes things clearer now.
Well the reason I'm doing SMARTS-SMARTS match is because I would like to
match functional groups with the reactants in reactions.
Regards,
Christos
Christos Kannas
Researcher
Ph.D Student
Mob (UK): +44 (0) 744770093
attachment points in hydrophobe
region core.
Is this the normal behaviour, or a bug?
Also if I merge the two families of Hydrophobe features then I do not get
the error.
Regards,
Christos
Christos Kannas
Researcher
Ph.D Student
Mob (UK): +44 (0) 7447700937
Mob (Cyprus): +357 99530608
[image: Vie
Hi JP,
I think smol = Chem.PathToSubmol(mol, path), where path is a list of
indices, will do what you want.
Best,
Christos
Christos Kannas
Researcher
Ph.D Student
Mob (UK): +44 (0) 7447700937
Mob (Cyprus): +357 99530608
[image: View Christos Kannas's profile on
LinkedIn]
Hi JP,
Well I've noticed the same thing on my tests, the only reason I can think
off is that it either takes the preceding or the ending atom to the tuple
of atom indices.
I hope Greg or someone else can shed some light into it.
Best,
Christos
Christos Kannas
Researcher
Ph.D Student
Mo
, if some ring atoms are mapped as hydrophobic, and I
also keep terminal carbons (CH3) connected to the adjacent hydrophobic
group, if any. I hope these assumptions are chemically correct.
Best,
Christos
Christos Kannas
Researcher
Ph.D Student
Mob (UK): +44 (0) 7447700937
Mob (Cyprus): +357 99
, kekulize=True)
For visualized output check
http://nbviewer.ipython.org/gist/anonymous/11248962/Sanitization_Errors.ipynb
Is this an expected behaviour?
Is there something I can do as a fix?
Regards,
Christos
Christos Kannas
Researcher
Ph.D Student
Mob (UK): +44 (0) 7447700937
Mob (Cypr
ith carbons so chloride
should be disconnected.
[N+]([Cl-])(C)(C)C -> [N+](C)(C)C.[Cl-]
Regards,
Christos
Christos Kannas
Researcher
Ph.D Student
Mob (UK): +44 (0) 7447700937
Mob (Cyprus): +357 99530608
[image: View Christos Kannas's profile on
Lin
Hi Jan,
AutoDock has a set of tools (MGLTools) that have tools to convert pdb to
pdbqt and vice-versa.
If I recall it can also convert pdbqt to mol2 also. See this discussion
http://autodock.1369657.n2.nabble.com/ADL-pdbqt-to-mol2-td6755769.html
Best,
Christos
Christos Kannas
Researcher
Ph.D
thing that should happen?
Attached is an ipython notebook showing this behaviour.
Best,
Christos
Christos Kannas
Researcher
Ph.D Student
Mob (UK): +44 (0) 7447700937
Mob (Cyprus): +357 99530608
[image: View Christos Kannas's profile on LinkedIn]
<http://cy.linkedin.com/in/christoskanna
x27;t have to
install NumPy, since it is bundled to it.
Best,
Christos
Christos Kannas
Researcher
Ph.D Student
Mob (UK): +44 (0) 7447700937
Mob (Cyprus): +357 99530608
[image: View Christos Kannas's profile on LinkedIn]
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On 24 July 20
if I did any update to gcc.
I will get back to you on Monday for this, except if you are in a hurry
I'll go from the office tomorrow to check my dev machine.
Best,
Christos
Christos Kannas
Researcher
Ph.D Student
Mob (UK): +44 (0) 7447700937
Mob (Cyprus): +357 99530608
[image: View Chr
/RDKit_2013_09_2
export LD_LIBRARY_PATH=$RDBASE/lib:path_to_boost_libs:$ LD_LIBRARY_PATH
export PYTHONPATH=$RDBASE:$PYTHONPATH
export PATH= /opt/anaconda/bin:$PATH
Best,
Christos
Christos Kannas
Researcher
Ph.D Student
Mob (UK): +44 (0) 7447700937
Mob (Cyprus): +357 99530608
[image: View Christos Kannas&#
Hi RDKiters,
How is UGM going?
Is there a tweet feed to follow?
Hope you are having a nice and interesting time!
