Re: [Rdkit-discuss] Problems building RDKit + JavaWrappers

2020-04-28 Thread Tim Dudgeon 

It's availalbe from the org.RDKit.RDKFuncs class. e.g:

String RDKFuncs.standardizeSmiles(String smiles)​

RWMol cleanup​(RWMol mol)

TIm

On 28/04/2020 15:09, Thomas Eckert wrote:
That helped, thanks! Didn't realize 'make install' was needed after 
building the wrappers - I had built without the wrappers first, trying 
to detect problems iteratively.


So now I'm able to use the wrappers in Java but noticed not all "core 
functionality" is covered by the wrappers. Specifically, I'm looking 
for a way to access

    rdkit.Chem.MolStandardize.rdMolStandardize
from Java. I could not 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 > wrote:


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 followed the
steps described at [1]. All dependencies installed via Ubuntu's
apt, no manually installed libs.

Cloned the RDKit sources to
    /home/thomas/git/rdkit
and set env variables
    RDBASE=/home/thomas/git/rdkit
LD_LIBRARY_PATH=/home/thomas/git/rdkit/lib:/lib/x86_64-linux-gnu/

Using this 'cmake' command
  cmake -DRDK_BUILD_PYTHON_WRAPPERS=OFF
-DRDK_BUILD_SWIG_WRAPPERS=ON ..
I get OK looking output except for
    CMake Warning (dev) at
/usr/share/cmake-3.13/Modules/UseSWIG.cmake:564 (message):
      Policy CMP0078 is not set.  Run "cmake --help-policy
CMP0078" for policy
      details.  Use the cmake_policy command to set the policy
and suppress this
      warning.
    Call Stack (most recent call first):
Code/JavaWrappers/gmwrapper/CMakeLists.txt:109 (SWIG_ADD_LIBRARY)
    This warning is for project developers.  Use -Wno-dev to
suppress it.
but as the warning states, this seems to be fine for
non-rdkit-dev users, so I just carry on.

'make' then runs happily with a few warnings on the first build
but no errors are reported. It even states
    (...)
    [ 99%] Built target GraphMolWrap_swig_compilation
    [ 99%] Built target GraphMolWrap
    [100%] building jar
    [100%] Built target GraphMolWrapJar
    [100%] building test classes
    [100%] Built target BuildJavaWrapperTests
which seems to mean the JavaWrappers were built. However this is
then the case
    ~/git/rdkit/build$ ls -lha Code/JavaWrappers/gmwrapper/
    total 16M
    drwxr-xr-x 3 thomas thomas 4,0K Apr 22 11:15 .
    drwxr-xr-x 4 thomas thomas 4,0K Apr 22 11:15 ..
    drwxr-xr-x 7 thomas thomas 4,0K Apr 22 11:15 CMakeFiles
    -rw-r--r-- 1 thomas thomas 2,6K Apr 22 10:47 cmake_install.cmake
    -rw-r--r-- 1 thomas thomas  13K Apr 22 10:47 CTestTestfile.cmake
    -rwxr-xr-x 1 thomas thomas  16M Apr 22 10:49 libGraphMolWrap.so
    -rw-r--r-- 1 thomas thomas  13K Apr 22 10:47 Makefile
so no JAR files to be found even though the shared library
mentioned in "Building the Java wrappers" at [1] is there.

Thus I ran the tests
   /git/rdkit/build$ ctest
Test project /home/thomas/git/rdkit/build
(...)
73% tests passed, 39 tests failed out of 143

