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Merge pull request #612 from bp-kelley/dev/filter-catalog-java-wrapper

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Dev/filter catalog java wrapper
This commit is contained in:
Greg Landrum
2015-09-26 05:38:49 -04:00
parent 209aa69e2a 7fe8fb5fb4
commit 2cb414e639
18 changed files with 587 additions and 27 deletions
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15
Code/JavaWrappers/CMakeLists.txt
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@@ -1,12 +1,24 @@
find_package(SWIG REQUIRED)
include(${SWIG_USE_FILE})
set(T_LIBS ${Boost_LIBRARIES})
find_package(Boost 1.39.0 COMPONENTS serialization)
if (Boost_SERIALIZATION_LIBRARY)
# don't add the boost serialization definitions, swig can't compile the
# headers. Hopefully it will stil link and run...
set(Boost_LIBRARIES ${T_LIBS} ${Boost_LIBRARIES})
else()
endif()
INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
SET(CMAKE_SWIG_FLAGS "")
if(WIN32)
set(RDKit_Wrapper_Libs
FilterCatalog
Catalogs
${Boost_SERIALIZATION_LIBRARY}
FMCS MolDraw2D
FileParsers SmilesParse
Depictor SubstructMatch ChemReactions Fingerprints ChemTransforms
@@ -27,6 +39,9 @@ if(WIN32)
endif(RDK_BUILD_AVALON_SUPPORT)
else()
set(RDKit_Wrapper_Libs
Catalogs_static
FilterCatalog_static
${Boost_SERIALIZATION_LIBRARY}
FMCS_static MolDraw2D_static
FileParsers_static SmilesParse_static
Depictor_static SubstructMatch_static ChemReactions_static Fingerprints_static ChemTransforms_static

