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initial addition of avalontoolkit support

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This commit is contained in:
Greg Landrum
2011-12-23 06:17:39 +00:00
parent 0c06670340
commit 2575bfbfb6
21 changed files with 2165 additions and 6 deletions
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41
Code/JavaWrappers/AvalonLib.i Executable file
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@@ -0,0 +1,41 @@
/*
* $Id$
*
* Copyright (c) 2010, 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.
*/
%include "std_pair.i"
%{
#include <AvalonTools/AvalonTools.h>
%}
%template(StringInt_Pair) std::pair<std::string, int >;
%include <AvalonTools/AvalonTools.h>

8
Code/JavaWrappers/CMakeLists.txt
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@@ -22,6 +22,9 @@ if(WIN32)
if(RDK_BUILD_INCHI_SUPPORT)
set(RDKit_Wrapper_Libs RDInchiLib ${INCHI_LIBRARIES} ${RDKit_Wrapper_Libs})
endif(RDK_BUILD_INCHI_SUPPORT)
if(RDK_BUILD_AVALON_SUPPORT)
set(RDKit_Wrapper_Libs AvalonLib avalon_clib ${RDKit_Wrapper_Libs})
endif(RDK_BUILD_AVALON_SUPPORT)
else()
set(RDKit_Wrapper_Libs
FileParsers_static SmilesParse_static
@@ -37,8 +40,9 @@ else()
if(RDK_BUILD_INCHI_SUPPORT)
set(RDKit_Wrapper_Libs RDInchiLib_static Inchi_static ${RDKit_Wrapper_Libs})
endif(RDK_BUILD_INCHI_SUPPORT)
if(RDK_BUILD_AVALON_SUPPORT)
set(RDKit_Wrapper_Libs AvalonLib_static avalon_clib_static ${RDKit_Wrapper_Libs})
endif(RDK_BUILD_AVALON_SUPPORT)
endif()
add_subdirectory(gmwrapper)

41
Code/JavaWrappers/gmwrapper/CMakeLists.txt
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@@ -1,5 +1,7 @@
project (jGraphMolJava Java)
include_directories( ${RDKit_ExternalDir} )
find_package(Java REQUIRED)
find_package(JNI REQUIRED)
@@ -21,7 +23,6 @@ INCLUDE_DIRECTORIES(${JNI_INCLUDE_DIRS})
SET_SOURCE_FILES_PROPERTIES(GraphMolJava.i PROPERTIES CPLUSPLUS ON )
FILE(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/../*.java COPY_SOURCE)
FILE(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/org/RDKit COPY_DEST)
@@ -47,6 +48,14 @@ else()
endif()
SET(CMAKE_SWIG_OUTDIR ${CMAKE_CURRENT_SOURCE_DIR}/src/org/RDKit )
if(RDK_BUILD_INCHI_SUPPORT)
SET(CMAKE_SWIG_FLAGS "-DBUILD_INCHI_SUPPORT" ${CMAKE_SWIG_FLAGS} )
endif()
if(RDK_BUILD_AVALON_SUPPORT)
SET(CMAKE_SWIG_FLAGS "-DBUILD_AVALON_SUPPORT" ${CMAKE_SWIG_FLAGS} )
endif()
# enable this line to build the ErrorGenerator class for testing handling of C++ errors in the JNI layer
#SET(CMAKE_SWIG_FLAGS ${CMAKE_SWIG_FLAGS} "-D INCLUDE_ERROR_GENERATOR" )
@@ -54,7 +63,6 @@ SWIG_ADD_MODULE(GraphMolWrap "java" GraphMolJava.i)
SET(SWIG_MODULE_GraphMolWrap_EXTRA_DEPS ../*.i)
SWIG_LINK_LIBRARIES(GraphMolWrap ${RDKit_Wrapper_Libs} )
# code adapted from the wrapper code for
@@ -97,9 +105,20 @@ ADD_CUSTOM_TARGET(GraphMolWrapJar ALL
## Tests -- note that building/rebuilding them keys on the file WrapperTests.class
SET(CMAKE_JAVA_TEST_OUTDIR ${CMAKE_CURRENT_SOURCE_DIR}/build-test )
FILE(GLOB JAVA_TEST_FILES "${CMAKE_CURRENT_SOURCE_DIR}/src-test/org/RDKit/*.java")
# we added all source files, now remove the ones that we're not supporting in this build:
if(NOT RDK_BUILD_AVALON_SUPPORT)
LIST(REMOVE_ITEM JAVA_TEST_FILES "${CMAKE_CURRENT_SOURCE_DIR}/src-test/org/RDKit/AvalonLibTests.java")
endif()
if(NOT RDK_BUILD_INCHI_SUPPORT)
LIST(REMOVE_ITEM JAVA_TEST_FILES "${CMAKE_CURRENT_SOURCE_DIR}/src-test/org/RDKit/InchiTests.java")
endif()
ADD_CUSTOM_COMMAND(
OUTPUT ${CMAKE_JAVA_TEST_OUTDIR}/org/RDKit/WrapperTests.class
COMMAND ${JAVA_COMPILE} -d ${CMAKE_JAVA_TEST_OUTDIR} -cp "${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar${PATH_SEP}${JUNIT_JAR}" "src-test/org/RDKit/*.java"
COMMAND ${JAVA_COMPILE} -d ${CMAKE_JAVA_TEST_OUTDIR} -cp "${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar${PATH_SEP}${JUNIT_JAR}" ${JAVA_TEST_FILES}
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar
)
@@ -208,7 +227,21 @@ ADD_TEST(JavaWrapperTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.WrapperTests)
if(RDK_BUILD_AVALON_SUPPORT)
ADD_TEST(JavaAvalonTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.AvalonLibTests)
endif(RDK_BUILD_AVALON_SUPPORT)
if (RDK_BUILD_INCHI_SUPPORT)
ADD_TEST(JavaInchiTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.InchiTests)
endif (RDK_BUILD_INCHI_SUPPORT)
#ADD_TEST(JavaMemoryTests
# java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
# -cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"

