Coords(m). And this
won't work unless AllChem is loaded.
Best,
Michal Krompiec
Merck KGaA
On Wed, 23 Sep 2020 at 16:56, Rocco Moretti wrote:
> Hi Norwid,
>
> There's a subtle but significant difference between the two examples:
>
> >>> AllChem.Compute2DCoords(m
Uhm, you’re right.
On Wed, Sep 23, 2020 at 7:46 PM Rocco Moretti wrote:
> Python translates object.method() to method(object).
>
>
> Well, yes and no. "Yes" in the sense that instance methods are internally
> implemented equivalently to a free method which takes an instance as the
> first parame
Hello RDKitters,
Are Dragon fingerprints (or something close) available in RDKit (or free
codes that depend on RDKit)? I'm trying to reproduce results from one paper.
Thanks,
Michal Krompiec
Merck KGaA
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elps,
> Nils
>
> Am 10.11.2020 um 23:11 schrieb Michal Krompiec:
> > Hello RDKitters,
> > Are Dragon fingerprints (or something close) available in RDKit (or free
> > codes that depend on RDKit)? I'm trying to reproduce results
Dear Anthony,
>From MMFF or UFF you shouldn’t expect reasonable structures of
metal-containing compounds. If you need a quick and qualitatively OK
method, I recommend xtb.
Best wishes,
Michal Krompiec, Merck KGaA
On Tue, Dec 1, 2020 at 1:09 PM Anthony Nash
wrote:
>
> Dear all,
>
tructure . As Jan suggested, I'm beginning to
> think that explicitly defining the Au-S and As-O bonds might be required!
>
> Thanks
> Anthony
>
> --
> *From:* Michal Krompiec
> *Sent:* 01 December 2020 15:07
> *To:* Anthony Nash
>
"brew install rdkit", but then rdkit is unimportable in
Python ("No module named 'rdkit'"). What am I doing wrong?
I'm using brew 3.2.0 on MacOS 11.4
Thanks in advance,
Michal Krompiec
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R
Thanks Maciek, Francois and Peter. A clean conda environment was all that
was needed…
Best,
Michal
On Fri, Jun 25, 2021 at 1:44 AM Francois Berenger wrote:
> On 25/06/2021 02:57, Michal Krompiec wrote:
> > Hello,
> > Is it possible to install RDKit on MacOSX in a Python
On Tuesday, 29 November 2016, Greg Landrum wrote:
>
> On Tue, Nov 29, 2016 at 5:17 PM, Bob Funchess > wrote:
>
>
>> PS: All I really need is the C# wrappers; if those could be included in
>> the binary distribution it would be extremely helpful for me.
>>
>
> Building these hasn't been automated
You need to sanitize the products, just run Chem.SanitizeMol on each
molecule. See
http://www.rdkit.org/docs/GettingStartedInPython.html#chemical-reactions :
"the molecules that are produced by the chemical reaction processing code
are not sanitized".
Best,
Michal
On 12 January 2017 at 17:22, Cur
Hello,
I can't install rdkit on anaconda with 32-bit python3 on Windows 7.
When I try "the usual", conda tries to install python2.7 into the
environment:
>conda create -c rdkit -n my-rdkit-env rdkit
Fetching package metadata .
Solving package specifications: .
Package plan for install
reluctant due to the amount of effort required.
> How many users do you need to support who are stuck on 32bit machines?
>
> -greg
>
>
> On Mon, Feb 20, 2017 at 2:18 PM, Michal Krompiec <
> michal.kromp...@gmail.com
> > wrote:
>
>> Hello,
>> I can't
;conda install -c
> rdkit rdkit" now and have things work. I will try python 2.7 tomorrow.
>
> It turns out that this isn't much extra effort, so assuming this build
> works I should be able to keep doing these.