173
Code/JavaWrappers/FilterCatalog.i Normal file
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@@ -0,0 +1,173 @@
/*
* Copyright (c) 2015, Novartis Institutes for BioMedical Research Inc.
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are
* met:
*
* * Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
* * Redistributions in binary form must reproduce the above
* copyright notice, this list of conditions and the following
* disclaimer in the documentation and/or other materials provided
* with the distribution.
* * Neither the name of Novartis Institutes for BioMedical Research Inc.
* nor the names of its contributors may be used to endorse or promote
* products derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
//%import "ROMol.i"
%include "std_string.i"
%include "std_vector.i"
%{
#include <../RDGeneral/Dict.h>
#include <../Catalogs/Catalog.h>
#include <../Catalogs/CatalogParams.h>
#include <GraphMol/FilterCatalog/FilterMatcherBase.h>
#include <GraphMol/FilterCatalog/FilterCatalogEntry.h>
#include <GraphMol/FilterCatalog/FilterCatalog.h>
// bug fix for swig, it removes these from their namespaces
typedef RDCatalog::Catalog<RDKit::FilterCatalogEntry, RDKit::FilterCatalogParams>::paramType_t paramType_t;
typedef RDCatalog::Catalog<RDKit::FilterCatalogEntry, RDKit::FilterCatalogParams>::entryType_t entryType_t;
typedef std::vector<std::string> STR_VECT;
%}
%template(FilterCatalogEntry_Vect) std::vector< boost::shared_ptr<RDKit::FilterCatalogEntry> >;
%template(FilterCatalogEntryVect) std::vector< const RDKit::FilterCatalogEntry* >;
%template(UChar_Vect) std::vector<unsigned char>;
%include "enums.swg"
%include <../RDGeneral/Dict.h>
%include <../Catalogs/Catalog.h>
%include <../Catalogs/CatalogParams.h>
%include <GraphMol/Substruct/SubstructMatch.h>
%typemap(javacode) RDKit::FilterCatalog %{
public static FilterCatalog Deserialize(byte[] b) {
UChar_Vect vec = new UChar_Vect();
vec.reserve(b.length);
for (int size=0;size<b.length;++size) {
vec.add(b[size]);
}
return new FilterCatalog(vec);
}
%}
%newobject RDKit::FilterCatalogEntry::getProp;
%extend RDKit::FilterCatalogEntry {
std::string getProp(const std::string key){
std::string res;
($self)->getProp(key, res);
return res;
}
}
%extend RDKit::FilterCatalog {
FilterCatalog(const std::vector<unsigned char> & data ) {
std::string str(data.begin(), data.end());
return new RDKit::FilterCatalog(str);
}
bool canSerialize() const {
return RDKit::FilterCatalogCanSerialize();
}
// boost does a bad job of wrapping shared_ptr<const T> so we will do the
// unthinkable and cast away const.
// Also we can't use FilterCatalog::SENTRY because swig thinks it is a new
// type. Bad swig!
boost::shared_ptr<RDKit::FilterCatalogEntry> getFirstMatch(const ROMol &mol) {
RDKit::FilterCatalog::CONST_SENTRY res = self->getFirstMatch(mol);
return boost::const_pointer_cast<RDKit::FilterCatalogEntry>(res);
}
std::vector<boost::shared_ptr<RDKit::FilterCatalogEntry> > getMatches(const ROMol &mol) {
std::vector<RDKit::FilterCatalog::CONST_SENTRY> matches = self->getMatches(mol);
std::vector<RDKit::FilterCatalog::SENTRY> res;
res.reserve(matches.size());
for (size_t i=0; i< matches.size(); ++i) {
res.push_back( boost::const_pointer_cast<RDKit::FilterCatalogEntry>(matches[i]) );
}
return res;
}
// re-wrap swig is making duplicate entries for some strange reason
unsigned int addEntry(boost::shared_ptr<RDKit::FilterCatalogEntry> entry) {
return self->addEntry(entry);
}
bool removeEntry(boost::shared_ptr<RDKit::FilterCatalogEntry> entry) {
return self->removeEntry(entry);
}
// swig const-ptr shenanigans again
boost::shared_ptr<RDKit::FilterCatalogEntry> getEntry(unsigned int idx) const {
return boost::const_pointer_cast<RDKit::FilterCatalogEntry>(
self->getEntry(idx));
}
unsigned int getIdxForEntry(const boost::shared_ptr<FilterCatalogEntry> &entry) const {
return self->getIdxForEntry(entry);
}
}
%ignore RDKit::FilterCatalog(const std::string &);
%ignore RDKit::FilterCatalog::getFirstMatch;
%ignore RDKit::FilterCatalog::getMatches;
%ignore RDKit::FilterCatalog::addEntry;
%ignore RDKit::FilterCatalog::removeEntry;
%ignore RDKit::FilterCatalog::setCatalogParams;
%ignore RDKit::FilterCatalog::getIdxForEntry;
%ignore RDKit::FilterCatalog::getEntryWithIdx;
//%ignore RDKit::FilterCatalogEntry::getPropList;
%ignore RDKit::Dict::getPropList;
%typemap(jni) std::string RDKit::FilterCatalog::Serialize "jbyteArray"
%typemap(jtype) std::string RDKit::FilterCatalog::Serialize "byte[]"
%typemap(jstype) std::string RDKit::FilterCatalog::Serialize "byte[]"
%typemap(javaout) std::string RDKit::FilterCatalog::Serialize {
return $jnicall;
}
%typemap(out) std::string RDKit::FilterCatalog::Serialize {
$result = JCALL1(NewByteArray, jenv, $1.size());
JCALL4(SetByteArrayRegion, jenv, $result, 0, $1.size(), (const jbyte*)$1.c_str());
}
%include <GraphMol/FilterCatalog/FilterMatcherBase.h>
%include <GraphMol/FilterCatalog/FilterCatalogEntry.h>
%include <GraphMol/FilterCatalog/FilterCatalog.h>
%pragma(java) modulecode=%{
public static FilterCatalog FilterCatalogDeserialize(byte[] b) {
UChar_Vect vec = new UChar_Vect();
vec.reserve(b.length);
for (int size=0;size<b.length;++size) {
vec.add(b[size]);
}
return new FilterCatalog(vec);
}
%}

