e's support for visualizing molecules from SMILES and CTAB, but
> currently no support for SDF properties out of the box.
>
> Cheers,
> p.
>
> On Thu, Mar 3, 2022 at 6:31 PM Tim Dudgeon wrote:
>
>> Is there a full list of the RDKit functionality that is available from
&g
Is there a full list of the RDKit functionality that is available from the
JavaScript bindings (
https://github.com/rdkit/rdkit/tree/master/Code/MinimalLib)? Maybe I'm
missing the obvious, but I can only find the examples e.g.
e the molecule and clear aromatic
> flags before starting to remove atoms, then sanitize:
>
> rwmol = Chem.RWMol(Chem.MolFromSmiles("c1c1"))
> Chem.Kekulize(rwmol, clearAromaticFlags=True)
> rwmol.RemoveAtom(0)
>
> Chem.SanitizeMol(rwmol)
> rdkit.Chem.rdmolops.Sa
I'm using mol.RemoveAtom(atom) to remove atoms from a molecule, and then
calling Chem.SanitizeMol(mol) at the end to clean up the molecule. Mostly
this works fine.
But when I delete atoms in an aromatic ring but leave a single ring atom
remaining in the molecule then the sanitize function fails:
;
> On Fri, Feb 11, 2022 at 3:49 PM Tim Dudgeon wrote:
>
>> Hi Greg,
>> yes, but my situation is that the X dimension is much larger than the Y
>> and most of the time things are aligned nicely. But not always. Here is an
>> example.
>> OC(C(=O)NC=1C=CC=
.com/greglandrum/12b793b240d27e3c0899c9c6c62d4f30
>
> -greg
>
>
> On Fri, Feb 11, 2022 at 10:20 AM Tim Dudgeon
> wrote:
>
>> At Dave Cosgrove's suggestion I raise this as a new topic, though it was
>> touched on briefly recently.
>>
>> I'd like to know if it
At Dave Cosgrove's suggestion I raise this as a new topic, though it was
touched on briefly recently.
I'd like to know if it's possible to depict a molecule in a way that takes
into account the dimensions of the box it will appear in. In my case I have
a rectangle that is short and wide (aspect
e
> default.")
> ```
> to $RDBASE/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp immediately after
> the analogous minFontSize entry
> HTH,
> Dave
>
>
>
> On Wed, Feb 9, 2022 at 10:31 AM Tim Dudgeon wrote:
>
>> OK, thanks. That's great to hear.
&g
ch, among other things,
> addresses exactly the need that you describe through the baseFontSize
> parameter, which is currently not exposed to Python. The PR is almost ready
> for merging and it should become part of the March release.
>
> Cheers,
> p.
>
> On Wed, Feb 9, 20
I'm confused over how the font is chosen when drawing molecules.
There are MolDrawOptions.minFontSize and MolDrawOptions.maxFontSize
properties, and if I set them to the same value then that sized font is
used. But if I set max to a larger size than min then it's not clear what
font size will be
And to clarify, the build completes OK. It's just that the Python
bindings don't work.
On Wed, Jan 26, 2022 at 2:42 PM Tim Dudgeon wrote:
> Yes, it sounds similar, but I'm not applying that fix (though on the
> Release_2021_09_4 tag I do also see that same problem).
> I'm just doin
lds
> fine for me too.
>
> Cheers,
> p.
>
> On Wed, Jan 26, 2022 at 2:58 PM Tim Dudgeon wrote:
>
>> I'm building RDKit from the latest code on the master branch.
>> The build is fine, but the python bindings seem broken:
>>
>> >>> from rdki
I'm building RDKit from the latest code on the master branch.
The build is fine, but the python bindings seem broken:
>>> from rdkit import Chem
Traceback (most recent call last):
File "", line 1, in
File "/data/github/rdkit/rdkit/rdkit/__init__.py", line 6, in
from . import rdBase
I think you have to add a step that removes the quote marks if they are
present?
Tim
On Mon, Jan 10, 2022 at 10:15 AM James Wallace wrote:
> As the subject suggests, I'm trying to find a universal solution for
> reading CSVs via the SmilesMolSupplier (as the input setup could be single
> column
I'm hitting problems when building from source on an Ubuntu system.
