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 <tdudgeon...@gmail.com
<mailto:tdudgeon...@gmail.com>> 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 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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