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#include "obtest.h"
#include <openbabel/mol.h>
#include <openbabel/obconversion.h>
#include <openbabel/builder.h>
#include <openbabel/forcefield.h>
#include <iostream>
#include <string>
#include <vector>
#include <algorithm>
using namespace std;
using namespace OpenBabel;
std::string GetFilename(const std::string &filename)
{
std::string path = TESTDATADIR + filename;
return path;
}
static unsigned int failed = 0;
static unsigned int testCount = 0;
void clearMolFlags(OBMol &mol)
{
// Both of these are needed or there's a crash.
mol.UnsetFlag(OB_SSSR_MOL);
mol.UnsetFlag(OB_AROMATIC_MOL);
// Not needed, doesn't cause crash
// mol.UnsetFlag(OB_RINGFLAGS_MOL);
// mol.UnsetFlag(OB_LSSR_MOL);
// mol.UnsetFlag(OB_KEKULE_MOL);
// mol.UnsetFlag(OB_CLOSURE_MOL);
// mol.UnsetFlag(OB_AROM_CORRECTED_MOL);
// mol.UnsetFlag(OB_RINGTYPES_MOL);
}
bool doBuildMoleculeTest(OBMol &mol)
{
testCount++;
OBBuilder builder;
OB_REQUIRE(builder.Build(mol));
// Does not need clearMolFlags -- crash still happens if you clear here
// and not after AddHydrogens()
OB_REQUIRE(mol.AddHydrogens());
OB_REQUIRE(mol.HasAromaticPerceived() == 0);
OB_REQUIRE(mol.HasSSSRPerceived() == 0);
// clearMolFlags(mol); // must clear here or you crash
// Should now be handled by AddHydrogens()
OBForceField* pff = OBForceField::FindType("mmff94");
OB_REQUIRE(pff != NULL);
cout << mol.GetTitle() << endl;
OB_REQUIRE(pff->Setup(mol));
// Check for explosions -- PR#3016479
pff->SteepestDescent(100);
OB_REQUIRE(!pff->DetectExplosion()); // no explosions please!
return true;
}
bool doMultiMoleculeFile(const std::string &filename)
{
cout << " Starting " << filename << endl;
std::string file = GetFilename(filename);
std::ifstream ifs;
ifs.open(file.c_str());
OB_REQUIRE( ifs );
OBMol mol;
OBConversion conv(&ifs, &cout);
OBFormat *format = conv.FormatFromExt(file.c_str());
OB_REQUIRE(format);
OB_REQUIRE(conv.SetInFormat(format));
bool result = true;
while (conv.Read(&mol, &ifs)) {
bool res = doBuildMoleculeTest(mol);
if (!res)
result = res;
}
return result;
}
bool doSMILESBuilderTest(string smiles)
{
cout << " SMILES " << smiles << endl;
testCount++;
OBMol mol;
OBConversion conv;
OBFormat *smilesFormat = conv.FindFormat("smi");
OB_REQUIRE(smilesFormat);
OB_REQUIRE(conv.SetInFormat(smilesFormat));
OB_REQUIRE(conv.ReadString(&mol, smiles));
OBBuilder builder;
OB_REQUIRE(builder.Build(mol));
return mol.Has3D();
}
int main(int argc, char **argv)
{
// Define location of file formats for testing
#ifdef FORMATDIR
char env[BUFF_SIZE];
snprintf(env, BUFF_SIZE, "BABEL_LIBDIR=%s", FORMATDIR);
putenv(env);
#endif
OB_ASSERT( doMultiMoleculeFile("forcefield.sdf") );
OB_ASSERT( doMultiMoleculeFile("filterset.sdf") );
// fails because of selenium
// OB_ASSERT( doMultiMoleculeFile("aromatics.smi") );
// fails because of stereo crash
// OB_ASSERT( doMultiMoleculeFile("nci.smi") );
// fails because of "organometallic" entries
// OB_ASSERT( doMultiMoleculeFile("attype.00.smi") );
// from Martin Guetlein to mailing list on July 14, 2010
OB_ASSERT( doSMILESBuilderTest("OC1=CC3=C([C@@]2([H])CC[C@@]4(C)[C@](CC[C@@H]4O)([H])[C@@]([H])2[C@H](CCCCCCCCCS(CCCC(F)(F)C(F)(F)F)=O)C3)C=C1") );
// from Thomas Womack -- PR#3016479
OB_ASSERT( doSMILESBuilderTest("O1C[C@H]2O[C@H]2c2ccc(Oc3c(O)ccc(CCC1=O)c3)cc2") );
// from Martin Guetlein -- PR#3107218 ("OBBuilder terminates while building 3d")
OB_ASSERT( doSMILESBuilderTest("N12[C@@H]([C@@H](NC([C@@H](c3ccsc3)C(=O)O)=O)C2=O)SC(C)(C)[C@@-]1C(=O)O") );
cout << "PASSED TESTS: " << testCount - failed << "/" << testCount << endl;
return 0;
}
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