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335 lines
7.8 KiB
C++
335 lines
7.8 KiB
C++
#include "obtest.h"
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#include <openbabel/mol.h>
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#include <openbabel/obconversion.h>
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#include <openbabel/isomorphism.h>
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#include <openbabel/query.h>
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#include <openbabel/elements.h>
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#include <openbabel/obiter.h>
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using namespace std;
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using namespace OpenBabel;
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void testIsomorphism1()
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{
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OBMol mol;
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OBConversion conv;
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conv.SetInFormat("smi");
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conv.ReadString(&mol, "CC1CCC(C)CC1");
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OBQuery *query = CompileMoleculeQuery(&mol);
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OBIsomorphismMapper *mapper = OBIsomorphismMapper::GetInstance(query);
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OBIsomorphismMapper::Mappings maps;
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mapper->MapAll(&mol, maps);
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OB_ASSERT( maps.size() == 4 );
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delete query;
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delete mapper;
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query = CompileSmilesQuery("C1(C)CCC(C)CC1");
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mapper = OBIsomorphismMapper::GetInstance(query);
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OBIsomorphismMapper::Mapping map;
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mapper->MapFirst(&mol, map);
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OB_ASSERT( map.size() == 8 );
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mapper->MapUnique(&mol, maps);
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OB_ASSERT( maps.size() == 1 );
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mapper->MapAll(&mol, maps);
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OB_ASSERT( maps.size() == 4 );
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delete query;
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delete mapper;
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}
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void testIsomorphism2()
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{
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cout << "testIsomorphism2" << endl;
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OBMol mol;
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OBConversion conv;
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conv.SetInFormat("smi");
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conv.ReadString(&mol, "Cc1ccc(C)cc1");
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OBQuery *query = CompileSmilesQuery("c1ccccc1");
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OBIsomorphismMapper *mapper = OBIsomorphismMapper::GetInstance(query);
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OBIsomorphismMapper::Mappings maps;
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mapper->MapUnique(&mol, maps);
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cout << maps.size() << endl;
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OB_ASSERT( maps.size() == 1 );
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delete query;
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delete mapper;
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}
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void testIsomorphism3()
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{
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cout << "testIsomorphism3" << endl;
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OBMol mol;
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OBConversion conv;
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conv.SetInFormat("smi");
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conv.ReadString(&mol, "C1CC1CC1CC1");
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OBQuery *query = CompileSmilesQuery("C1CC1");
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OBIsomorphismMapper *mapper = OBIsomorphismMapper::GetInstance(query);
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OBIsomorphismMapper::Mappings maps;
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mapper->MapUnique(&mol, maps);
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cout << maps.size() << endl;
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OB_ASSERT( maps.size() == 2 );
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delete query;
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delete mapper;
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}
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void testIsomorphism4()
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{
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cout << "testIsomorphism4" << endl;
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OBMol mol;
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OBConversion conv;
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conv.SetInFormat("smi");
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conv.ReadString(&mol, "C12C(C2)C1");
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OBQuery *query = CompileSmilesQuery("C1CC1");
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OBIsomorphismMapper *mapper = OBIsomorphismMapper::GetInstance(query);
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OBIsomorphismMapper::Mappings maps;
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mapper->MapUnique(&mol, maps);
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cout << maps.size() << endl;
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OB_ASSERT( maps.size() == 2 );
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delete query;
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delete mapper;
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}
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void testIsomorphismMask()
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{
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// read file: 3 6-rings
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//
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// /\ /\ /\
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// | | | |
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// \/ \/ \/
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//
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OBMol mol;
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OBConversion conv;
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conv.SetInFormat("cml");
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std::ifstream ifs(OBTestUtil::GetFilename("isomorphism1.cml").c_str());
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OB_REQUIRE( ifs );
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conv.Read(&mol, &ifs);
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OBQuery *query = CompileSmilesQuery("C1CCCCC1");
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OBIsomorphismMapper *mapper = OBIsomorphismMapper::GetInstance(query);
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// no mask
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OBIsomorphismMapper::Mappings maps;
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mapper->MapUnique(&mol, maps);
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cout << maps.size() << endl;
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OB_ASSERT( maps.size() == 3 );
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// mask first ring
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OBBitVec mask;
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for (int i = 0; i < 6; ++i)
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mask.SetBitOn(i+1);
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mapper->MapUnique(&mol, maps, mask);
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cout << maps.size() << endl;
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OB_ASSERT( maps.size() == 1 );
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// mask second ring also
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for (int i = 6; i < 10; ++i)
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mask.SetBitOn(i+1);
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mapper->MapUnique(&mol, maps, mask);
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cout << maps.size() << endl;
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OB_ASSERT( maps.size() == 2 );
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// just mask last ring (atomIds 7-8, 10-13)
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mask.Clear();
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for (int i = 10; i < 14; ++i)
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mask.SetBitOn(i+1);
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mask.SetBitOn(7 + 1); mask.SetBitOn(8 + 1);
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mapper->MapUnique(&mol, maps, mask);
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cout << maps.size() << endl;
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OB_ASSERT( maps.size() == 1 ); // Should be same result as masking just the first ring
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delete query;
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delete mapper;
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}
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void testAutomorphismMask() {
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// read file: 3 6-rings
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//
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// /\ /\ /\
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// | | | |
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// \/ \/ \/
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//
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cout << "testAutomorphismMask" << endl;
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OBMol mol;
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OBConversion conv;
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conv.SetInFormat("cml");
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std::ifstream ifs(OBTestUtil::GetFilename("isomorphism1.cml").c_str());
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OB_REQUIRE( ifs );
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conv.Read(&mol, &ifs);
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OBIsomorphismMapper::Mappings maps;
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// First of all, how many automorphisms are there without any mask?