I've installed the dependencies (e.g. boost) using apt and think I have
everything set properly, but cmake is failing. Early on it says:
-- Found Boost:
/usr/lib/x86_64-linux-gnu/cmake/Boost-1.71.0/BoostConfig.cmake (found
I've found that a source of molecules that I use now has some smiles
that contain the * character, whereas earlier versions did not. This is now
causing downstream problems.
Whilst it would be pretty simple to check the smiles for * characters I
think there should be a more general solution here
Worked it out for myself.
I needed to use:
Chem.AddHs(mol, addCoords=True)
Doh!
On Tue, Dec 14, 2021 at 5:45 PM Tim Dudgeon wrote:
> I'm seeing lots of failures when minimising molecules using
> MMFFOptimizeMolecule.
> A large proportion of seemingly valid molecules seem to fail.
>
I'm seeing lots of failures when minimising molecules using
MMFFOptimizeMolecule.
A large proportion of seemingly valid molecules seem to fail.
Am I doing something stupid here?
Example:
from rdkit import Chem
from rdkit.Chem import AllChem
molblock = '''
RDKit 3D
5 4 0 0 0
I'm having problems building with Debian bullseye release.
Bullseye now has swig4.0, but RDKit build seems to require exactly 3.0.
Error is:
CMake Error at
/usr/share/cmake-3.18/Modules/FindPackageHandleStandardArgs.cmake:165
(message):
Could NOT find SWIG: Found unsuitable version "4.0.2", but
I'm looking into the current status of techniques that use RDKit to perform
3D alignments based on shape (e.g. not using AlignMol()) and struggling to
find what the best tools are and the status of each.
The Open3D align tools are relatively straightforward to use, but in my
hands do not seem to
I am needing to access the text of each record of a SDF, as well as
creating a mol instance.
I was successfully doing this using SDMolSupplier.GetItemText().
Then I needed to switch to handling gzipped SD files, and SDMolSupplier can
only take a file name in its constructor.
ForwardSDMolSupplier
and
> only sanitize at the end of the insertion process.
>
> Cheers,
> p.
>
> On Mon, Oct 25, 2021 at 1:15 PM Tim Dudgeon wrote:
>
>> I'm trying to merge two molecules into one, and it looks like the
>> InsertMol() function is supposed to do this. But when I try the
I'm trying to merge two molecules into one, and it looks like the
InsertMol() function is supposed to do this. But when I try the merged
molecule is messed up.
[image: image.png]
Am I doing the right thing?
Thanks
Tim
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Chem.RemoveHs(mol) will remove all Hs.
Do you really want to only remove them from sp3 carbons?
On Tue, Oct 19, 2021 at 7:08 PM Alfredo Quevedo
wrote:
> Dear all,
>
> I am trying to figure out if there is a way to remove all hydrogens bond
> to sp3 carbons in my molecule?
>
> thanks in advance
le.
>
> -Brian
>
>
> On Sep 27, 2021, at 8:06 AM, Tim Dudgeon wrote:
>
>
> I have Python code to enumerate undefined chiral centres in a molecule.
> Mostly this works fine, but for some constrained structures this can
> generate stereochemistry that makes no s
I have Python code to enumerate undefined chiral centres in a molecule.
Mostly this works fine, but for some constrained structures this can
generate stereochemistry that makes no sense. For
instance consider NC1CC2CCC1C2:
[image: #1 (2).png]
These two make sense:
[image: #2.png]
[image: #3.png]
I'm wanting to pick the molecules in one set that are most similar to those
in a seed set.
Seems like I should be able to use the MaxMinPicker to do this by using a
function of (1 - tanimoto).
Would this work, or is there a better approach?
Thanks
Tim
>>> parsers? Have they been sanitized?
>>>
>>> Another thing you might have already tried, but it's worth checking
>>> anyway: can you force your web app to only run a single thread at a time?
>>> That shouldn't be a problem with the morgan fingerprinting co
already tried, but it's worth checking
> anyway: can you force your web app to only run a single thread at a time?
> That shouldn't be a problem with the morgan fingerprinting code, but it's
> still worth the experiment.
>
> -greg
>
>
> On Tue, Feb 2, 2021 at 7:14 P
Wondering if anyone had any thoughts on this core dump from Java.
What other info would be useful?