Total Test time (real) =  98.60 sec

The following tests FAILED:
        105 - JavaAromaticTests (Failed)
        106 - JavaAtomPairsTests (Failed)
        107 - JavaBasicMoleculeTests (Failed)
        108 - JavaBasicMolecule2Tests (Failed)
        109 - JavaChemAtomTests (Failed)
        110 - JavaChemBondTests (Failed)
        111 - JavaChemReactionTests (Failed)
        112 - JavaChemSmartsTests (Failed)
        113 - JavaChemTests (Failed)
        114 - JavaChemv2Tests (Failed)
        115 - JavaConformerTests (Failed)
        116 - JavaDescriptorTests (Failed)
        117 - JavaDistanceGeometryTests (Failed)
        118 - JavaErrorHandlingTests (Failed)
        119 - JavaFingerprintsTests (Failed)
        120 - JavaForceFieldsTests (Failed)
        121 - JavaHManipulationsTests (Failed)
        122 - JavaLipinskiTests (Failed)
        123 - JavaPicklingTests (Failed)
        124 - JavaSmilesCreationTests (Failed)
        125 - JavaSmilesDetailsTests (Failed)
        126 - JavaSmilesTests (Failed)
        127 - JavaSuppliersTests (Failed)
        128 - JavaTrajectoryTests (Failed)
        129 - JavaWrapperTests (Failed)
        130 - JavaChemTransformsTests (Failed)
        131 - JavaFMCSTests (Failed)
        132 - JavaPDBTests (Failed)
        133 - JavaSequenceTests (Failed)
        134 - JavaAlignTests (Failed)
        135 - JavaMolQueryTests (Failed)

Re: [Rdkit-discuss] Problems building RDKit + JavaWrappers

2020-04-28 Thread Thomas Eckert 
That helped, thanks! Didn't realize 'make install' was needed after
building the wrappers - I had built without the wrappers first, trying to
detect problems iteratively.

So now I'm able to use the wrappers in Java but noticed not all "core
functionality" is covered by the wrappers. Specifically, I'm looking for a
way to access
rdkit.Chem.MolStandardize.rdMolStandardize
from Java. I could not 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  wrote:

> 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 followed the steps
> described at [1]. All dependencies installed via Ubuntu's apt, no manually
> installed libs.
>
> Cloned the RDKit sources to
> /home/thomas/git/rdkit
> and set env variables
> RDBASE=/home/thomas/git/rdkit
> LD_LIBRARY_PATH=/home/thomas/git/rdkit/lib:/lib/x86_64-linux-gnu/
>
> Using this 'cmake' command
>   cmake -DRDK_BUILD_PYTHON_WRAPPERS=OFF -DRDK_BUILD_SWIG_WRAPPERS=ON ..
> I get OK looking output except for
> CMake Warning (dev) at /usr/share/cmake-3.13/Modules/UseSWIG.cmake:564
> (message):
>   Policy CMP0078 is not set.  Run "cmake --help-policy CMP0078" for
> policy
>   details.  Use the cmake_policy command to set the policy and
> suppress this
>   warning.
> Call Stack (most recent call first):
>   Code/JavaWrappers/gmwrapper/CMakeLists.txt:109 (SWIG_ADD_LIBRARY)
> This warning is for project developers.  Use -Wno-dev to suppress it.
> but as the warning states, this seems to be fine for non-rdkit-dev users,
> so I just carry on.
>
> 'make' then runs happily with a few warnings on the first build but no
> errors are reported. It even states
> (...)
> [ 99%] Built target GraphMolWrap_swig_compilation
> [ 99%] Built target GraphMolWrap
> [100%] building jar
> [100%] Built target GraphMolWrapJar
> [100%] building test classes
> [100%] Built target BuildJavaWrapperTests
> which seems to mean the JavaWrappers were built. However this is then the
> case
> ~/git/rdkit/build$ ls -lha Code/JavaWrappers/gmwrapper/
> total 16M
> drwxr-xr-x 3 thomas thomas 4,0K Apr 22 11:15 .
> drwxr-xr-x 4 thomas thomas 4,0K Apr 22 11:15 ..
> drwxr-xr-x 7 thomas thomas 4,0K Apr 22 11:15 CMakeFiles
> -rw-r--r-- 1 thomas thomas 2,6K Apr 22 10:47 cmake_install.cmake
> -rw-r--r-- 1 thomas thomas  13K Apr 22 10:47 CTestTestfile.cmake
> -rwxr-xr-x 1 thomas thomas  16M Apr 22 10:49 libGraphMolWrap.so
> -rw-r--r-- 1 thomas thomas  13K Apr 22 10:47 Makefile
> so no JAR files to be found even though the shared library mentioned in
> "Building the Java wrappers" at [1] is there.
>
> Thus I ran the tests
>/git/rdkit/build$ ctest
> Test project /home/thomas/git/rdkit/build
> (...)
> 73% tests passed, 39 tests failed out of 143
>
> Total Test time (real) =  98.60 sec
>
> The following tests FAILED:
> 105 - JavaAromaticTests (Failed)
> 106 - JavaAtomPairsTests (Failed)
> 107 - JavaBasicMoleculeTests (Failed)
> 108 - JavaBasicMolecule2Tests (Failed)
> 109 - JavaChemAtomTests (Failed)
> 110 - JavaChemBondTests (Failed)
> 111 - JavaChemReactionTests (Failed)
> 112 - JavaChemSmartsTests (Failed)
> 113 - JavaChemTests (Failed)
> 114 - JavaChemv2Tests (Failed)
> 115 - JavaConformerTests (Failed)
> 116 - JavaDescriptorTests (Failed)
> 117 - JavaDistanceGeometryTests (Failed)
> 118 - JavaErrorHandlingTests (Failed)
> 119 - JavaFingerprintsTests (Failed)
> 120 - JavaForceFieldsTests (Failed)
> 121 - JavaHManipulationsTests (Failed)
> 122 - JavaLipinskiTests (Failed)
> 123 - JavaPicklingTests (Failed)
> 124 - JavaSmilesCreationTests (Failed)
> 125 - JavaSmilesDetailsTests (Failed)
> 126 - JavaSmilesTests (Failed)
> 127 - JavaSuppliersTests (Failed)
> 128 - JavaTrajectoryTests (Failed)
> 129 - JavaWrapperTests (Failed)
> 130 - JavaChemTransformsTests (Failed)
> 131 - JavaFMCSTests (Failed)
> 132 - JavaPDBTests (Failed)
> 133 - JavaSequenceTests (Failed)
> 134 - JavaAlignTests (Failed)
> 135 - JavaMolQueryTests (Failed)
> 136 - JavaFilterCatalogTests (Failed)
> 137 - JavaSubstructLibraryTests (Failed)
> 138 - JavaRGroupDecompositionTests (Failed)
> 139 - JavaScaffoldNetworkTests (Failed)
> 140 - JavaMolHashTest (Failed)
> 141 - JavaDiversityPickerTests (Failed)
> 142 - JavaBitOpsTests (Failed)
> 143 - MolStandardizeTest (Failed)
> Errors