4
Code/JavaWrappers/gmwrapper/GraphMolJava.i
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@@ -249,6 +249,10 @@ typedef unsigned long long int uintmax_t;
}
%include "../Descriptors.i"
#ifdef BUILD_AVALON_SUPPORT
%include "../AvalonLib.i"
#endif
#ifdef BUILD_INCHI_SUPPORT
%include "../Inchi.i"
#endif

83
Code/JavaWrappers/gmwrapper/src-test/org/RDKit/AvalonLibTests.java Normal file
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@@ -0,0 +1,83 @@
/*
* $Id$
*
* Copyright (c) 2010, 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.Test;
public class AvalonLibTests extends GraphMolTest {
@Test public void testAvalonTools1() {
ROMol m1;
m1 = RWMol.MolFromSmiles("n1ccccc1");
String newsmi=RDKFuncs.getCanonSmiles(m1);
assertEquals(newsmi,"c1ccncc1",newsmi);
newsmi=RDKFuncs.getCanonSmiles("n1ccccc1",true);
assertEquals(newsmi,"c1ccncc1",newsmi);
}
@Test public void testStereochem() {
ROMol m1;
m1 = RWMol.MolFromSmiles("C[C@H](F)C(F)Cl");
RDKFuncs.assignStereochemistry(m1,true,true,true);
int nKnown=0;
int nPossible=0;
for(int i=0;i<m1.getNumAtoms();i++){
if(m1.getAtomWithIdx(i).hasProp("_CIPCode")){
nKnown++;
nPossible++;
} else if(m1.getAtomWithIdx(i).hasProp("_ChiralityPossible")){
nPossible++;
}
}
assertEquals(nKnown,1);
assertEquals(nPossible,2);
}
@Test public void testAvalonTools2() {
StringInt_Pair res;
res=RDKFuncs.checkMolString("c1ccccn1",true);
assertEquals(res.getSecond(),0,res.getSecond());
assertFalse(res.getFirst(),""==res.getFirst());
res=RDKFuncs.checkMolString("c1c(R)cccc1C1(CC-C(C)C1)",true);
assertEquals(1,res.getSecond());
assertEquals(res.getFirst(),"",res.getFirst());
}
public static void main(String args[]) {
org.junit.runner.JUnitCore.main("org.RDKit.AvalonLibTests");
}
}

54
Code/JavaWrappers/gmwrapper/src-test/org/RDKit/InchiTests.java Executable file
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@@ -0,0 +1,54 @@
/*
* $Id: ChemTests.java 131 2011-01-20 22:01:29Z ebakke $
*
* Copyright (c) 2010, 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.Test;
public class InchiTests extends GraphMolTest {
@Test public void testInchi() {
ROMol m1;
m1 = RWMol.MolFromSmiles("C[C@H](F)C(F)Cl");
ExtraInchiReturnValues evs=new ExtraInchiReturnValues();
String inchi=RDKFuncs.MolToInchi(m1,evs);
String key=RDKFuncs.InchiToInchiKey(inchi);
assertEquals(inchi,"InChI=1S/C3H5ClF2/c1-2(5)3(4)6/h2-3H,1H3/t2-,3?/m0/s1");
assertEquals(key,"NCBHZPYEURSCDF-SCQFTWEKSA-N");
}
public static void main(String args[]) {
org.junit.runner.JUnitCore.main("org.RDKit.InchiTests");
}
}