Tim
On Tue, Jan 12, 2021 at 12:55 PM Tim Dudgeon wrote:
> I'm struggling to work out a stange core dump I'm getting when calculating
> Morgan fingerprints from Java. This seems to
I'm struggling to work out a stange core dump I'm getting when calculating
Morgan fingerprints from Java. This seems to happen with the
Release_2020_09 releases but not with the Release_2019_09 ones. It does not
happen when calculating RDKit fingerprints. The exact Java code involved is:
ppened to be bonded, but that's not necessary, here's the atom1 -
> atom6 - atom3 angle:
> In [15]: (ps[6]-ps[1]).AngleTo(ps[6]-ps[3])
> Out[15]: 0.4862648980647286
>
> Is that what you're looking for?
>
> -greg
>
>
>
> On Mon, Sep 7, 2020 at 3:06 PM Tim Dud
Hi RDKitters,
I was wondering whether anyone has any RDKit code that checks on the
geometry of a H-bond.
e.g. once a donor and acceptor are located within a reasonable distance of
each other to check on the angles involved to establish if that is a
reasonable H-bond.
Tim
I've encountered a strange problem when doing constrained embedding that
seems to be related to chirality.
The example is here:
https://gist.github.com/tdudgeon/c4604f3ee9124eeec60668b5eefe465e
The molecule being embedded has a single chiral carbon, and while that atom
is tethered, only one of
ConstrainedEmbed should be what you need. If it's saying that your molecule
doesn't match the core then that's where you need to look. Maybe the core
is not an exact substructure?
If you still have difficulties you could generate the MCS between the
structures and use that as the core.
Greg's blog
RDKit can read PDB files but is there any functionality to work with the
resulting molecule at the chain and residue level?
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The points in a featuremap seem to have a 'weight' property that is set to
1.0 as default.
When merging featuremaps with the CombineFeatMaps() the weight of the
merged points remains as 1.0. Is it possible to change this behaviour so
that the meged point has an increased weight? Either a weight
I'm needing to save a FeatMap to a file so that I can load it back later.
I've been using a pickle for this, but am now told that this will not be
permitted for security reasons.
Is there a better way to do this?
Thanks
Tim
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>
> The code behaves this way because otherwise it would need to guess what
> the user intended (as well as how they interpret/use the chiral flag).
>
> -greg
>
>
> On Mon, Jul 13, 2020 at 1:28 PM Tim Dudgeon wrote:
>
>> I've noticed that when writing a 3D molfile th
I've noticed that when writing a 3D molfile that has been generated by
RDKit (in my case using AllChem.EmbedMolecule) and has chirality present
that the chiral flag is not set. At least it is not always set, I can't be
exactly sure. My exact scenario is to read a chiral SMILES, convert to 3D
using
mations/blob/4f3c5ef47f66708defc64196c94e427a956b8f15/get_conformations.py#L16
>
> On 30 May 2020, at 13.38, Tim Dudgeon wrote:
>
> Is there an easy way to ask whether a particular bond is rotatable?
> ___
> Rdkit-discuss mailing list
> Rd
What is the best way to swap 2 bonds that are attached to an atom without
changing the 3D coordinates of the other atoms.
As an example, I have a tetrahedral carbon with bonds 1, 2, 3 and 4. I want
to switch bonds 1 and 2, including relocating any atoms attached to the
other atom in those bonds,
Is there an easy way to ask whether a particular bond is rotatable?
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error if I try to run your command from
> rdkit/Code/JavaWrappers/gmwrapper/build rather than from rdkit/build, as
> in that case the main CMakeLists.txt file is not sourced.
>
> Cheers,
> p.
> On 28/05/2020 17:01, Tim Dudgeon wrote:
>
> well, I am running it from a subdirecto
you might be running cmake in a subdirectory rather than in
> the RDKit root directory.
>
> HTH, cheers
> p.
>
> On 28/05/2020 16:28, Tim Dudgeon wrote:
>
> I'm not able to build form source (master branch) from a new machine I've
> recently set up (Ubuntu 20.04).
I'm not able to build form source (master branch) from a new machine I've
recently set up (Ubuntu 20.04).
$ cmake -DPYTHON_EXECUTABLE=/usr/bin/python3 -DRDK_BUILD_INCHI_SUPPORT=ON
-DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_PYTHON_WRAPPERS=ON
-DRDK_BUILD_SWIG_WRAPPERS=ON ..