76
Code/JavaWrappers/FilterCatalogParams_doc.i Normal file
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@@ -0,0 +1,76 @@
/*
*
* Copyright (c) 2015, Novartis Institutes for BioMedical Research Inc.
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are
* met:
*
* * Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
* * Redistributions in binary form must reproduce the above
* copyright notice, this list of conditions and the following
* disclaimer in the documentation and/or other materials provided
* with the distribution.
* * Neither the name of Novartis Institutes for BioMedical Research Inc.
* nor the names of its contributors may be used to endorse or promote
* products derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
%typemap(javaimports) RDKit::FilterCatalogParams "
/**
<p>
Paramter Class for initializing a FilterCatalog with the specified set of FilterCatalogs. Current
catalogs include:
<pre><code>
FilterCatalogParams.FilterCatalogs.ALL
FilterCatalogParams.FilterCatalogs.BRENK
FilterCatalogParams.FilterCatalogs.PAINS_A
FilterCatalogParams.FilterCatalogs.PAINS_B
FilterCatalogParams.FilterCatalogs.PAINS_C
FilterCatalogParams.FilterCatalogs.PAINS
FilterCatalogParams.FilterCatalogs.ZINC
</pre></code>
Details:
<h4>Brenk</h4>
<ul>
<li>Reference: <a href=\"http://www.ncbi.nlm.nih.gov/pubmed/18064617\">Brenk</a> Lessons Learnt from Assembling Screening Libraries for Drug Discovery for Neglected Diseases</li>
<li>Scope: unwanted functionality due to potential tox reasons or unfavourable pharmacokinetic properties</li>
</ul>
<h4>NIH</h4>
<ul>
<li>Reference: <a href=\"http://pubs.rsc.org/en/Content/ArticleLanding/2015/OB/c4ob02287d#!divAbstract\">NIH</a> A Unified Lead-oriented Synthesis of over Fifty Molecular Scaffolds. </li>
<li>Reference: <a href=\"http://pubs.acs.org/doi/abs/10.1021/jm901070c\">NIH</a> Quantitative Analyses of Aggregation, Autofluorescence, and Reactivity Artifacts in a Screen for Inhibitors of a Thiol Protease</li>
<li>Scope: uannotate compounds with problematic functional groups </li>
</ul>
<h4>PAINS</h4>
<ul>
<li>Reference: <a href=\"http://pubs.rsc.org/en/Content/ArticleLanding/2015/OB/c4ob02287d#!divAbstract\">NIH</a> New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in Bioassays </li>
<li>Scope: PAINS filters </li>
</ul>
<h4>ZINC</h4>
<ul>
<li>Reference: <a href=\"http://blaster.docking.org/filtering/\">ZINC</a></li>
<li>Scope: drug-likeness and unwanted functional group filters </li>
</ul>
**/"

63
Code/JavaWrappers/FilterCatalog_doc.i Normal file
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@@ -0,0 +1,63 @@
/*
*
* Copyright (c) 2015, Novartis Institutes for BioMedical Research Inc.
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are
* met:
*
* * Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
* * Redistributions in binary form must reproduce the above
* copyright notice, this list of conditions and the following
* disclaimer in the documentation and/or other materials provided
* with the distribution.
* * Neither the name of Novartis Institutes for BioMedical Research Inc.
* nor the names of its contributors may be used to endorse or promote
* products derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
%typemap(javaimports) RDKit::FilterCatalog "
/** FilterCatalog Class used to filter out undesireable molecules
<br>
Basic usage:
<pre><code>
FilterCatalog catalog = new FilterCatalog(
FilterCatalogParams.FilterCatalogs.PAINS_A);
// go through a mol supplier
while (!molSupplier.atEnd()) {
ROMol m = suppl.next();
FilterCatalogEntry_Vect matches = catalog.getMatches(mol);
if( matches.size() ) {
// reject -- get descriptions of rejection
for (int entryIdx = 0; entryIdx < matches.size(); ++entryIdx) {
entry = matches.get(entryIdx);
String description = entry.getDescription(); // why
// optional properties
String reference = entry.getProp(\"Reference\");
String scope = entry.getProp(\"Scope\");
}
}
else {
// accept
}
}
</code></pre>
**/
"