Re: [Rdkit-discuss] Problems building RDKit + JavaWrappers

2020-04-22 Thread Tim Dudgeon 
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 followed the steps 
described at [1]. All dependencies installed via Ubuntu's apt, no 
manually installed libs.


Cloned the RDKit sources to
    /home/thomas/git/rdkit
and set env variables
    RDBASE=/home/thomas/git/rdkit
LD_LIBRARY_PATH=/home/thomas/git/rdkit/lib:/lib/x86_64-linux-gnu/

Using this 'cmake' command
  cmake -DRDK_BUILD_PYTHON_WRAPPERS=OFF -DRDK_BUILD_SWIG_WRAPPERS=ON ..
I get OK looking output except for
    CMake Warning (dev) at 
/usr/share/cmake-3.13/Modules/UseSWIG.cmake:564 (message):
      Policy CMP0078 is not set.  Run "cmake --help-policy CMP0078" 
for policy
      details.  Use the cmake_policy command to set the policy and 
suppress this

      warning.
    Call Stack (most recent call first):
      Code/JavaWrappers/gmwrapper/CMakeLists.txt:109 (SWIG_ADD_LIBRARY)
    This warning is for project developers.  Use -Wno-dev to suppress it.
but as the warning states, this seems to be fine for non-rdkit-dev 
users, so I just carry on.