>
> -greg
>
>
> On Mon, Feb 20, 2017 at 9:33 PM
Hi Thomas,
I had a similar problem, but in my case checking for unusually long bonds
(e.g. longer than typical bond length times an experimental multiplier) and
"additional" close contacts, i.e. more close contacts (excluding h-bonds)
between atoms separated by at least 4 bonds (if I remember corre
Hi Alexis,
Try aromatic form instead of Kekule notation.
Best,
Michal
On 17 May 2017 at 12:55, Alexis Parenty
wrote:
> Hi everyone,
>
> I am looking for substructure match between a smarts and a smiles, but I
> want any heteroatom from the smarts to match any heteroatom from a smiles:
>
>
> [ima
Hi Germano,
You can also install rdkit in the default environment:
conda install -c rdkit rdkit
Best,
Michal
On 29 June 2017 at 14:22, Germano Massullo
wrote:
> Hi there, I am experiencing some troubles in letting jupyter use rdkit
> on Fedora 25
> I installed Anaconda 4.4.0
> then following [
Dear Stephen,
You have installed RDKit in the environment my-rdkit-env, you need to
activate the environment in order to use it (btw, it seems that you
installed it in "mr-rdkit-env").
But you can also install RDKit in the default environment: conda install
rdkit -c rdkit
Best wishes,
Michal
On 1
I'm afraid it won't work in the general case (i.e. you can make it work for
some classes of compounds, but not without unwanted side effects on others)
if the aromaticity model of the other cartridge is different - and it seems
to be the case here...
On Wednesday, 13 September 2017, Michał Nowotka
+1 vote for Symmetrizer. It would be very useful for preparing input for
computational chemistry codes.
Best,
Michal Krompiec
Merck KGaA
On Mon, 15 Jan 2018 at 15:21, Jason Biggs wrote:
>
>- I've had this on my to-do list for a few months now, implementing
>the algorith
I’ve just done an analysis of frequency of hash collisions for Morgan
fingerprints, on a combinatorial library of 1M potential organic
semiconductors. To reduce collisions below 0.5% (meaning: >99.5%
fingerprints are unique), the radius has to be at least 5 (corresponding to
ECFP10) and number of b
etro Giuria, 9 - 10125 Torino (Italy)
> Tel: +39 011 670 7680 | Mob: +39 348 5537206
> Fax: +39 011 670 7687 | E-mail: paolo.to...@unito.it
> http://open3dqsar.org | http://open3dalign.org
> ==
>
>
>
> On 5 Nov 2013,
. Can anybody
point me to a toolkit (or RDKit hack) that can handle these?
Best,
Michal
Dr. Michal Krompiec
Adjunct Professor
School of Chemistry, University of Southampton
Highfield, Southampton SO17 1BJ, UK
and
Head of Computational Modelling | Performance Materials | Early Research
and Bus
> structures in them.
>
> If you have some examples you can share, I'd be happy to take a look to
> see if I can suggest ways to read them in.
>
> Best,
> -greg
>
>
> On Wed, Sep 12, 2018 at 10:30 PM Michal Krompiec <
> michal.kromp...@gmail.com> wrot
... and yet another example, bis-mu-dichloro-bis(allyl)dipalladium(II),
drawn according to ChemAxon's instructions:
https://docs.chemaxon.com/display/docs/How+to+draw+coordination+compounds
Michal
On Thu, 13 Sep 2018 at 14:45, Michal Krompiec
wrote:
> Hi Greg,
> Thanks for your
lot you can do
>>> with them once you've loaded them), the difficult part almost always ends
>>> up being finding input files that have reasonably machine-readable
>>> structures in them.
>>>
>>> If you have some examples you can share, I'd
t it may be possible to add the ability
> to directly parse and interpret this information; that would make things
> easier and the drawings would be less crappy.