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// This takes about 20 seconds, so you may want to comment this out while debugging
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FindAutomorphisms(&mol, maps);
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cout << maps.size() << endl;
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OB_ASSERT( maps.size() == 4 );
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// Now, let's remove the bridge (atomId 6) of the central ring.
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//
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// /\ /\ /\
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// | | | |
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// \/ \/
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// both rings can be flipped around exocyclic bond, the whole molecule can be mirrored
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// horizontally, this results in 2 x 2 x 2 = 8 automorphisms
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OBBitVec mask;
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mask.SetRangeOn(1, mol.NumAtoms());
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mask.SetBitOff(6+1);
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FindAutomorphisms(&mol, maps, mask);
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cout << maps.size() << endl;
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for (unsigned int i = 0; i < maps.size(); ++i) {
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OBIsomorphismMapper::Mapping::const_iterator j;
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for (j = maps[i].begin(); j != maps[i].end(); ++j)
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cout << j->second << " ";
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cout << endl;
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}
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OB_ASSERT( maps.size() == 8 );
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// Verify that atom Id 6 does not occur anywhere in the mappings
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OBIsomorphismMapper::Mappings::const_iterator a;
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OBIsomorphismMapper::Mapping::const_iterator b;
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for (a = maps.begin(); a != maps.end(); ++a)
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for (b = a->begin(); b!= a->end(); ++b) {
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OB_ASSERT( b->first != 6 );
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OB_ASSERT( b->second != 6 );
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}
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}
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void testAutomorphismMask2()
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{
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// The test molecule is progesterone, a steroid (four fused non-planar rings)
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cout << "testAutomorphismMask2" << endl;
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OBMol mol;
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OBConversion conv;
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conv.SetInFormat("sdf");
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std::ifstream ifs(OBTestUtil::GetFilename("progesterone.sdf").c_str());
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OB_REQUIRE( ifs );
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OB_REQUIRE( conv.Read(&mol, &ifs) );
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Automorphisms _aut;
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OBBitVec _frag_atoms;
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FOR_ATOMS_OF_MOL(a, mol) {
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if (a->GetAtomicNum() != OBElements::Hydrogen)
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_frag_atoms.SetBitOn(a->GetIdx());
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}
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FindAutomorphisms((OBMol*)&mol, _aut, _frag_atoms);
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OB_ASSERT( _aut.size() == 1 );
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}
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void testAutomorphismPreMapping()
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{
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cout << "testAutomorphismPreMapping" << endl;
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OBMol mol;
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OBConversion conv;
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conv.SetInFormat("smi");
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conv.ReadString(&mol, "c1(C)c(C)c(C)c(C)c(C)c1");
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Automorphisms aut;
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FindAutomorphisms((OBMol*)&mol, aut);
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cout << aut.size() << endl;
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OB_ASSERT( aut.size() == 2 );
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}
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// https://github.com/openbabel/openbabel/issues/1929
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void testIsomorphism9()
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{
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cout << "testIsomorphism9" << endl;
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OBMol mol;
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OBConversion conv;
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conv.SetInFormat("smi");
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conv.ReadString(&mol, "Cc1onc(C)c1");
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OBQuery *query = CompileMoleculeQuery(&mol);
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OBIsomorphismMapper *mapper = OBIsomorphismMapper::GetInstance(query);
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OBIsomorphismMapper::Mappings maps;
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mapper->MapAll(&mol, maps);
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OB_ASSERT(maps.size() == 1);
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OBIsomorphismMapper::Mapping map;
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OBIsomorphismMapper::Mapping::const_iterator iter;
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map = maps[0];
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for (iter=map.begin(); iter!=map.end(); ++iter)
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OB_ASSERT( iter->first == iter->second);
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delete query;
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delete mapper;
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}
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int isomorphismtest(int argc, char* argv[])
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{
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int defaultchoice = 1;
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int choice = defaultchoice;
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if (argc > 1) {
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if(sscanf(argv[1], "%d", &choice) != 1) {
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printf("Couldn't parse that input as a number\n");
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return -1;
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}
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}
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// Define location of file formats for testing
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#ifdef FORMATDIR
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char env[BUFF_SIZE];
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snprintf(env, BUFF_SIZE, "BABEL_LIBDIR=%s", FORMATDIR);
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putenv(env);
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#endif
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switch(choice) {
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case 1:
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testIsomorphism1();
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break;
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case 2:
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testIsomorphism2();
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break;
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case 3:
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testIsomorphism3();
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break;
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case 4:
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testIsomorphism4();
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break;
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case 5:
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testIsomorphismMask();
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break;
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case 6:
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testAutomorphismMask();
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break;
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case 7:
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testAutomorphismMask2();
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break;
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case 8:
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testAutomorphismPreMapping();
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break;
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case 9:
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testIsomorphism9();
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break;
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default:
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cout << "Test number " << choice << " does not exist!\n";
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return -1;
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}
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return 0;
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}
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