CMake Error at
of the replacement feature.
The other two possibilities are Average (does a non-weighted average)
and UseLarger which just keeps the location and weight of the feature
point with the larger weight.
does that help?
-greg
On Wed, May 6, 2020 at 5:27 PM Tim Dudgeon <mailto:tdudgeon...@gmail.
I'm trying to use the FeatureMaps functionality in RDKit (described here
http://rdkit.blogspot.com/2017/11/using-feature-maps.html) and have a
question on the parameters for CombineFeatMaps.
See here:
I'm using the rdShapeHelpers.ShapeProtrudeDist() method to generate a
protrude distance score like this:
protrude_dist = rdShapeHelpers.ShapeProtrudeDist(ref_mol,
query_mol,allowReordering=False)
Is it possible to determine the contributions that each atom of a
molecule makes to the score?
t find any matching Java class nor function. Is
this functionality supported via the Java wrappers ?
Thanks & Regards,
Thomas
On Wed, Apr 22, 2020 at 11:55 AM Tim Dudgeon <mailto:tdudgeon...@gmail.com>> wrote:
Have a look in 'Code/JavaWrappers/gmwrapper/' not
'build/Code
the MCS query, so you don't need to rebuild the query molecule
out of the SMARTS pattern.
p.
On 18/04/2020 10:27, Tim Dudgeon wrote:
I also updated the Jupyter notebook with the solution.
Out of interest, I now need to get the atom indices of the part of
the molecule that matched.
As Jupyter
Would it be possible to add improving the docs for Java to the list?
e.g. https://sourceforge.net/p/rdkit/mailman/message/36929992/
Tim
On 23/04/2020 16:17, Scalfani, Vincent wrote:
Dear RDKit Community,
Greg and I are putting together an application for the Google Season
of the Docs
Have a look in 'Code/JavaWrappers/gmwrapper/' not
'build/Code/JavaWrappers/gmwrapper/' ?
Tim
On 22/04/2020 10:36, Thomas Eckert wrote:
Hi folks,
Trying to build RDKit + JavaWrappers from scratch but, in the end, the
JAR files are missing.
Working on a freshly installed Ubuntu 19.10 and
. But I can't find it.
Also note that |rdFMCS.||MCSResult| has a |queryMol |property that
encode the MCS query, so you don't need to rebuild the query molecule
out of the SMARTS pattern.
Good. I'll use that.
p.
On 18/04/2020 10:27, Tim Dudgeon wrote:
I also updated the Jupyter notebook
and atom properties but can't find anything that
suggests "highlight me".
How is this encoded?
Tim
On 17/04/2020 19:02, Paolo Tosco wrote:
Hi Tim,
I’ll take a look later and get back to you.
Cheers,
p.
On 17 Apr 2020, at 18:55, Tim Dudgeon wrote:
I'm wanting to use AllChem.Constr
19:02, Paolo Tosco wrote:
Hi Tim,
I’ll take a look later and get back to you.
Cheers,
p.
On 17 Apr 2020, at 18:55, Tim Dudgeon wrote:
I'm wanting to use AllChem.ConstrainedEmbed() to generate a conformer of a
molecule tethered to a molecule that should always have some MCS. I found some
I'm wanting to use AllChem.ConstrainedEmbed() to generate a conformer of
a molecule tethered to a molecule that should always have some MCS. I
found some code on the internet that mostly works, but I don't fully
understand.
It generally works as planned, but for a small number of examples it
Thanks Paolo, that fixed it.
On 30/03/2020 15:05, Paolo Tosco wrote:
Hi Tim,
try rm -rf External/CoordGen/coordgen* External/CoordGen/maeparser*
you might have some outdated coordgen libs. Deleting those and
re-running cmake will download them afresh.
Cheers,
p.
On 30/03/2020 14:51, Tim
, Tim Dudgeon wrote:
I'm finding an error building from source (on master branch).
Any ideas?
cmake -DPYTHON_EXECUTABLE=/usr/bin/python3
-DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON
-DRDK_BUILD_PYTHON_WRAPPERS=ON -DRDK_BUILD_SWIG_WRAPPERS=ON ..
make -j 8
[ 66%] Building CXX
, 2020, at 4:07 AM, Tim Dudgeon wrote:
I'm finding that if I create a pandas dataframe using
PandasTools.LoadSDF() and then write the dataframe out using
df.to_pickle() then I can read that pickle back in as a dataframe,
but the RDKit molecules don't get handled correctly.