>
> -greg
>
>
>
> On Fri, Sep 14, 2018 at 10:55 AM Michal Krompiec <
> michal.kromp...@gmail.com> wrote:
>
Hello,
Is it possible to control the number of significant digits of XYZ
coordinates? I am modifying coordinates of my molecules
using SetAtomPosition but when I save them into an SDF it seems that the
precision is limited to 4 digits after the decimal point (I'd like 10
instead...).
Best wishes,
M
.0. C 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0
> M END
>
> >>> print(Chem.MolToMolBlock(m, forceV3000=True))
>
> RDKit 2D
>
> 0 0 0 0 0 0 0 0 0 0999 V3000
> M V30 BEGIN CTAB
> M V30 COUNTS 2 1 0 0 0
> M V30
6 digits seems perfectly fine for me.
On Fri, 5 Oct 2018 at 14:26, Greg Landrum wrote:
>
> On Fri, Oct 5, 2018 at 2:42 PM Ivan Tubert-Brohman <
> ivan.tubert-broh...@schrodinger.com> wrote:
>
>> In the newer "V3000", the atom line is not column-based, which I believe
>> gives more freedom to imp
Hi all,
I have a slightly off-topic question. I'm trying to train a neural network
on a dataset of small molecules and their melting points. I did get a
not-so-bad accuracy with Morgan fingerprints, but I've realised that
regardless of FP radius and bitvector length, several dozen molecules have
th
Hi Thomas,
Radius 2, 2048 bits, 5200 data points.
On Wed, 10 Oct 2018 at 13:13, Thomas Evangelidis wrote:
> What's your bitvector length and radius? How many training samples do you
> have?
>
> On Wed, 10 Oct 2018 at 13:51, Michal Krompiec
> wrote:
>
>> Hi all,
&
challenges with a descriptor as simple as a
> molecular fingerprint - regardless of bit-length, collisions etc. is
> probably over optimistic...
>
> Regards,
> Chris Earnshaw
>
> On Wed, 10 Oct 2018 at 13:16, Michal Krompiec
> wrote:
>
>> Hi Thomas,
>&
e number of collisions in these RDKit blog posts:
> http://rdkit.blogspot.com/2014/02/colliding-bits.html
> http://rdkit.blogspot.com/2014/03/colliding-bits-ii.html
> http://rdkit.blogspot.com/2016/02/colliding-bits-iii.html
>
> I hope this helps a bit,
> -greg
> [1] Here's
Isn't this patch already incorporated in the master branch?
On Tue, 13 Nov 2018 at 12:35, Malgorzata Werner <
malgorzata.wer...@molecularhealth.com> wrote:
> Hi Henrique,
>
> You could try using v3000 sd files.
>
> Here's a blog about this:
> https://www.wildcardconsulting.dk/useful-information/h
Dear Stamatia,
If the molecules are processed completely independently by your code, it
may be simpler to split the SDF into chunks (e.g. with csplit in a bash
script) and then run separate instances of your python code on each chunk,
wait until all are finished and finally collate the output. Thus
Hello,
Let mol be a molecule with a conformer with 3D coordinates, consisting of 2
fragments. Chem.GetMolFrags(mol, asMols=true) returns these fragments as
Molecule objects, but the 3D coordinates are lost. Is there any way to
preserve them?
Best,
Michal
> 1 2 2 0
> 2 3 1 0
> 3 4 2 0
> 4 5 1 0
> 5 6 2 0
> 6 1 1 0
> 1 8 1 0
> 2 9 1 0
> 3 10 1 0
> 4 11 1 0
> 5 12 1 0
> 6 13 1 0
> 7 14 1 0
> 7 15 1 0
> 7 16 1 0
> M END
>
>
>
&
Hello,
I'd like to check if a particular axis is a C2 symmetry axis of a
conformer. How do I rotate my conformer around an axis? (apart from
extracting the coordinates into numpy, multiplying by a rotation matrix and
updating the coordinates)
Can TransformConformer function be used for this?
Thanks
z axis.