57
Code/JavaWrappers/FilterCatalogs_doc.i Normal file
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@@ -0,0 +1,57 @@
/*
*
* Copyright (c) 2015, Novartis Institutes for BioMedical Research Inc.
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are
* met:
*
* * Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
* * Redistributions in binary form must reproduce the above
* copyright notice, this list of conditions and the following
* disclaimer in the documentation and/or other materials provided
* with the distribution.
* * Neither the name of Novartis Institutes for BioMedical Research Inc.
* nor the names of its contributors may be used to endorse or promote
* products derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
%typemap(javaimports) RDKit::FilterCatalogParams::FilterCatalog "
/**
<p>
Initialize a FilterCatalog with the specified set of FilterCatalogs. Current
catalogs include:
<pre><code>
FilterCatalogParams.FilterCatalogs.ALL
FilterCatalogParams.FilterCatalogs.BRENK
FilterCatalogParams.FilterCatalogs.PAINS_A
FilterCatalogParams.FilterCatalogs.PAINS_B
FilterCatalogParams.FilterCatalogs.PAINS_C
FilterCatalogParams.FilterCatalogs.PAINS
FilterCatalogParams.FilterCatalogs.ZINC
</pre></code>
Details:
<h4>Brenk</h4>
<ul>
<li><pre># Reference: Brenk R et al. Lessons Learnt from Assembling Screening Libraries for Drug Discovery for Neglected Diseases. ChemMedChem 3 (2008) 435-444. doi:10.1002/cmdc.200700139.</pre></li>
<li><Scope: unwanted functionality due to potential tox reasons or unfavourable pharmacokinetic properties</li>
</ul>
**/"

1
Code/JavaWrappers/ROMol.i
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@@ -31,6 +31,7 @@
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
%include "std_pair.i"
%include "std_string.i"
%include "std_vector.i"
%{
#include <RDGeneral/types.h>

15
Code/JavaWrappers/gmwrapper/CMakeLists.txt
View File

@@ -82,7 +82,7 @@ SWIG_ADD_MODULE(GraphMolWrap "java" GraphMolJava.i )
# as of Oct 2012 using boost 1.51 under at least ubuntu 12.04 we get a
# link error if they aren't there.
SWIG_LINK_LIBRARIES(GraphMolWrap ${RDKit_Wrapper_Libs}
${RDKit_THREAD_LIBS})
${Boost_SERIALIZATION_LIBRARY} ${RDKit_THREAD_LIBS})
# code adapted from the wrapper code for
# GDCM: http://gdcm.svn.sf.net/viewvc/gdcm/trunk/Wrapping/Java/CMakeLists.txt?view=markup
@@ -153,6 +153,12 @@ ADD_CUSTOM_TARGET(RunJavaWrapperTests
COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/runUnitTests.sh
)
# need to add boost libs for testing
SET (CTEST_ENVIRONMENT
"LD_LIBRARY_PATH=${Boost_LIBRARY_DIRS}"
"DYLD_LIBRARY_PATH=${Boost_LIBRARY_DIRS}"
)
ADD_TEST(JavaAromaticTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
@@ -291,5 +297,12 @@ ADD_TEST(JavaMolQueryTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.MolQueryTests)
ADD_TEST(JavaFilterCatalogTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.FilterCatalogTests)
INSTALL(TARGETS GraphMolWrap
DESTINATION ${CMAKE_CURRENT_SOURCE_DIR} )

5
Code/JavaWrappers/gmwrapper/GraphMolJava.i
View File

@@ -112,6 +112,7 @@ typedef unsigned long long int uintmax_t;
%shared_ptr(ForceFields::UFF::vdWContrib);
%shared_ptr(ForceFields::UFF::TorsionAngleContrib);
%shared_ptr(ForceFields::UFF::InversionContrib);
%shared_ptr(RDKit::FilterCatalogEntry);
/* Some utility classes for passing arrays in and out */
%array_class(double, Double_Array);
@@ -140,6 +141,9 @@ typedef unsigned long long int uintmax_t;
%include "../TDTWriter_doc.i"
%include "../Transform2D_doc.i"
%include "../Transform3D_doc.i"
%include "../FilterCatalog_doc.i"
%include "../FilterCatalogParams_doc.i"
%include "../FilterCatalogs_doc.i"
// DO THIS BEFORE ANY OF THE OTHER INCLUDES
%include "../RDKitExceptions.i"
@@ -185,6 +189,7 @@ typedef unsigned long long int uintmax_t;
%include "../MolTransforms.i"
%include "../FMCS.i"
%include "../MolDraw2D.i"
%include "../FilterCatalog.i"
// Create a class to throw various sorts of errors for testing. Required for unit tests in ErrorHandlingTests.java
#ifdef INCLUDE_ERROR_GENERATOR

