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Fixes #1837 (#1839)

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* Fixes #1837

* do not expose the takeOwnership forms of addAtom and addBond
This commit is contained in:
Greg Landrum
2018-04-26 21:02:22 +01:00
parent 1fa8216532
commit ad080a8484
2 changed files with 41 additions and 16 deletions
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9
Code/JavaWrappers/RWMol.i
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@@ -41,11 +41,10 @@
#include <GraphMol/FileParsers/MolFileStereochem.h>
%}
%ignore RDKit::RWMol::addAtom(Atom *atom);
%ignore RDKit::RWMol::addAtom(Atom *atom,bool updateLabel);
%ignore RDKit::RWMol::addBond(Atom *beginAtom, Atom *endAtom, Bond::BondType order);
%ignore RDKit::RWMol::addBond(Atom *beginAtom, Atom *endAtom);
%ignore RDKit::RWMol::addBond(Bond *bond);
// ignore the methods that allow the molecule to take ownership of atoms/Bonds
// (instead of copying them). This just leads to memory problems with Java
%ignore RDKit::RWMol::addAtom(Atom *atom,bool updateLabel,bool takeOwnership);
%ignore RDKit::RWMol::addBond(Bond *bond,bool takeOwnership);
%shared_ptr(RDKit::RWMol)
%include "enums.swg"

48
Code/JavaWrappers/gmwrapper/src-test/org/RDKit/BasicMoleculeTests.java
View File

@@ -1,21 +1,21 @@
/*
/*
* $Id: BasicMoleculeTests.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:
* met:
*
* * Redistributions of source code must retain the above copyright
* * 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
* 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
* * 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
@@ -37,7 +37,7 @@ import static org.junit.Assert.*;
import org.junit.*;
public class BasicMoleculeTests extends GraphMolTest {
private ROMol mol1;
@Before public void setUp() {
String smiles="c1ccccc1";
@@ -117,7 +117,7 @@ public class BasicMoleculeTests extends GraphMolTest {
assertEquals(1,mv.get(0).getSecond());
assertEquals(1,mv.get(1).getFirst());
assertEquals(0,mv.get(1).getSecond());
}
}
@Test public void testSubstruct4() {
ROMol p;
Match_Vect_Vect mvv;
@@ -201,9 +201,35 @@ public class BasicMoleculeTests extends GraphMolTest {
assertEquals(failedAt,SanitizeFlags.SANITIZE_KEKULIZE.swigValue());
ops ^= SanitizeFlags.SANITIZE_KEKULIZE.swigValue();
failedAt=RDKFuncs.sanitizeMol(mol,ops);
assertEquals(failedAt,0);
assertEquals(failedAt,0);
}
@Test public void testAddAtomsAndBonds() {
RWMol mol = new RWMol();
assertEquals(mol.getNumBonds(),0);
Atom carbon = new Atom(6);
mol.addAtom(carbon,false);
mol.addAtom(carbon,false);
assertEquals(mol.getNumAtoms(),2);
Bond single = new Bond(Bond.BondType.SINGLE);
single.setOwningMol(mol);
single.setBeginAtomIdx(1);
single.setEndAtomIdx(0);
mol.addBond(single);
assertEquals(mol.getNumBonds(),1);
assertEquals(mol.getBondWithIdx(0).getBeginAtomIdx(),1);
assertEquals(mol.getBondWithIdx(0).getEndAtomIdx(),0);
// the molecule has copied the bond, so if we change it, there's
// no impact on the molecule itself:
single.setBeginAtomIdx(0);
single.setEndAtomIdx(1);
assertEquals(mol.getBondWithIdx(0).getBeginAtomIdx(),1);
assertEquals(mol.getBondWithIdx(0).getEndAtomIdx(),0);
}
/* @Test -- the contents of this test now in UnitTestPickling, testIssue219
public void testConformer(){
}