>
> https://nbviewer.jupyter.org/github/iwatobipen/playground/blob/master/rotation_mol.ipynb
>
> Unfortunately molecule will not render on github but you can view molecule
> if you run the code on your PC.
> I hope this would be some of help.
>
> Best regards,
> T
It’s because the molecule with atom indices is a tautomer of the other one
(H at the other N), hence different Kekule structure and different
behaviour of the aromaticity perception code.
Best,
Michal
On Wed, 6 Mar 2019 at 10:04, Colin Bournez
wrote:
> Hi Greg,
>
> Indeed it seems one bond is no
Dear Omar,
Probably, but it is not trivial: you’d need to optimise geometries of a few
1:1 complexes and calculate average interaction energy. Why use rdkit for
that?
Michal
On Tue, 11 Jun 2019 at 01:48, Omar H94 wrote:
> Dear RDKit users,
> Is there a way to calculate the VDW energy between two
Dear Mike,
Try changing all metal-ligand bonds to "dative" or "ionic, and
standardize afterwards (but disable adjusting of implicit Hs). This
way, I was able to process (in KNIME) >99% of organometallics (incl.
metallocenes) downloaded from Reaxys.
Example snippet (which doesn't check the "directio
It depends what you need it for, but if you want a more realistic
conformational analysis instead, CREST is the tool of choice.
https://xtb-docs.readthedocs.io/en/latest/crest.html
Best,
Michal
On Tue, Dec 17, 2019 at 16:26 topgunhaides . wrote:
> Hi guys,
>
> Can anyone tell me more about the
Are you looking for the global minimum or an ensemble of conformers? Either
way, this is already very fast. Bear in mind, however, that MMFF’s accuracy
isn’t great for this type of tasks (see for example
https://arxiv.org/pdf/1705.04308.pdf ). In other words, I don’t see a use
case for generation o
n to slow things down, but not quite sure.
> Any suggestions are very welcome!
>
> Best,
> Leon
>
>
>
>
>
>
>
> On Wed, Dec 18, 2019 at 7:08 PM Michal Krompiec
> wrote:
>>
>> Are you looking for the global minimum or an ensemble of conformers? Either
>
everything into a graph library like networkx...
Best wishes,
Michal Krompiec
Merck KGaA
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(3,4).GetIdx())fragmented=Chem.FragmentOnBonds(cx,bonds)
>
> mat = Chem.GetDistanceMatrix(cx)
>
> mat[1, 2]
>
> 1.0
>
> Chem.GetShortestPath(cx, 1, 2)
>
> (1, 2)
>
> mat = Chem.GetDistanceMatrix(fragmented)
>
> mat[1, 2]
>
> 1.0
>
> Chem.GetShor
Hello, I noticed this was discussed before and I'm wondering if anything's
changed.
Is it possible to extract a substructure from a molecule, based on atom
indices? I understand that Chem.PathToSubmol does something similar, but
takes bond indices.
Best,
Michal
_
msToUse":
>
> e.g.
>
> rdkit.Chem.rdmolfiles.MolFragmentToSmiles(mol, atomsToUse=[11,13,22,15])
>
> Kangway
> --
> *From:* Michal Krompiec
> *Sent:* Thursday, June 4, 2020 10:45 AM
> *To:* RDKit Discuss
> *Subject:* [Rdkit-discuss] PathToSubmol on atom indices?
>
> He
, a[0], a[1],
a[2], a[3], newangle) #this one will crash as well
angle=rdMolTransforms.GetDihedralDeg(mol.GetConformer(), a[0],
a[1], a[2], a[3])
print("angle between atoms {}".format(a)+" is
{}".format(angle))
Best wishes,
Michal Krompiec
Hello,
Is it possible to construct a Mol (or EditableMol) object out of a
list of 3D coordinates? I am trying to write a bridge between cclib
and RDKit, and I need a function to convert 3D geometries to SDF.