128
Code/JavaWrappers/gmwrapper/src-test/org/RDKit/FilterCatalogTests.java Normal file
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@@ -0,0 +1,128 @@
/*
*
* Copyright (c) 2015, Novartis Institutes for BioMedical Research Inc.
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are
* met:
*
* * Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
* * Redistributions in binary form must reproduce the above
* copyright notice, this list of conditions and the following
* disclaimer in the documentation and/or other materials provided
* with the distribution.
* * Neither the name of Novartis Institutes for BioMedical Research Inc.
* nor the names of its contributors may be used to endorse or promote
* products derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
package org.RDKit;
import static org.junit.Assert.*;
import org.junit.*;
public class FilterCatalogTests extends GraphMolTest {
private ROMol mol;
@Before public void setUp() {
}
@Test
public void test1Basics() {
FilterCatalog catalog = new FilterCatalog();
assertEquals(0, catalog.getNumEntries());
//assertEquals(16, catalog.getNumEntries());
}
@Test
public void test2Basics() {
FilterCatalog catalog = new FilterCatalog(
FilterCatalogParams.FilterCatalogs.PAINS_A);
assertEquals(16, catalog.getNumEntries());
mol = RWMol.MolFromSmiles("O=C(Cn1cnc2c1c(=O)n(C)c(=O)n2C)N/N=C/c1c(O)ccc2c1cccc2");
FilterCatalogEntry entry = catalog.getFirstMatch(mol);
Str_Vect props = entry.getPropList();
String ref = entry.getProp("Reference");
String source = entry.getProp("Scope");
assertEquals(ref,
"Baell JB, Holloway GA. New Substructure Filters for " +
"Removal of Pan Assay Interference Compounds (PAINS) " +
"from Screening Libraries and for Their Exclusion in " +
"Bioassays. J Med Chem 53 (2010) 2719D40. " +
"doi:10.1021/jm901137j.");
assertEquals(source, "PAINS filters (family A)");
assertEquals(entry.getDescription(),"hzone_phenol_A(479)");
// check the getMatches api point
FilterCatalogEntry_Vect matches = catalog.getMatches(mol);
assertEquals(1, matches.size());
for (int entryIdx = 0; entryIdx < matches.size(); ++entryIdx) {
entry = matches.get(entryIdx);
String refa = entry.getProp("Reference");
String sourcea = entry.getProp("Scope");
assertEquals(refa,
"Baell JB, Holloway GA. New Substructure Filters for " +
"Removal of Pan Assay Interference Compounds (PAINS) " +
"from Screening Libraries and for Their Exclusion in " +
"Bioassays. J Med Chem 53 (2010) 2719D40. " +
"doi:10.1021/jm901137j.");
assertEquals(source, "PAINS filters (family A)");
assertEquals(entry.getDescription(),"hzone_phenol_A(479)");
}
if (catalog.canSerialize()) {
byte pickle[] = catalog.Serialize();
System.out.println(pickle);
assertTrue(pickle != null);
FilterCatalog catalog2 = FilterCatalog.Deserialize(pickle);
assertFalse(catalog2 == null);
assertEquals(16, catalog2.getNumEntries());
entry = catalog2.getFirstMatch(mol);
assertEquals(entry.getDescription(),"hzone_phenol_A(479)");
}
}
@Test
public void testRemoveEntry() {
FilterCatalog catalog = new FilterCatalog(
FilterCatalogParams.FilterCatalogs.PAINS_A);
assertEquals(16, catalog.getNumEntries());
mol = RWMol.MolFromSmiles("O=C(Cn1cnc2c1c(=O)n(C)c(=O)n2C)N/N=C/c1c(O)ccc2c1cccc2");
FilterCatalogEntry entry = catalog.getFirstMatch(mol);
assertEquals(entry.getDescription(),"hzone_phenol_A(479)");
assertTrue(catalog.removeEntry(entry));
FilterCatalogEntry entry_removed = catalog.getFirstMatch(mol);
assertEquals(entry_removed, null);
catalog.addEntry(entry);
entry = catalog.getFirstMatch(mol);
assertEquals(entry.getDescription(),"hzone_phenol_A(479)");
}
public static void main(String args[]) {
org.junit.runner.JUnitCore.main("org.RDKit.FilterCatalogTests");
}
}