Hi all,
I have a list of compounds that I want to know their topological and molecular
properties to be able to generate a model for QSAR. I have over a hundred
compounds contained in an MS Excel file in csv format since we only downloaded
these compounds from existing chemical databases that
You can open the csv file directly into Schrodinger's Maestro. The free version
can open CSV files.
--
Gustavo Seabra
From: ITS RDC
Sent: Thursday, May 28, 2020 9:11:42 AM
To: RDKit Discuss
Subject: [Rdkit-discuss] Converting csv/xls file containing SMILES to
Hi Joanna,
If you load the molecules from SMILES with RDKit, you can write them out
using AllChem.SDWriter.
Best,
Jennifer
On Thu, May 28, 2020 at 9:51 AM Gustavo Seabra
wrote:
> You can open the csv file directly into Schrodinger's Maestro. The free
> version can open CSV files.
>
> --
>
Hi Tim,
could you please run a pwd in your build directory? Also, could you try
deleting CMakeCache.txt and re-running cmake?
With "subdirectory" I was asking whether your build directory was a
subdirectory of the RDKit root dir or a subdirectory of gmwrapper,
because I get that error if I
Thanks Paulo. Deleting CMakeCache.txt seems to have fixed the problem.
I then hit a problem being unable to build against boost 1.71 but when I
switched back to 1.67 it was OK.
Seems to be building fine now.
Tim
On Thu, May 28, 2020 at 5:09 PM Paolo Tosco
wrote:
> Hi Tim,
>
> could you please
well, I am running it from a subdirectory - the build subdirectory which is
where it has always been run from.
e.g.
mkdir build
cd build
cmake -DPYTHON_EXECUTABLE=/usr/bin/python3 -DRDK_BUILD_INCHI_SUPPORT=ON
-DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_PYTHON_WRAPPERS=ON
Hi Tim,
downloadAndCheckMD5 is a function defined in
Code/cmake/Modules/RDKitUtils.cmake, which is included by the main
CMakeLists.txt file and then is available to all children CMakeLists.txt
files.
From the line number where the error occurs
$ grep -n downloadAndCheckMD5 `find . -name
Hi Joanna,
I put a small gist here:
https://gist.github.com/ptosco/49bdfc55db7277c7c94aca71b69f64b5
which reads SMILES and compound names from a CSV string; you may easily
modify the code to read from a CSV file.
Note that you could actually even just use
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
Hi Tim,
great. For the Boost problem you could try adding
|-DBoost_NO_BOOST_CMAKE=ON|
to your cmake command; it will probably fix the problem.
Cheers,
p.
On 28/05/2020 18:01, Tim Dudgeon wrote:
Thanks Paulo. Deleting CMakeCache.txt seems to have fixed the problem.
I then hit a problem being
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