Thanks,
Michal
---
Hello,
Is Se defined in UFF and/or MMFF94? Apparently, molecules with
selenophene moieties don't optimize in RDKit, and a warning appears in
the log: UFFTYPER: Unrecognized atom type: Se2+2
Is it possible to define/modify the force field by hand? (for example,
use the parametrs of S for Se)
Thanks,
olecule):
> tmp = Chem.MolFromPDBFile(yourfilename)
> template = Chem.MolFromSmiles(yoursmiles)
> mol = AllChem.AssignBondOrdersFromTemplate(template, tmp)
>
> I don't know if this is what you were looking for.
>
> Best,
> Sereina
>
>
>
> 2013/11/4 Michal Kro
===
>
>
>
> On 5 Nov 2013, at 07:20, Greg Landrum wrote:
>
> Hi Michal,
>
>
> On Mon, Nov 4, 2013 at 11:45 AM, Michal Krompiec
> wrote:
>>
>> Hello,
>> Is Se defined in UFF and/or MMFF94? Apparently, molecules with
>> selenophe
Hello,
I have a question about AllChem.ReplaceSubstructs(mol,
query,replacement). As I understand, it replaces 'query' pattern in
'mol' by 'replacement' fragment. It is clear which atom from 'mol' is
the joining atom, but which is the joining atom in 'replacement'? The
atom with index=0? Is it poss
in a molecule (i.e. to have a chosen
atom at index 0)?
Best wishes,
Michal
On 7 November 2013 11:38, Michal Krompiec wrote:
> Hello,
> I have a question about AllChem.ReplaceSubstructs(mol,
> query,replacement). As I understand, it replaces 'query' pattern in
> 'mol
Hello,
In the Python API, is it possible to read the 3D coordinates of an
atom (from a Mol object created from an SDF file with 3D coords)?
Thanks,
Michal
--
November Webinars for C, C++, Fortran Developers
Accelerate appl
rue, False)
> mol = supplier[0]
> for i in range(0, mol.GetNumAtoms()):
> pos = mol.GetConformer().GetAtomPosition(i)
> print '{0:12.4f}{1:12.4f}{2:12.4f}'.format(pos.x, pos.y, pos.z)
>
>
> Cheers,
> p.
>
>
> On 11/08/2013 01:01 PM, Michal Krompiec wro
Hello,
Substructure matching with SMARTS behaves strangely sometimes - see code below.
The pattern with [H] matches, but the pattern with [H,F] does not
(both should match).
from rdkit import Chem
mol=Chem.MolFromSmiles('Clc2sccc2[H]')
mol=Chem.AddHs(mol)
p1=Chem.MolFromSmarts('c2sccc2[H]')
p2=Che
Dear Greg,
Thanks a lot! This solves my problem.
Best wishes,
Michal
On 18 November 2013 10:27, Greg Landrum wrote:
> Dear Michal,
>
> On Mon, Nov 18, 2013 at 10:55 AM, Michal Krompiec
> wrote:
>>
>> Hello,
>> Substructure matching with SMARTS behaves strangely
Dear Paolo,
Is it possible to add also the option to freeze certain internal
coordinates (I am particularly interested in freezing the dihedral
angles)?
Best wishes,
Michal
On 26 November 2013 18:09, Paolo Tosco wrote:
> Dear James,
>
> I will try to get it done during the weekend - I'll get back
Suppose we have 2 fragments, A and B, with free valences marked as
some dummy atoms. For example, A=CH3* and B=HO*. We want a general
method to combine A and B, in this example the result should be CH3OH.
There are at least 3 ways to do it.
1. Use the trick from SMILIB: replace dummies with %11, a
Dear Greg,
But does CombineMols create any new bonds?
What is the simplest/fastest way of joining two molecules (fragments)
together? (i.e. is there anything simpler than using
ReplaceSubstructs)
Best wishes,
Michal
On 1 December 2013 04:40, Greg Landrum wrote:
> This is the approach I would us
Dear Greg,
Thanks for the answer.