Is there a way
I'm finding an error building from source (on master branch).
Any ideas?
cmake -DPYTHON_EXECUTABLE=/usr/bin/python3
-DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON
-DRDK_BUILD_PYTHON_WRAPPERS=ON -DRDK_BUILD_SWIG_WRAPPERS=ON ..
make -j 8
[ 66%] Building CXX object
search - within 3 secs
I tried to store the converted molecules and fingerprints in a file to
get better performance while trying the pyspark program but was not
able to do so.
Regards,
DA
On Wednesday, February 26, 2020, 12:57:43 AM GMT+5:30, Tim Dudgeon
wrote:
I think you need to explain
I think you need to explain what benchmarks you are running and what is
really meant by "faster".
And what hardware (for Spark how many nodes, how big; for PostgreSQL
what size server, what settings esp. the shared_buffers setting).
A very obvious critique of what you reported is that what you
/MolStandardizeTest.java
I will try to make some time to improve the situation here with the
goal of
a) have better tests
b) making it more obvious how to use the code from Java
-greg
On Thu, Dec 26, 2019 at 4:55 PM Tim Dudgeon <mailto:tdudgeon...@gmail.com>> wrote:
I'm trying to get my h
Yes, not a typo!
RDKit has excellent docs for Python, but the Java side of things have
received less love ;-)
Would there be interest from the community in helping put together a
guide that is similar in principle to the "Getting Started with the
RDKit in Python" page [1]. I'd be happy to
Greg is too modest to mention it, but he recently blogged on performance
aspects of the cartridge which covers many aspects of how it works:
http://rdkit.blogspot.com/2020/01/some-thoughts-on-performance-of-rdkit.html
On 25/01/2020 05:11, Greg Landrum wrote:
Hi Changge,
On Fri, Jan 24, 2020
/README.md
Tim
On 16/01/2020 16:34, dmaziuk via Rdkit-discuss wrote:
On 1/16/2020 10:20 AM, Greg Landrum wrote:
It does look like Tim Dudgeon is creating docker images for the RDKit +
cartridge:
https://hub.docker.com/r/informaticsmatters/rdkit-cartridge-debian
Have you looked at those
/latest/module/UseJava.html
set(CMAKE_JAVA_COMPILE_FLAGS"-source 8")
might do the trick.
Cheers,
p.
On 03/01/2020 17:41, Tim Dudgeon wrote:
Hi Paolo,
I'm afraid that's not working for me. Still getting Java11 class files.
My cmake command is:
cmake -Wno-dev\
-DPYTHON_EXECUTABLE=/usr/b
compile rdkit for Java?
Last time I tried on a Mac, it did not work:
https://github.com/rdkit/homebrew-rdkit/issues/38
Thanks a lot,
F.
On 26/12/2019 23:22, Tim Dudgeon wrote:
When building the Java wrappers from source (the
-DRDK_BUILD_SWIG_WRAPPERS=ON option) is possible to specify options
everything still
builds OK!
Tim
On 26/12/2019 15:39, Paolo Tosco wrote:
Hi Tim,
Try adding this to your CMake command:
-DJAVA_COMPILE="/usr/bin/javac -source 8"
Cheers,
p.
On 26/12/2019 15:22, Tim Dudgeon wrote:
When building the Java wrappers from source (the
-DRDK_BUILD_SWI
I'm trying to get my head round using the new standardizer code from Java.
Looks like this should be accessible from the RDKFuncs class, but I'm
failing at stage 1.
Simple example is:
package org.exmple;
import org.RDKit.RDKFuncs;
import org.RDKit.RWMol;
public class Simple {
static {
When building the Java wrappers from source (the
-DRDK_BUILD_SWIG_WRAPPERS=ON option) is possible to specify options to
pass on to javac.
Specifically I'm wanting to use the '-source 8' option as most distros
now come with java11 (and make it difficult to install an earlier one)
but I want
there any correlation between the maxAttempts and numConfs?
For instance, do I need to set a higher maxAttempts value if I request
a higher numConfs value?
Or to put it another way, what maxAttempts value can be considered as
"enough"?
Best,
Leon
On Tue, Dec 17, 2019 at
This is in regard to the pruneRmsThresh option which removes very
similar conformers.