'make' then runs happily with a few warnings on the first build but no 
errors are reported. It even states

    (...)
    [ 99%] Built target GraphMolWrap_swig_compilation
    [ 99%] Built target GraphMolWrap
    [100%] building jar
    [100%] Built target GraphMolWrapJar
    [100%] building test classes
    [100%] Built target BuildJavaWrapperTests
which seems to mean the JavaWrappers were built. However this is then 
the case

    ~/git/rdkit/build$ ls -lha Code/JavaWrappers/gmwrapper/
    total 16M
    drwxr-xr-x 3 thomas thomas 4,0K Apr 22 11:15 .
    drwxr-xr-x 4 thomas thomas 4,0K Apr 22 11:15 ..
    drwxr-xr-x 7 thomas thomas 4,0K Apr 22 11:15 CMakeFiles
    -rw-r--r-- 1 thomas thomas 2,6K Apr 22 10:47 cmake_install.cmake
    -rw-r--r-- 1 thomas thomas  13K Apr 22 10:47 CTestTestfile.cmake
    -rwxr-xr-x 1 thomas thomas  16M Apr 22 10:49 libGraphMolWrap.so
    -rw-r--r-- 1 thomas thomas  13K Apr 22 10:47 Makefile
so no JAR files to be found even though the shared library mentioned 
in "Building the Java wrappers" at [1] is there.


Thus I ran the tests
   /git/rdkit/build$ ctest
Test project /home/thomas/git/rdkit/build
(...)
73% tests passed, 39 tests failed out of 143

Total Test time (real) =  98.60 sec

The following tests FAILED:
        105 - JavaAromaticTests (Failed)
        106 - JavaAtomPairsTests (Failed)
        107 - JavaBasicMoleculeTests (Failed)
        108 - JavaBasicMolecule2Tests (Failed)
        109 - JavaChemAtomTests (Failed)
        110 - JavaChemBondTests (Failed)
        111 - JavaChemReactionTests (Failed)
        112 - JavaChemSmartsTests (Failed)
        113 - JavaChemTests (Failed)
        114 - JavaChemv2Tests (Failed)
        115 - JavaConformerTests (Failed)
        116 - JavaDescriptorTests (Failed)
        117 - JavaDistanceGeometryTests (Failed)
        118 - JavaErrorHandlingTests (Failed)
        119 - JavaFingerprintsTests (Failed)
        120 - JavaForceFieldsTests (Failed)
        121 - JavaHManipulationsTests (Failed)
        122 - JavaLipinskiTests (Failed)
        123 - JavaPicklingTests (Failed)
        124 - JavaSmilesCreationTests (Failed)
        125 - JavaSmilesDetailsTests (Failed)
        126 - JavaSmilesTests (Failed)
        127 - JavaSuppliersTests (Failed)
        128 - JavaTrajectoryTests (Failed)
        129 - JavaWrapperTests (Failed)
        130 - JavaChemTransformsTests (Failed)
        131 - JavaFMCSTests (Failed)
        132 - JavaPDBTests (Failed)
        133 - JavaSequenceTests (Failed)
        134 - JavaAlignTests (Failed)
        135 - JavaMolQueryTests (Failed)
        136 - JavaFilterCatalogTests (Failed)
        137 - JavaSubstructLibraryTests (Failed)
        138 - JavaRGroupDecompositionTests (Failed)
        139 - JavaScaffoldNetworkTests (Failed)
        140 - JavaMolHashTest (Failed)
        141 - JavaDiversityPickerTests (Failed)
        142 - JavaBitOpsTests (Failed)
        143 - MolStandardizeTest (Failed)
Errors while running CTest

At this point I cannot find anything in the documentation to proceed 
further. I'm not familiar with most of the stack used with/for RDKit 
either, so I don't know where to look. Any hints on where to look or 
what to check ?


Regards,
  Thomas

[1] https://www.rdkit.org/docs/Install.html#building-from-source


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[Rdkit-discuss] Problems building RDKit + JavaWrappers

2020-04-22 Thread Thomas Eckert 
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 followed the steps
described at [1]. All dependencies installed via Ubuntu's apt, no manually
installed libs.

Cloned the RDKit sources to
/home/thomas/git/rdkit
and set env variables
RDBASE=/home/thomas/git/rdkit
LD_LIBRARY_PATH=/home/thomas/git/rdkit/lib:/lib/x86_64-linux-gnu/

Using this 'cmake' command
  cmake -DRDK_BUILD_PYTHON_WRAPPERS=OFF -DRDK_BUILD_SWIG_WRAPPERS=ON ..
I get OK looking output except for
CMake Warning (dev) at /usr/share/cmake-3.13/Modules/UseSWIG.cmake:564
(message):
  Policy CMP0078 is not set.  Run "cmake --help-policy CMP0078" for
policy
  details.  Use the cmake_policy command to set the policy and suppress
this
  warning.
Call Stack (most recent call first):
  Code/JavaWrappers/gmwrapper/CMakeLists.txt:109 (SWIG_ADD_LIBRARY)
This warning is for project developers.  Use -Wno-dev to suppress it.
but as the warning states, this seems to be fine for non-rdkit-dev users,
so I just carry on.