> ReplaceSubstructs() is designed for the very simple case of replacing a
> piece of the molecule that is connected via one bond. It has the significant
> limitation that it (currently) assumes that the bond will be formed to the
> first atom in the replacement.
I
Hello,
Is there any simpler (=faster) way of calculating the shortest
distance between non-bonded atoms in a molecule?
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import rdMolTransforms
import numpy
mol=Chem.MolFromSmiles("Cc2ccsc2c1sccc1C")
mol=Chem.AddHs(mol)
AllChem.Em
C. Firth | PhD Student | Cancer Therapeutics
> The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton |
> Surrey | SM2 5NG
>
> T 020 8722 4033 | E nicholas.fi...@icr.ac.uk | W www.icr.ac.uk | Twitter
> @ICRnews
>
> Facebook www.facebook.com/theinstituteofcancerrese
ve not looked but there must be
>> some sort of euclidean distance using the Point3D class in RDKit.
>>
>> Best,
>> Nick
>>
>> Nicholas C. Firth | PhD Student | Cancer Therapeutics
>> The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton |
&g
Sorry for spamming the list. This is the correct version:
from rdkit import Chem
from rdkit.Chem import AllChem
mol = Chem.MolFromSmiles('')
mol=Chem.AddHs(mol)
AllChem.EmbedMolecule(mol)
AllChem.UFFOptimizeMolecule(mol)
conf = mol.GetConformer()
natom=mol.GetNumAtoms()
conf=mol.GetConformer()
Hello,
Is it possible to suppress kekulization by SDWriter? I get the
following error on a call to SDWriter.write:
ValueError: Sanitization error: Can't kekulize mol
But some molecules can't be kekulized using RDKit's algorithm, even
though they are otherwise 'correct'.
I browsed the sources and it
it is not a bug in your code, unless you consider the fused
thiadiazole ring aromatic.
Best wishes,
Michal
On 5 December 2013 12:19, Greg Landrum wrote:
> Hi Michal,
>
> On Thu, Dec 5, 2013 at 11:52 AM, Michal Krompiec
> wrote:
>>
>> Hello,
>> Is it possible to sup
with kekulization).
But IMHO both representations are correct, am I wrong?
Best wishes,
Michal
On 5 December 2013 12:19, Greg Landrum wrote:
> Hi Michal,
>
> On Thu, Dec 5, 2013 at 11:52 AM, Michal Krompiec
> wrote:
>>
>> Hello,
>> Is it possible to suppress kekul
Hello,
We've been using the RDKit nodes in KNIME for quite a while without
any problems. But suddenly they ceased to work on some computers,
while still working on other ones. Tried with a fresh KNIME
installation with latest RDKit nodes - same problem. What could be
wrong? I pasted the warning/err
Hello Jan,
Thanks for your reply. Yes, it was the missing DLL. Copying
msvcp100.dll to KNIME\jre\bin solved the problem.
Best wishes,
Michal
On 21 February 2014 11:25, Jan Holst Jensen wrote:
> On 2014-02-21 11:04, Michal Krompiec wrote:
>>
>> Hello,
>> We've been usin
Hello, I have just noticed this:
>>> Chem.MolToSmiles(Chem.MolFromSmiles("[H]c1c([H])sc([H])c1[H]"))
'c1ccsc1'
>>> Chem.MolToSmiles(Chem.MolFromSmiles("[H]c1c([H])sc([H])c1[H]",sanitize=False))
'[H]c1sc([H])c([H])c1[H]'
>>> Chem.MolToSmiles(Chem.RemoveHs(Chem.MolFromSmiles("[H]c1c([H])sc([H])c1[H]"
Thanks Greg, this is exactly what I wanted to know. Would you consider
adding an optional removeHs argument to MolFromSmiles(), as in
mol/mol2/sdf parsers?
