diff --git a/Code/JavaWrappers/MonomerInfo.i b/Code/JavaWrappers/MonomerInfo.i new file mode 100644 index 000000000..337308987 --- /dev/null +++ b/Code/JavaWrappers/MonomerInfo.i @@ -0,0 +1,42 @@ +/* +* $Id$ +* +* Copyright (c) 2013, 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_string.i" + +%{ +#include +%} + +%include + + diff --git a/Code/JavaWrappers/gmwrapper/CMakeLists.txt b/Code/JavaWrappers/gmwrapper/CMakeLists.txt index bd39ea7cd..d52e14da0 100644 --- a/Code/JavaWrappers/gmwrapper/CMakeLists.txt +++ b/Code/JavaWrappers/gmwrapper/CMakeLists.txt @@ -269,6 +269,10 @@ ADD_TEST(JavaChemTransformsTests 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.ChemTransformsTests) +ADD_TEST(JavaPDBTests + 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.PDBTests) INSTALL(TARGETS GraphMolWrap DESTINATION ${CMAKE_CURRENT_SOURCE_DIR} ) diff --git a/Code/JavaWrappers/gmwrapper/GraphMolJava.i b/Code/JavaWrappers/gmwrapper/GraphMolJava.i index edba8c4d9..f5325e46a 100644 --- a/Code/JavaWrappers/gmwrapper/GraphMolJava.i +++ b/Code/JavaWrappers/gmwrapper/GraphMolJava.i @@ -155,6 +155,7 @@ typedef unsigned long long int uintmax_t; %include "../QueryAtom.i" %include "../QueryBond.i" %include "../QueryOps.i" +%include "../MonomerInfo.i" %include "../PeriodicTable.i" %include "../SanitException.i" %include "../SmilesParse.i" diff --git a/Code/JavaWrappers/gmwrapper/src-test/org/RDKit/PDBTests.java b/Code/JavaWrappers/gmwrapper/src-test/org/RDKit/PDBTests.java new file mode 100644 index 000000000..edd598b6c --- /dev/null +++ b/Code/JavaWrappers/gmwrapper/src-test/org/RDKit/PDBTests.java @@ -0,0 +1,76 @@ +/* + * $Id: ForceFieldsTests.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 java.io.File; + +import org.junit.Test; + +public class PDBTests extends GraphMolTest { + + File testDataDir = new File(getRdBase(), + "Code/GraphMol/FileParsers/test_data"); + + @Test + public void testPDBReadBasic () { + File molFile = new File(testDataDir, "1CRN.pdb"); + ROMol m = RWMol.MolFromPDBFile(molFile.getPath()); + assertEquals(327, m.getNumAtoms()); + assertEquals(337, m.getNumBonds()); + AtomMonomerInfo mi=new AtomMonomerInfo(m.getAtomWithIdx(0).getMonomerInfo()); + assert(mi instanceof AtomPDBResidueInfo); + // FIX: need to actually test this + } + + @Test + public void testPDBWriteBasic () { + File molFile = new File(testDataDir, "1CRN.pdb"); + ROMol m = RWMol.MolFromPDBFile(molFile.getPath()); + String mb = new String(m.MolToPDBBlock()); + ROMol m2 = RWMol.MolFromPDBBlock(mb); + assertEquals(327, m2.getNumAtoms()); + assertEquals(337, m2.getNumBonds()); + AtomMonomerInfo mi=new AtomMonomerInfo(m2.getAtomWithIdx(0).getMonomerInfo()); + assert(mi instanceof AtomPDBResidueInfo); + // FIX: need to actually test this + + } + + + public static void main(String args[]) { + org.junit.runner.JUnitCore.main("org.RDKit.PDBTests"); + } + +}