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make sure that the global EmbedParameter objects are not writeable from Java (#1824)

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This commit is contained in:
Greg Landrum
2018-04-17 13:37:04 +02:00
committed by GitHub
parent 10496f750f
commit 404df80b8a
2 changed files with 45 additions and 3 deletions
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34
Code/JavaWrappers/DistGeom.i
View File

@@ -57,8 +57,42 @@
%ignore RDKit::DGeomHelpers::EmbedMolecule;
%ignore RDKit::DGeomHelpers::EmbedMultipleConfs;
// make sure the struct has a copy constructor:
%copyctor RDKit::DGeomHelpers::EmbedParameters;
// we want to ignore the const global parameter objects because SWIG does a
// poor job of making them read-only when they are exposed to Java.
%ignore RDKit::DGeomHelpers::KDG;
%ignore RDKit::DGeomHelpers::ETDG;
%ignore RDKit::DGeomHelpers::ETKDG;
%ignore RDKit::DGeomHelpers::ETKDGv2;
%include <GraphMol/DistGeomHelpers/Embedder.h>
// create functions to return copies of the global parameter objects
%newobject RDKit::DGeomHelpers::getKDG;
%newobject RDKit::DGeomHelpers::getETDG;
%newobject RDKit::DGeomHelpers::getETKDG;
%newobject RDKit::DGeomHelpers::getETKDGv2;
%inline {
namespace RDKit{
namespace DGeomHelpers {
EmbedParameters *getKDG() {
return new EmbedParameters(KDG);
}
EmbedParameters *getETDG() {
return new EmbedParameters(ETDG);
}
EmbedParameters *getETKDG() {
return new EmbedParameters(ETKDG);
}
EmbedParameters *getETKDGv2() {
return new EmbedParameters(ETKDGv2);
}
}
}
}
// A class to hang special distance geometry methods on.
%inline {
namespace DistGeom {

14
Code/JavaWrappers/gmwrapper/src-test/org/RDKit/DistanceGeometryTests.java
View File

@@ -481,13 +481,21 @@ public class DistanceGeometryTests extends GraphMolTest {
ROMol ref=RWMol.MolFromMolFile(molFile.getPath(), true, false);;
ROMol test = RWMol.MolFromSmiles("OCCC").addHs(false,false);
assertTrue(test.getNumAtoms()==ref.getNumAtoms());
EmbedParameters eps = RDKFuncs.getETKDG();
EmbedParameters eps = new EmbedParameters(RDKFuncs.getETKDG());
eps.setRandomSeed(42);
int cid = DistanceGeom.EmbedMolecule(test,eps);
assertTrue(cid>-1);
double ssd;
ssd = test.alignMol(ref);
assertTrue(ssd < 0.1);
// make sure we didn't change the global params
EmbedParameters eps2 = RDKFuncs.getETKDG();
cid = DistanceGeom.EmbedMolecule(test,eps2);
assertTrue(cid>-1);
ssd = test.alignMol(ref);
assertTrue(ssd > 0.1);
}
@Test
public void test9ETDGParams2() {
@@ -520,10 +528,10 @@ public class DistanceGeometryTests extends GraphMolTest {
assertTrue(ssd < 0.1);
}
public static void main(String args[]) {
System.out.print("STARTING\n");
org.junit.runner.JUnitCore.main("org.RDKit.DistanceGeometryTests");
System.out.print("FINISHED\n");
}
}