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#include "obtest.h"
#include <openbabel/stereo/stereo.h>
#include <openbabel/mol.h>
#include <openbabel/obconversion.h>
#include <openbabel/graphsym.h>
#include <algorithm>
using namespace std;
using namespace OpenBabel;
void test_MakeRefs()
{
OBStereo::Refs refs = OBStereo::MakeRefs(1, 3, 5);
OB_ASSERT( refs.size() == 3 );
OB_ASSERT( refs[0] == 1 );
OB_ASSERT( refs[1] == 3 );
OB_ASSERT( refs[2] == 5 );
refs = OBStereo::MakeRefs(1, 3, 5, 7);
OB_ASSERT( refs.size() == 4 );
OB_ASSERT( refs[0] == 1 );
OB_ASSERT( refs[1] == 3 );
OB_ASSERT( refs[2] == 5 );
OB_ASSERT( refs[3] == 7 );
}
void test_ContainsSameRefs()
{
OB_ASSERT( OBStereo::ContainsSameRefs(OBStereo::MakeRefs(1, 2, 3),
OBStereo::MakeRefs(2, 3, 1)) );
OB_ASSERT( !OBStereo::ContainsSameRefs(OBStereo::MakeRefs(1, 2, 3),
OBStereo::MakeRefs(2, 7, 1)) );
// different sizes
OB_ASSERT( !OBStereo::ContainsSameRefs(OBStereo::MakeRefs(1, 2, 3),
OBStereo::MakeRefs(2, 3, 1, 4)) );
}
void test_NumInversions()
{
OB_ASSERT( OBStereo::NumInversions(OBStereo::MakeRefs(1, 2, 3)) == 0 );
OB_ASSERT( OBStereo::NumInversions(OBStereo::MakeRefs(1, 3, 2)) == 1 );
OB_ASSERT( OBStereo::NumInversions(OBStereo::MakeRefs(2, 1, 3)) == 1 );
OB_ASSERT( OBStereo::NumInversions(OBStereo::MakeRefs(2, 3, 1)) == 2 );
OB_ASSERT( OBStereo::NumInversions(OBStereo::MakeRefs(3, 1, 2)) == 2 );
OB_ASSERT( OBStereo::NumInversions(OBStereo::MakeRefs(3, 2, 1)) == 3 );
}
void test_Permutate()
{
OBStereo::Refs refs = OBStereo::MakeRefs(1, 2, 3);
OBStereo::Permutate(refs, 1, 2);
OB_ASSERT( refs[0] == 1 );
OB_ASSERT( refs[1] == 3 );
OB_ASSERT( refs[2] == 2 );
// test out of range indexes for crashes
OBStereo::Permutate(refs, -1, 1);
OBStereo::Permutate(refs, 1, -1);
OBStereo::Permutate(refs, 9, 1);
OBStereo::Permutate(refs, 1, 9);
}
void test_Permutated()
{
OBStereo::Refs refs = OBStereo::MakeRefs(1, 2, 3);
OBStereo::Refs mutant = OBStereo::Permutated(refs, 1, 2);
OB_ASSERT( refs[0] == 1 );
OB_ASSERT( refs[1] == 2 );
OB_ASSERT( refs[2] == 3 );
OB_ASSERT( mutant[0] == 1 );
OB_ASSERT( mutant[1] == 3 );
OB_ASSERT( mutant[2] == 2 );
}
std::string GetFilename(const std::string &filename)
{
string path = TESTDATADIR + filename;
return path;
}
bool doStereoPerception(OBMol &mol, int numTetrahedral, int numCisTrans)
{
// need to calculate symmetry first
std::vector<unsigned int> symmetry_classes;
OpenBabel::OBGraphSym graphsym(&mol);
graphsym.GetSymmetry(symmetry_classes);
OBStereoUnitSet units = FindStereogenicUnits(&mol, symmetry_classes);
int tetrahedralCount = 0;
int cistransCount = 0;
for (unsigned int i = 0; i < units.size(); ++i) {
switch (units.at(i).type) {
case OBStereo::Tetrahedral:
tetrahedralCount++;
break;
case OBStereo::CisTrans:
cistransCount++;
break;
}
}
OB_COMPARE(tetrahedralCount, numTetrahedral);
OB_COMPARE(cistransCount, numCisTrans);
return (tetrahedralCount == numTetrahedral) && (cistransCount == numCisTrans);
}
bool doStereoPerception2(OBMol &mol, int numTetrahedral, int numCisTrans)
{
// need to calculate symmetry first
std::vector<unsigned int> symmetry_classes;
OpenBabel::OBGraphSym graphsym(&mol);
graphsym.GetSymmetry(symmetry_classes);
Automorphisms G;
FindAutomorphisms(&mol, G, symmetry_classes);
std::vector<OpenBabel::OBStereoUnit> units = FindStereogenicUnits(&mol, symmetry_classes, G);
int tetrahedralCount = 0;
int cistransCount = 0;
for (unsigned int i = 0; i < units.size(); ++i) {
switch (units.at(i).type) {
case OBStereo::Tetrahedral:
tetrahedralCount++;
break;
case OBStereo::CisTrans:
cistransCount++;
break;
}
}
OB_COMPARE(tetrahedralCount, numTetrahedral);
OB_COMPARE(cistransCount, numCisTrans);
return (tetrahedralCount == numTetrahedral) && (cistransCount == numCisTrans);
}
OBStereoUnitSet Units(const OBStereoUnit &u1)
{ OBStereoUnitSet units; units.push_back(u1); return units; }