Best,
Christos
Christos Kannas
Researcher
Ph.D Student
[image: View Christos Kannas's profile on LinkedIn]
<http://cy.linkedin.com/in/christ
Hi Greg,
Could you provide a compiled version of the patched RDKit for Python 64bit
on Windows,
Thanks,
Christos
Christos Kannas
Researcher
Ph.D Student
Mob (UK): +44 (0) 7447700937
Mob (Cyprus): +357 99530608
[image: View Christos Kannas's profile on LinkedIn]
<http://cy.linkedi
Sergio,
You have to use GetSubstructMatches.
Look at my sample here
<http://nbviewer.ipython.org/gist/CKannas/5a762b97c52e389d492e>.
Best,
Christos
Christos Kannas
Researcher
Ph.D Student
Mob (UK): +44 (0) 7447700937
Mob (Cyprus): +357 99530608
[image: View Christos Kannas's
,
Christos
Christos Kannas
Researcher
Ph.D Student
Mob (UK): +44 (0) 7447700937
Mob (Cyprus): +357 99530608
[image: View Christos Kannas's profile on LinkedIn]
<http://cy.linkedin.com/in/christoskannas>
On 2 February 2015 at 09:03, Reutlinger, Michael <
michael.reutlin...@roche.com>
Hi Samuel,
The problem is that x is a tuple in your case not an rdkit molecule object.
Check your code to see what mols list actually has inside. I'm guessing
that x is a tuple containing a molecule object plus some other info.
Best.
Christos
Christos Kannas
Researcher
Ph.D Student
Mo
Hi Steve,
Make sure that PYTHONPATH has the correct location of RDKit, and
LD_LIBRARY_PATH has the location of boost libraries.
Regards,
Christos
Christos Kannas
Researcher
Ph.D Student
Mob (UK): +44 (0) 7447700937
Mob (Cyprus): +357 99530608
[image: View Christos Kannas's profi
safe.
Best,
Christos Kannas
Sent from my Galaxy Note 4.
On 2 Mar 2015 17:50, "Bennion, Brian" wrote:
> Hello,
>
> I am relatively new to rdkit but have found it to be very useful in
> creating compounds with the reaction functions.
>
> Currently my project involves
Hi Brian,
Can you provide a complete block of code of the serial code or the parallel
block and synthesize function?
Best,
Christos
Christos Kannas
Researcher
Ph.D Student
Mob (UK): +44 (0) 7447700937
Mob (Cyprus): +357 99530608
[image: View Christos Kannas's profile on LinkedIn]
that extra
information,you can convert your molecules to PropertyMol, e.g. from
rdkit.Chem.PropertyMol import PropertyMol pmol = PropertyMol(mol)
Hope the information above helps a bit.
Regards,
Christos
Christos Kannas
Researcher
Ph.D Student
[image: View Christos Kannas's profile on Lin
common problem with Python especially if you are dealing with the
various parallel computation packages, that exchange messages across python
processes via pickled messages.
Regards,
Christos
Christos Kannas
Researcher
Ph.D Student
Mob (UK): +44 (0) 7447700937
Mob (Cyprus): +357 99530608
Hi Tim,
I'm not sure about this, but I think that in order to use the cartridge you
have to build RDKit and cartridge from source.
Regards,
Christos Kannas
Sent from my Galaxy Note 4.
On 24 Apr 2015 13:47, "Tim Dudgeon" wrote:
> Is it possible when using the packages?
>
att)
C
In [4]:
pm = m.GetSubstructMatches(patt)
print len(pm)
8
Regards,
Christos
Christos Kannas
Researcher
Ph.D Student
Mob (UK): +44 (0) 7447700937
Mob (Cyprus): +357 99530608
[image: View Christos Kannas's profile on LinkedIn]
<http://cy.linkedin.com/in/christoskannas>
On 7 October 20
Hi Greg,
I want to use RDKit to quantify Shape Similarity between molecules and have
tried the following:
from rdkit.Chem import AllChem
mol1 = AllChem.MolFromSmiles("C(=O)(C(c1ccc(cc1)CC(C)C)C)NO")
AllChem.CanonicalizeMol(mol1)
AllChem.EmbedMolecule(mol1)
AllChem.UFFOptimizeMolec
: ckan...@noesisinformatics.com
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Shape Similarity
Dear Christos,
2009/3/23 Christos Kannas :
>
> I want to use RDKit to quantify Shape Similarity between molecules and
have
> tried the following:
>
> from rdkit.Chem im
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