Best wishes,
Michal
On 25 February 2014 04:23, Greg Landrum wrote:
> Hi Michal,
>
> On Mon, Feb 24, 2014 at 4:48 PM, Michal
Hello,
I am trying to implement substructure searching with fingerprint-based
screening in Knime, using RDKit fingerprints (I know that a database
would be the preferred solution, but for some reasons I'd rather use
Knime).
In order to do this, I need an equivalent of
DataStructs.AllProbeBitsMatch(
quite slow for large systems.
That's why I switched to CORINA, btw.
Best wishes,
Michal Krompiec
On 5 April 2014 18:05, JP wrote:
> I don't know about the "ultimate way": but this works for me (to generate n
> conformers):
>
> writer = Chem.SDWriter('
On 5 April 2014 19:11, Paul Emsley wrote:
> On 05/04/14 19:04, Michal Krompiec wrote:
>
>
>> For example, it does not work well
>> for long conjugated oligomers - sometimes it produces molecular knots
>> instead of straight strands, and is quite slow for large systems.
On 6 April 2014 05:36, Greg Landrum wrote:
>> Some substituted oligoarenes with at least 8 rings in the chain, not
>> particularly fancy (I think the problem is related more to the length
>> of the molecule than to the nature of the repeat units). I tried
>> various options in the EmbedMolecule fu
Hello, has anybody tried to compile a portable Windows binary of
PostgreSQL with RDKit cartridge? There is a portable PostreSQL at
http://sourceforge.net/projects/postgresqlportable/ and I wonder if it
is possible to use it with the cartridge.
Best regards,
Michal
-
simplify the
lives of many ;)
Best wishes,
Michal
On 28 August 2014 15:04, Jan Holst Jensen wrote:
> On 2014-08-28 14:34, Michal Krompiec wrote:
>>
>> Hello, has anybody tried to compile a portable Windows binary of
>> PostgreSQL with RDKit cartridge? There is a portable
Dear Greg,
Fair enough;). Indeed this is quite complex and a bit separate from
the "core" of RDKit's purpose. Nevertheless, I'm sure quite a few
people would appreciate such a build.
Best regards,
Michal
On 28 August 2014 15:37, Greg Landrum wrote:
>
>
> On Thur
Hello, has anybody tried to implement substructure searching in an Oracle
database using PYPL and RDKit? Is it just a matter of writing a wrapper
function for molecule.HasSubstructMatch(pattern) or is the overhead of
calling pypl each time too costly timewise? Do consecutive pypl calls
always share
emented a suite of rdkit functions
> for postgres using plpython
> https://github.com/tjod/rdchord
> and the overhead is minimal
> since most of the heavy lifting of substructure searching
> is done by rdkit.
>
> I think the same would be true of oracle.
> ---
>
Hello,
I understand that the index for substructure searching is created by,
for example:
create index molidx on mols using gist(m)
where m is the molecule column in mols table. Is this correct?
How do I select the type of fingerprint used for the index? I just
suspect that my dataset may requi
Hello,
I'm trying to build RDKit on Cygwin, on Windows 7 32-bit (current
GitHub version).
So far, everything looked fine, but some tests failed:
The following tests FAILED:
13 - testUFFForceField (OTHER_FAULT)
66 - testFMCS (SEGFAULT)
79 - pythonTestDbCLI (Failed) - that
Hi Greg,
Thanks. I haven't started tests yet, so we'll see.
Best wishes,
Michal
On 17 Mar 2015 15:08, "Greg Landrum" wrote:
> Hi Michal,
>
> On Tue, Mar 17, 2015 at 3:02 PM, Michal Krompiec <
> michal.kromp...@gmail.com> wrote:
>
>> Hello,
>
t; 6, 8) << std::endl;
>
> and tell me what the return value of
> MolTransforms::getDihedralDeg(mol->getConformer(), 1, 3, 6, 8) actually is?