If let's say numConfs is set to 10 and maxAttempts is set to 20 then it
will use UP TO 20 attempts to generate 10 conformers.
If too many conformers get rejected due to pruneRmsThresh then you will
end up with
you might want to look at these that we're been using for several years:
https://hub.docker.com/r/informaticsmatters/rdkit-cartridge-debian/tags
This the GitHub repo for this and several other flavours of RDKit
container images:
https://github.com/InformaticsMatters/docker-rdkit
Tim
On
stuff there for isotopes, but I couldn't figure out how to use
this.
On 12/12/2019 16:39, Rafal Roszak wrote:
On Wed, 11 Dec 2019 10:53:47 +
Tim Dudgeon wrote:
I'm wanting to write isomeric smiles that does not include isotope
information.
I also had sytuation when I need to generate
I'm wanting to write isomeric smiles that does not include isotope
information.
The standard Chem.MolToSmiles(m, isomericSmiles=True) includes isotope
information which is what I'm wanting to exclude.
I note that there is a Atom.SetIsotope(int) method and after a bit of
hacking around I found
tom.GetExplicitValence() # returns 1
atom.GetTotalValence() *# returns 1*
atom.GetNumImplicitHs() *# returns 0***
Chem.MolToSmiles(mw) *# returns '[Xe]c1c1'*
On Wed, Sep 4, 2019 at 9:35 AM Tim Dudgeon <mailto:tdudgeon...@gmail.com>> wrote:
I'm finding that if I add a Xenon atom to
I'm finding that if I add a Xenon atom to a molecule it seems to get an
unwanted hydrogen added to it.
Example notebook here:
https://gist.github.com/tdudgeon/ba3497341d9de95b4d78f3e5ed9fc0f7
Basic code is like this:
from rdkit import Chem
m = Chem.MolFromSmiles("c1c1")
mw = Chem.RWMol(m)
/
Does it help?
Hongbin Yang
*发件人: *Tim Dudgeon <mailto:tdudgeon...@gmail.com>
*发送时间: *2019年8月26日21:08
*收件人: *rdkit-discuss@lists.sourceforge.net
<mailto:rdkit-discuss@lists.sourceforge.net>
*主题: *[Rdkit-discuss] Generating R-group representation
I have a set of molecules that sh
I was very happy to hear about the integration of MolVS into RDKit core
in the talk by Susan Leung at the recent UGM.
https://github.com/rdkit/UGM_2018/blob/master/Presentations/Leung_GSoC_RDKit-MolVS_Integration.pdf
This is going to be incredibly useful once it gets released.
To help with
As some of you will know I am creating various Docker images for RDKit.
See [1] and [2] if you want to know more.
The key to these is building RPM and DEB packages using `cpack`.
This is mostly working pretty well as you will see in those links.
Now I'm wanting to extend this to building
com
<mailto:greg.land...@gmail.com>> wrote:
Yeah, thats another change that has been made. I will update the docs.
Thanks for pointing out the oversight
-greg
On Thu, 5 Apr 2018 at 17:30, Tim Dudgeon <tdudgeon...@gmail.com
<mailto:tdudgeon...@gmail.com>> wrote:
will update the docs.
Thanks for pointing out the oversight
-greg
On Thu, 5 Apr 2018 at 17:30, Tim Dudgeon <tdudgeon...@gmail.com
<mailto:tdudgeon...@gmail.com>> wrote:
Greg,
Does this explain problems I'm seeing with building on Centos:
From the current docs:
cma
Greg,
Does this explain problems I'm seeing with building on Centos:
From the current docs:
cmake. You need version 2.6 (or more recent)
With a current centos7 distro after a `yum install cmake`
# cmake --version
cmake version 2.8.12.2
When you build from current master branch you get this
Incorporating and "industrialising" Matt's MolVS tautomer and
standardizer code?
http://molvs.readthedocs.io/en/latest/index.html
On 15/01/18 07:09, Greg Landrum wrote:
Dear all,
We've been invited again to participate in the OpenChemistry
application for Google Summer of Code.
In order
Agreed. Good support for reading and writing mol2 format would indeed be
useful.
But not convinced this alone is sexy enough for GSoC.