OBStereoUnitSet Units(const OBStereoUnit &u1, const OBStereoUnit &u2)
{ OBStereoUnitSet units = Units(u1); units.push_back(u2); return units; }
OBStereoUnitSet Units(const OBStereoUnit &u1, const OBStereoUnit &u2,
const OBStereoUnit &u3)
{ OBStereoUnitSet units = Units(u1, u2); units.push_back(u3); return units; }
OBStereoUnitSet Units(const OBStereoUnit &u1, const OBStereoUnit &u2,
const OBStereoUnit &u3, const OBStereoUnit &u4)
{ OBStereoUnitSet units = Units(u1, u2, u3); units.push_back(u4); return units; }
OBStereoUnitSet Units(const OBStereoUnit &u1, const OBStereoUnit &u2,
const OBStereoUnit &u3, const OBStereoUnit &u4, const OBStereoUnit &u5)
{ OBStereoUnitSet units = Units(u1, u2, u3, u4); units.push_back(u5); return units; }
#define TH(id) OBStereoUnit(OBStereo::Tetrahedral, id)
std::vector< std::vector<OpenBabel::OBStereoUnit> > DepUnits(const OBStereoUnitSet &u1)
{ std::vector< std::vector<OpenBabel::OBStereoUnit> > sets; sets.push_back(u1); return sets; }
std::vector< std::vector<OpenBabel::OBStereoUnit> > DepUnits(const OBStereoUnitSet &u1,
const OBStereoUnitSet &u2)
{ std::vector< std::vector<OpenBabel::OBStereoUnit> > sets = DepUnits(u1); sets.push_back(u2); return sets; }
std::vector< std::vector<OpenBabel::OBStereoUnit> > DepUnits(const OBStereoUnitSet &u1,
const OBStereoUnitSet &u2, const OBStereoUnitSet &u3)
{ std::vector< std::vector<OpenBabel::OBStereoUnit> > sets = DepUnits(u1, u2); sets.push_back(u3); return sets; }
bool doStereoPerception3(OBMol &mol, const OBStereoUnitSet &refUnits = OBStereoUnitSet(),
const OBStereoUnitSetOfSets refInterdependent =
OBStereoUnitSetOfSets())
{
std::vector<OBAtom*> atoms;
FOR_ATOMS_OF_MOL(atom, mol)
atoms.push_back(&*atom);
for (int i = 0; i < 100; ++i) {
std::random_shuffle(atoms.begin(), atoms.end());
mol.RenumberAtoms(atoms);
// need to calculate symmetry first
std::vector<unsigned int> symmetry_classes;
OpenBabel::OBGraphSym graphsym(&mol);
int nclasses = graphsym.GetSymmetry(symmetry_classes);
cout << "nclasses = " << nclasses << endl;
OB_ASSERT( nclasses == 7 );
Automorphisms G;
FindAutomorphisms(&mol, G, symmetry_classes);
cout << "G.size " << G.size() << endl;
std::vector<OpenBabel::OBStereoUnit> units = FindStereogenicUnits(&mol, symmetry_classes, G);
OB_COMPARE(units.size(), refUnits.size());
for (unsigned int i = 0; i < units.size(); ++i) {
bool foundUnit = false;
for (unsigned int j = 0; j < refUnits.size(); ++j) {
if (units[i].type == refUnits[j].type)
if (units[i].id == refUnits[j].id)
foundUnit = true;
}
OB_ASSERT( foundUnit );
}
}
return true;
}
/**
* Test detection of stereocenters
*
*
*/
void test_StereoPerception()
{
OBMol mol;
OBConversion conv;
OB_ASSERT( conv.SetInFormat("mol") );
/*
cout << "structure break1" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/break1.mol")) );
// need to calculate symmetry first
std::vector<unsigned int> symmetry_classes;
OpenBabel::OBGraphSym graphsym(&mol);
cout << "nclasses = " << graphsym.GetSymmetry(symmetry_classes, false) << endl;
Automorphisms G = FindAutomorphisms(&mol, symmetry_classes);
cout << "G.size " << G.size() << endl;
OB_ASSERT( doStereoPerception3(mol, Units(TH(0), TH(4), TH(3), TH(9), TH(15)),
DepUnits(Units(TH(0), TH(4)), Units(TH(3), TH(9)), Units(TH(15)))) );
*/
cout << "structure perception1" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/perception1.mol")) );
OB_ASSERT( doStereoPerception(mol, 0, 0) );
OB_ASSERT( doStereoPerception2(mol, 0, 0) );
cout << "structure perception2" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/perception2.mol")) );
OB_ASSERT( doStereoPerception(mol, 0, 0) );
OB_ASSERT( doStereoPerception2(mol, 0, 0) );
cout << "structure perception3" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/perception3.mol")) );
OB_ASSERT( doStereoPerception(mol, 2, 0) );
OB_ASSERT( doStereoPerception2(mol, 2, 0) );
