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
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
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 on Ubuntu 14.04 as per
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.
PYTHON_EXECUTAB
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 David Hall's suggestion h
Hello,
In the past, I've had very good experience with the rooted fingerprints.
They were introduced by Vulpetti et al. as a description of local
environment of fluorine (LEF) atoms. Later on, we used it to compare
ionization sites in a Moka retraining study (Gedeck et al.).
The LEF code in the R
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
illustrate a great opport
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 probab
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,
Pete
Hello
In cases like this i know that Greg did the valid implementation according
to the standard. If you check the ctfile definition (
http://c4.cabrillo.edu/404/ctfile.pdf#page41) you will see that the data
header is pretty flexible. The only requirement is that it starts with a >.
Usually we fin
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 écr
Hello,
I thought we had removed all of these by now. I'll open an issue and fix
the code.
Best,
Peter
On Tue, Dec 20, 2016 at 6:01 AM David Hall wrote:
> The replace and split methods were removed from the string module in
> python3. You can replace the code as follows:
>
> s = s.replace
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,
Looks like you have a very old version of RDkit. The additional option was
included in RDkit 2016.03.1. Check
import rdkit
print(rdkit.__version__)
Best,
Peter
On Sat, Jan 21, 2017 at 3:39 PM Janusz Petkowski wrote:
> Czesc again,
>
> Many thanks for the code snippet. I thought that I use i
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
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,
r?
> So, if a radius is greater than the number of available bonds in all
> directions from the rooted atom the function will return empty list as it
> considers that such environment does not exist. Is this a correct
> expectation?
>
>
> Pavel.
>
>
> On 03/27/2017 03:5
ee from test examples for the 0 atom in CC1CC1 an environment
> with radius 3 exists. Thus, radius should be interpreted as a number of
> bonds from the rooted atom, not a number of atoms. I did not expect this as
> well.
>
>
> Pavel.
>
> On 03/27/2017 04:22 PM, Peter Gedeck wro
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:
> Hello Christian:
>
> I
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 r
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
hello Paul
If you look at your fragments you see that in your decomposition you have
overlapping fragments:
set(['[3*]OCC(O[3*])C1CC1', '[4*]CC([4*])C1CC1', '[3*]Oc1ncncn1',
'[14*]c1ncncn1', '[3*]OCC([4*])C1CC1', '[3*]OC(C[4*])C1CC1',
'[3*]OC1CNC1', '[15*]C1CNC1'])
This indicated that the fragme
Hello Yingfeng,
The molecular formula in the inchi key is not the same as the one from the
molecule that is encoded. It ignores charges. You can see this when you
convert the mol to a SMILES:
>>> sInchi =
"InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-1/t3-/m0/s1"
>>> curre
-- Forwarded message --
From: Peter Gedeck
Date: 19 December 2013 11:43
Subject: Re: [Rdkit-discuss] compound mass calculation
To: Yingfeng Wang
Hello,
Here is RDkit code that will neutralize a compound:
http://code.google.com/p/rdkit/wiki/NeutralisingCompounds
If you are
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
mailto
Hi
If we had known that the helpdesk advice would work here, ... ;-)
Best,
Peter
On 24 March 2014 19:05, Gerebtzoff, Gregori wrote:
> Hi guys,
>
> Many thanks for your help and suggestions!
> Don't ask me why but restarting PostgreSQL did the trick, now my "C12CC(C1)C2"
> smiles can be rea
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 = Chem.MolFromMolBlock(s
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 <
s.balasupraman...@
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 9:57 PM, Bodle, Christopher
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))
molsin2[0].GetProp('PUBCHEM_ATOM_DEF_STER
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.
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 t
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 b
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