Could there be something in a more general project to bridge the
compound (mol/smiles), sequence (protein/nucleotide seq + alignments)
and structure
I think the MaxMinPicker can do what you want.
A blog on using this can be found here:
https://rdkit.blogspot.co.uk/2017/11/revisting-maxminpicker.html
On 03/01/18 19:53, Sundar wrote:
Hi RDKit users,
Is it possible to pick a subset of (diverse) compounds that have less
than a particular
fine.
On 05/12/17 07:18, Greg Landrum wrote:
On Fri, Dec 1, 2017 at 7:24 PM, Tim Dudgeon <tdudgeon...@gmail.com
<mailto:tdudgeon...@gmail.com>> wrote:
If upgrading PostgreSQL to a new version of the RDKit cartridge is
any maintenance needed?
Either rebuild
.
Tim
On 04/12/17 00:16, Francois BERENGER wrote:
Please report your problems in the rdkit bugtracker.
What you do exactly to test, on which distro, etc.
If you don't, this issue will be forgotten.
Regards,
F.
On 12/02/2017 02:53 AM, Tim Dudgeon wrote:
Read back to the top of this thread for all
If upgrading PostgreSQL to a new version of the RDKit cartridge is any
maintenance needed?
Either rebuild the indexes or regenerate the fingerprints and rebuild
the indexes?
--
Check out the vibrant tech community
In what way? Given a single PubChem compound or substance ID you just
want to pull the smiles or molfile into RDKit?
Tim
On 01/12/17 17:26, Sundar wrote:
Hi RDkit users,
I was wondering if RDkit has a means of downloading compounds from
Pubchem.
Also let me other ways that helps here.
/12/17 17:51, Gianluca Sforna wrote:
On Fri, Dec 1, 2017 at 6:04 PM, Tim Dudgeon <tdudgeon...@gmail.com> wrote:
Maciek
The 'cpack -G RPM' command does not seem to create a rdkit_package_file.rpm.
The ones that are created are:
RDKit-2018.03.1.dev1-Linux-Development.rpm
RDKit-2018.03.1.dev1
Francois,
I'm assuming you are meaning to install those packages on the debian
system prior to installing the RDKit-2018.03.1.dev1-Linux-*.deb files.
Unfortunately that didn't help.
Tim
On 27/11/2017 23:50, Francois BERENGER wrote:
On 11/28/2017 12:42 AM, Tim Dudgeon wrote:
I see exactly
ia
gdebi which does this automatically.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl <mailto:mac...@wojcikowski.pl>
2017-11-28 0:50 GMT+01:00 Francois BERENGER
<beren...@bioreg.kyushu-u.ac.jp <mailto:beren...@bioreg.kyushu-u.ac.jp>>:
On 11/28/201
I see exactly the same when I build with those cmake args.
On 27/11/2017 09:11, Francois BERENGER wrote:
On 11/27/2017 06:01 PM, Tim Dudgeon wrote:
I did:
cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_INSTALL_INTREE=OFF
-DCMAKE_INSTALL_PREFIX=/usr/ ..
Try this instead, just for the cmake part
:
https://github.com/rdkit/rdkit/pull/1655
Regards,
F.
On 11/25/2017 12:50 AM, Tim Dudgeon wrote:
I got round to testing the debs and rpms but without success.
For the debs the following were built:
RDKit-2018.03.1.dev1-Linux-Development.deb
RDKit-2018.03.1.dev1-Linux-Extras.deb
RDKit-2018.03.1
e "help", "copyright", "credits" or "license" for more information.
>>> import rdkit
Traceback (most recent call last):
File "", line 1, in
ImportError: No module named rdkit
>>>
On 15/11/2017 20:18, David Hall wrote:
apt in
I've got some dockerfiles that might be worth a look.
https://github.com/InformaticsMatters/docker_jupyter
Not sure if they will help.
Tim
On 21/11/2017 15:25, JP wrote:
Yo RDKitters,
I am running a CADD workshop for a group of MSc students and would
like to show them some some RDKit
get you rpmbuild
-David
On Nov 15, 2017, at 2:59 PM, Tim Dudgeon <tdudgeon...@gmail.com
<mailto:tdudgeon...@gmail.com>> wrote:
OK, makes sense, but I'm building on a Debian system. So neither 'yum
install rpm-build' nor 'apt-get install rpm-build' doesn't work.
So (sorry fo
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