cout << "structure perception4" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/perception4.mol")) );
OB_ASSERT( doStereoPerception(mol, 0, 0) );
OB_ASSERT( doStereoPerception2(mol, 0, 0) );
cout << "structure perception5" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/perception5.mol")) );
OB_ASSERT( doStereoPerception(mol, 0, 0) );
OB_ASSERT( doStereoPerception2(mol, 0, 0) );
cout << "structure perception6" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/perception6.mol")) );
OB_ASSERT( doStereoPerception(mol, 0, 2) );
OB_ASSERT( doStereoPerception2(mol, 0, 2) );
cout << "structure perception7" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/perception7.mol")) );
OB_ASSERT( doStereoPerception(mol, 0, 0) );
OB_ASSERT( doStereoPerception2(mol, 0, 0) );
cout << "structure perception8" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/perception8.mol")) );
OB_ASSERT( doStereoPerception(mol, 0, 0) );
OB_ASSERT( doStereoPerception2(mol, 0, 0) );
cout << "structure perception9" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/perception9.mol")) );
OB_ASSERT( doStereoPerception(mol, 0, 0) );
OB_ASSERT( doStereoPerception2(mol, 0, 0) );
cout << "structure perception10" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/perception10.mol")) );
OB_ASSERT( doStereoPerception(mol, 1, 1) );
OB_ASSERT( doStereoPerception2(mol, 1, 1) );
cout << "structure perception11" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/perception11.mol")) );
OB_ASSERT( doStereoPerception(mol, 3, 0) );
OB_ASSERT( doStereoPerception2(mol, 3, 0) );
cout << "structure perception12" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/perception12.mol")) );
OB_ASSERT( doStereoPerception(mol, 0, 0) );
OB_ASSERT( doStereoPerception2(mol, 0, 0) );
cout << "structure perception13" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/perception13.mol")) );
OB_ASSERT( doStereoPerception(mol, 0, 0) );
OB_ASSERT( doStereoPerception2(mol, 0, 0) );
cout << "structure perception14" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/perception14.mol")) );
OB_ASSERT( doStereoPerception(mol, 0, 0) );
OB_ASSERT( doStereoPerception2(mol, 0, 0) );
cout << "structure perception15" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/perception15.mol")) );
OB_ASSERT( doStereoPerception(mol, 0, 0) );
OB_ASSERT( doStereoPerception2(mol, 0, 0) );
cout << "structure perception16" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/perception16.mol")) );
OB_ASSERT( doStereoPerception(mol, 1, 2) );
OB_ASSERT( doStereoPerception2(mol, 1, 2) );
cout << "structure perception17" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/perception17.mol")) );
OB_ASSERT( doStereoPerception(mol, 2, 0) );
OB_ASSERT( doStereoPerception2(mol, 2, 0) );
cout << "structure perception18" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/perception18.mol")) );
OB_ASSERT( doStereoPerception(mol, 3, 1) );
OB_ASSERT( doStereoPerception2(mol, 3, 1) );
cout << "structure perception19" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/perception19.mol")) );
OB_ASSERT( doStereoPerception(mol, 2, 0) );
OB_ASSERT( doStereoPerception2(mol, 2, 0) );
cout << "structure perception20" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/perception20.mol")) );
OB_ASSERT( doStereoPerception(mol, 4, 0) );
OB_ASSERT( doStereoPerception2(mol, 4, 0) );
/*
* J. Chem. Inf. Comput. Sci., Vol. 33, No. 6, 1993
*
* Figure 1. Examples of compounds containing parastereocenters
*/
cout << "Razinger paper, fig. 1: structure a" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/razinger_fig1_a.mol")) );
OB_ASSERT( doStereoPerception(mol, 0, 2) );
OB_ASSERT( doStereoPerception2(mol, 0, 2) );
cout << "Razinger paper, fig. 1: structure b" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/razinger_fig1_b.mol")) );
OB_ASSERT( doStereoPerception(mol, 2, 2) );
OB_ASSERT( doStereoPerception2(mol, 2, 2) );
