Re: [Rdkit-discuss] Unknown CMake command "downloadAndCheckMD5"
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 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
mailto:paolo.tosco.m...@gmail.com>> wrote:
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 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 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 -DRDK_BUILD_SWIG_WRAPPERS=ON ..
Tim
On Thu, May 28, 2020 at 4:46 PM Paolo Tosco
mailto:paolo.tosco.m...@gmail.com>>
wrote:
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 CMakeLists.txt`
./Code/JavaWrappers/gmwrapper/CMakeLists.txt:21:
downloadAndCheckMD5(${JUNIT_URL}
"${RDKit_JavaLibDir}/junit.jar" ${JUNIT_MD5SUM})
it looks like 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).
$ 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 CMakeLists.txt:21 (downloadAndCheckMD5):
Unknown CMake command "downloadAndCheckMD5".
-- Configuring incomplete, errors occurred!
See also
"/home/timbo/github/rdkit/rdkit_2020_03/CMakeFiles/CMakeOutput.log".
$ cmake --version
cmake version 3.16.3
Has anything changed with cmake recently?
Tim
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Re: [Rdkit-discuss] Unknown CMake command "downloadAndCheckMD5"
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 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 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 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
> -DRDK_BUILD_SWIG_WRAPPERS=ON ..
>
>
>
> Tim
>
> On Thu, May 28, 2020 at 4:46 PM Paolo Tosco
> wrote:
>
>> 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 CMakeLists.txt`
>> ./Code/JavaWrappers/gmwrapper/CMakeLists.txt:21:
>> downloadAndCheckMD5(${JUNIT_URL} "${RDKit_JavaLibDir}/junit.jar"
>> ${JUNIT_MD5SUM})
>> it looks like 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).
>>
>> $ 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 CMakeLists.txt:21 (downloadAndCheckMD5):
>> Unknown CMake command "downloadAndCheckMD5".
>>
>>
>> -- Configuring incomplete, errors occurred!
>> See also
>> "/home/timbo/github/rdkit/rdkit_2020_03/CMakeFiles/CMakeOutput.log".
>>
>> $ cmake --version
>> cmake version 3.16.3
>>
>> Has anything changed with cmake recently?
>>
>> Tim
>>
>>
>> ___
>> Rdkit-discuss mailing
>> listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
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Re: [Rdkit-discuss] Unknown CMake command "downloadAndCheckMD5"
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 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 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 -DRDK_BUILD_SWIG_WRAPPERS=ON ..
Tim
On Thu, May 28, 2020 at 4:46 PM Paolo Tosco
mailto:paolo.tosco.m...@gmail.com>> wrote:
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 CMakeLists.txt`
./Code/JavaWrappers/gmwrapper/CMakeLists.txt:21:
downloadAndCheckMD5(${JUNIT_URL} "${RDKit_JavaLibDir}/junit.jar"
${JUNIT_MD5SUM})
it looks like 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).
$ 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 CMakeLists.txt:21 (downloadAndCheckMD5):
Unknown CMake command "downloadAndCheckMD5".
-- Configuring incomplete, errors occurred!
See also
"/home/timbo/github/rdkit/rdkit_2020_03/CMakeFiles/CMakeOutput.log".
$ cmake --version
cmake version 3.16.3
Has anything changed with cmake recently?
Tim
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Re: [Rdkit-discuss] Unknown CMake command "downloadAndCheckMD5"
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
-DRDK_BUILD_SWIG_WRAPPERS=ON ..
Tim
On Thu, May 28, 2020 at 4:46 PM Paolo Tosco
wrote:
> 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 CMakeLists.txt`
> ./Code/JavaWrappers/gmwrapper/CMakeLists.txt:21:
> downloadAndCheckMD5(${JUNIT_URL} "${RDKit_JavaLibDir}/junit.jar"
> ${JUNIT_MD5SUM})
> it looks like 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).
>
> $ 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 CMakeLists.txt:21 (downloadAndCheckMD5):
> Unknown CMake command "downloadAndCheckMD5".
>
>
> -- Configuring incomplete, errors occurred!
> See also
> "/home/timbo/github/rdkit/rdkit_2020_03/CMakeFiles/CMakeOutput.log".
>
> $ cmake --version
> cmake version 3.16.3
>
> Has anything changed with cmake recently?
>
> Tim
>
>
> ___
> Rdkit-discuss mailing
> listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
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Re: [Rdkit-discuss] Unknown CMake command "downloadAndCheckMD5"
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 CMakeLists.txt`
./Code/JavaWrappers/gmwrapper/CMakeLists.txt:21:
downloadAndCheckMD5(${JUNIT_URL} "${RDKit_JavaLibDir}/junit.jar"
${JUNIT_MD5SUM})
it looks like 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).
$ 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 CMakeLists.txt:21 (downloadAndCheckMD5):
Unknown CMake command "downloadAndCheckMD5".
-- Configuring incomplete, errors occurred!
See also
"/home/timbo/github/rdkit/rdkit_2020_03/CMakeFiles/CMakeOutput.log".
$ cmake --version
cmake version 3.16.3
Has anything changed with cmake recently?
Tim
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[Rdkit-discuss] Unknown CMake command "downloadAndCheckMD5"
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 CMakeLists.txt:21 (downloadAndCheckMD5): Unknown CMake command "downloadAndCheckMD5". -- Configuring incomplete, errors occurred! See also "/home/timbo/github/rdkit/rdkit_2020_03/CMakeFiles/CMakeOutput.log". $ cmake --version cmake version 3.16.3 Has anything changed with cmake recently? Tim ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Converting csv/xls file containing SMILES to .sdf
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 Chem.SmilesMolSupplierFromText() if you already know the indices of the columns containing SMILES and compound name; you may check the documentation of the function here: http://rdkit.org/docs/source/rdkit.Chem.rdmolfiles.html?highlight=smilesmolsupplier#rdkit.Chem.rdmolfiles.SmilesMolSupplierFromText Cheers, p. On 28/05/2020 14:11, ITS RDC wrote: 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 do not offer the sdf format. I think it is not convenient to manually open each compound in ChemDraw to pool all compounds. I am looking into PandasTools but the documentation only indicated that sdf can be converted to csv and not vice versa. Has anyone worked with similar task before? Your response is very much appreciated. Thank you. Joanna ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Converting csv/xls file containing SMILES to .sdf
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. > > -- > 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 > .sdf > > 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 do not > offer the sdf format. I think it is not convenient to manually open each > compound in ChemDraw to pool all compounds. I am looking into PandasTools > but the documentation only indicated that sdf can be converted to csv and > not vice versa. Has anyone worked with similar task before? Your response > is very much appreciated. Thank you. > > Joanna > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Converting csv/xls file containing SMILES to .sdf
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 .sdf 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 do not offer the sdf format. I think it is not convenient to manually open each compound in ChemDraw to pool all compounds. I am looking into PandasTools but the documentation only indicated that sdf can be converted to csv and not vice versa. Has anyone worked with similar task before? Your response is very much appreciated. Thank you. Joanna ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Converting csv/xls file containing SMILES to .sdf
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 do not offer the sdf format. I think it is not convenient to manually open each compound in ChemDraw to pool all compounds. I am looking into PandasTools but the documentation only indicated that sdf can be converted to csv and not vice versa. Has anyone worked with similar task before? Your response is very much appreciated. Thank you. Joanna ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