> It might just be a periodicity problem.
>
> Thanks for your collaboration, kind regards
> Paolo
>
>
> On 17/03/2015 14:48, Mi
What could it be? My suspicion is that it a wrong version of some dll
is loaded, but how do I trace it?
Best wishes,
Michal
On 17 March 2015 at 14:48, Michal Krompiec wrote:
> Hello,
> I'm trying to build RDKit on Cygwin, on Windows 7 32-bit (current
> GitHub version).
> So far, ev
Hello,
I am struggling to build RDKit on Cygwin, under 32-bit Windows 7,
using gcc 4.9.2, boost 1.55 and python 2.7.8, with the standard
options:
cmake .. && make && make install
The building itself did not raise any errors, but the python tests
fail, for example:
$ python -v -c 'from rdkit impor
Dear All,
I know that building on Cygwin is not a popular topic here, but perhaps
someone will have some ideas. I'm trying to build on 32-bit Cygwin under
Windows 7 32-bit. The build seems successful and C tests are passed, but
importing the python bindings causes python to crash silently:
$ pytho
Dear All,
In case this may be useful to anybody in the future:
RDKit (current github version) builds nicely on Cygwin 64-bit without
any modifications (GCC 4.9.2, boost 1.55).
The following tests fail:
13 - testUFFForceField (SEGFAULT) - rounding error
15 - pyForceFieldConstraints (Failed) - roun
2014 at 04:23, Greg Landrum wrote:
> Hi Michal,
>
> On Mon, Feb 24, 2014 at 4:48 PM, Michal Krompiec <
> michal.kromp...@gmail.com> wrote:
>
>> Hello, I have just noticed this:
>> >>> Chem.MolToSmiles(Chem.MolFromSmiles("[H]c1c([H])sc([H])c1[H]"
Hi Greg,
Thank you, this is exactly what I needed.
On 2 April 2015 at 05:22, Greg Landrum wrote:
>
> Skipping sanitization, as you propose, isn't going to help here: the
> kekulized form of the ring will not be converted to aromatic and you won't
> get the matches you are looking for.
>
Indeed.
ooking for. I have already added
>> the feature to the cartridge and will check it in later today/tomorrow
>> morning.
>>
>> -greg
>>
>> On Thursday, April 2, 2015, Michal Krompiec
>> wrote:
>>
>>> Hi Greg,
>>> Thank you, this is e
Dear All,
I have just found an interesting behaviour of the RDKit Interactive Table
node in Knime.
My workflow contains two such nodes and they contain pretty much the same
data. If I hilite a molecule in one node, it is automatically hilited in
the other one as well.
I'm using KNIME 2.10.4 with th
Hello,
I'm trying to manipulate out-of-plane bends of substituents attached to
aromatic rings. Obviously, they should lie in the plane of the ring, but
sometimes (after constrained optimization) they come slightly out of plane
and there doesn't seem to be a way to push/rotate them back to the ring
it hydrogens? If the latter, how can I check this using
> RDKit without writing my own SDF parser?
>
> Michał Nowotka
>
> On Tue, Apr 7, 2015 at 11:50 AM, Greg Landrum
> wrote:
> >
> > On Tue, Apr 7, 2015 at 12:13 PM, Michal Krompiec <
> michal.kromp.
different approach, i.e. it minimizes only the methyl group in
> 2-methylthiophene while keeping the rest fixed, effectively pushing it back
> in plane. Would that work for you?
>
> Best,
> Paolo
>
>
> On 04/15/2015 10:57 AM, Michal Krompiec wrote:
>
> Hello,
>
Hello,
I was trying to generate 3D coordinates for an europium complex,
[Eu(acac)3(phen)], with UFF, using RDKit nodes in KNIME (UFF is
parametrized for lanthanides). Whereas the generation of coordinates seems
to produce an almost sensible structure:
[image: Inline images 3]
subsequent geometry
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