cout << "Razinger paper, fig. 1: structure c" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/razinger_fig1_c.mol")) );
OB_ASSERT( doStereoPerception(mol, 2, 0) );
OB_ASSERT( doStereoPerception2(mol, 2, 0) );
cout << "Razinger paper, fig. 1: structure d" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/razinger_fig1_d.mol")) );
OB_ASSERT( doStereoPerception(mol, 3, 0) );
OB_ASSERT( doStereoPerception2(mol, 3, 0) );
cout << "Razinger paper, fig. 1: structure e" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/razinger_fig1_e.mol")) );
OB_ASSERT( doStereoPerception(mol, 6, 0) );
OB_ASSERT( doStereoPerception2(mol, 6, 0) );
cout << "Razinger paper, fig. 1: structure f" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/razinger_fig1_f.mol")) );
OB_ASSERT( doStereoPerception(mol, 2, 1) );
OB_ASSERT( doStereoPerception2(mol, 2, 1) );
cout << "Razinger paper, fig. 1: structure g" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/razinger_fig1_g.mol")) );
OB_ASSERT( doStereoPerception(mol, 0, 0) );
OB_ASSERT( doStereoPerception2(mol, 0, 0) );
cout << "Razinger paper, fig. 1: structure h" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/razinger_fig1_h.mol")) );
OB_ASSERT( doStereoPerception(mol, 2, 0) );
OB_ASSERT( doStereoPerception2(mol, 2, 0) );
cout << "Razinger paper, fig. 1: structure i" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/razinger_fig1_i.mol")) );
OB_ASSERT( doStereoPerception(mol, 3, 0) ); // rule 2a
OB_ASSERT( doStereoPerception2(mol, 3, 0) );
cout << "Razinger paper, fig. 1: structure j" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/razinger_fig1_j.mol")) );
OB_ASSERT( doStereoPerception(mol, 7, 0) ); // rule 2b
OB_ASSERT( doStereoPerception2(mol, 7, 0) );
cout << "Razinger paper, fig. 1: structure k" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/razinger_fig1_k.mol")) );
OB_ASSERT( doStereoPerception(mol, 3, 0) ); // counter example to j
OB_ASSERT( doStereoPerception2(mol, 3, 0) );
cout << "Razinger paper, fig. 1: structure l" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/razinger_fig1_l.mol")) );
OB_ASSERT( doStereoPerception(mol, 13, 0) ); // rule 2b
OB_ASSERT( doStereoPerception2(mol, 13, 0) );
cout << "Razinger paper, fig. 1: structure m" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/razinger_fig1_m.mol")) );
OB_ASSERT( doStereoPerception(mol, 12, 0) ); // counter example to l
OB_ASSERT( doStereoPerception2(mol, 12, 0) );
cout << "Razinger paper, fig. 1: structure n" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/razinger_fig1_n.mol")) );
OB_ASSERT( doStereoPerception(mol, 5, 0) );
OB_ASSERT( doStereoPerception2(mol, 5, 0) );
cout << "Razinger paper, fig. 1: structure o" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/razinger_fig1_o.mol")) );
OB_ASSERT( doStereoPerception(mol, 2, 0) );
OB_ASSERT( doStereoPerception2(mol, 2, 0) );
cout << "Razinger paper, fig. 1: structure p" << endl;
OB_ASSERT( conv.ReadFile(&mol, GetFilename("stereo/razinger_fig1_p.mol")) );
OB_ASSERT( doStereoPerception(mol, 5, 2) );
OB_ASSERT( doStereoPerception2(mol, 5, 2) );
// conv.ReadString(&mol, "CC1CCC(C)CC1");
}
int stereotest(int argc, char* argv[])
{
int defaultchoice = 1;
int choice = defaultchoice;
if (argc > 1) {
if(sscanf(argv[1], "%d", &choice) != 1) {
printf("Couldn't parse that input as a number\n");
return -1;
}
}
// Define location of file formats for testing
#ifdef FORMATDIR
char env[BUFF_SIZE];
snprintf(env, BUFF_SIZE, "BABEL_LIBDIR=%s", FORMATDIR);
putenv(env);
#endif
switch(choice) {
case 1:
test_MakeRefs();
break;
case 2:
test_ContainsSameRefs();
break;
case 3:
test_NumInversions();
break;
case 4:
test_Permutate();
break;
case 5:
test_Permutated();
break;
case 6:
test_StereoPerception();
break;
default:
cout << "Test number " << choice << " does not exist!\n";
return -1;
}
return 0;
}
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