'make' then runs happily with a few warnings on the first build but no
errors are reported. It even states
(...)
[ 99%] Built target GraphMolWrap_swig_compilation
[ 99%] Built target GraphMolWrap
[100%] building jar
[100%] Built target GraphMolWrapJar
[100%] building test classes
[100%] Built target BuildJavaWrapperTests
which seems to mean the JavaWrappers were built. However this is then the
case
~/git/rdkit/build$ ls -lha Code/JavaWrappers/gmwrapper/
total 16M
drwxr-xr-x 3 thomas thomas 4,0K Apr 22 11:15 .
drwxr-xr-x 4 thomas thomas 4,0K Apr 22 11:15 ..
drwxr-xr-x 7 thomas thomas 4,0K Apr 22 11:15 CMakeFiles
-rw-r--r-- 1 thomas thomas 2,6K Apr 22 10:47 cmake_install.cmake
-rw-r--r-- 1 thomas thomas  13K Apr 22 10:47 CTestTestfile.cmake
-rwxr-xr-x 1 thomas thomas  16M Apr 22 10:49 libGraphMolWrap.so
-rw-r--r-- 1 thomas thomas  13K Apr 22 10:47 Makefile
so no JAR files to be found even though the shared library mentioned in
"Building the Java wrappers" at [1] is there.

Thus I ran the tests
   /git/rdkit/build$ ctest
Test project /home/thomas/git/rdkit/build
(...)
73% tests passed, 39 tests failed out of 143

Total Test time (real) =  98.60 sec

The following tests FAILED:
105 - JavaAromaticTests (Failed)
106 - JavaAtomPairsTests (Failed)
107 - JavaBasicMoleculeTests (Failed)
108 - JavaBasicMolecule2Tests (Failed)
109 - JavaChemAtomTests (Failed)
110 - JavaChemBondTests (Failed)
111 - JavaChemReactionTests (Failed)
112 - JavaChemSmartsTests (Failed)
113 - JavaChemTests (Failed)
114 - JavaChemv2Tests (Failed)
115 - JavaConformerTests (Failed)
116 - JavaDescriptorTests (Failed)
117 - JavaDistanceGeometryTests (Failed)
118 - JavaErrorHandlingTests (Failed)
119 - JavaFingerprintsTests (Failed)
120 - JavaForceFieldsTests (Failed)
121 - JavaHManipulationsTests (Failed)
122 - JavaLipinskiTests (Failed)
123 - JavaPicklingTests (Failed)
124 - JavaSmilesCreationTests (Failed)
125 - JavaSmilesDetailsTests (Failed)
126 - JavaSmilesTests (Failed)
127 - JavaSuppliersTests (Failed)
128 - JavaTrajectoryTests (Failed)
129 - JavaWrapperTests (Failed)
130 - JavaChemTransformsTests (Failed)
131 - JavaFMCSTests (Failed)
132 - JavaPDBTests (Failed)
133 - JavaSequenceTests (Failed)
134 - JavaAlignTests (Failed)
135 - JavaMolQueryTests (Failed)
136 - JavaFilterCatalogTests (Failed)
137 - JavaSubstructLibraryTests (Failed)
138 - JavaRGroupDecompositionTests (Failed)
139 - JavaScaffoldNetworkTests (Failed)
140 - JavaMolHashTest (Failed)
141 - JavaDiversityPickerTests (Failed)
142 - JavaBitOpsTests (Failed)
143 - MolStandardizeTest (Failed)
Errors while running CTest

At this point I cannot find anything in the documentation to proceed
further. I'm not familiar with most of the stack used with/for RDKit
either, so I don't know where to look. Any hints on where to look or what
to check ?

Regards,
  Thomas

[1] https://www.rdkit.org/docs/Install.html#building-from-source
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