bool OBChemTsfm::Apply(OBMol &mol)
{
if (!_bgn.Match(mol))
return(false);
mol.BeginModify();
vector<vector<int> > mlist = _bgn.GetUMapList();
obErrorLog.ThrowError(__FUNCTION__,
"Ran OpenBabel::OBChemTransform", obAuditMsg);
if (!_vchrg.empty()) //modify charges
{
vector<vector<int> >::iterator i;
vector<pair<int,int> >::iterator j;
for (i = mlist.begin();i != mlist.end();++i)
for (j = _vchrg.begin();j != _vchrg.end();++j)
if (j->first < (signed)i->size()) { //goof proofing
OBAtom *atom = mol.GetAtom((*i)[j->first]);
int old_charge = atom->GetFormalCharge();
atom->SetFormalCharge(j->second);
int new_hcount = atom->GetImplicitHCount() + (j->second - old_charge);
if (new_hcount < 0)
new_hcount = 0;
atom->SetImplicitHCount(new_hcount);
}
}
if (!_vbond.empty()) //modify bond orders
{
OBBond *bond;
vector<vector<int> >::iterator i;
vector<pair<pair<int,int>,int> >::iterator j;
for (i = mlist.begin();i != mlist.end();++i)
for (j = _vbond.begin();j != _vbond.end();++j)
{
bond = mol.GetBond((*i)[j->first.first],(*i)[j->first.second]);
if (!bond)
{
obErrorLog.ThrowError(__FUNCTION__, "unable to find bond", obDebug);
continue;
}
unsigned int old_bond_order = bond->GetBondOrder();
bond->SetBondOrder(j->second);
for (int k = 0; k < 2; ++k) {
OBAtom* atom = k == 0 ? bond->GetBeginAtom() : bond->GetEndAtom();
int new_hcount = atom->GetImplicitHCount() - (j->second - old_bond_order);
if (new_hcount < 0)
new_hcount = 0;
atom->SetImplicitHCount(new_hcount);
}
}
}
if (!_vadel.empty() || !_vele.empty()) //delete atoms and change elements
{
vector<int>::iterator j;
vector<vector<int> >::iterator i;
if (!_vele.empty())
{
vector<pair<int,int> >::iterator k;
for (i = mlist.begin();i != mlist.end();++i)
for (k = _vele.begin();k != _vele.end();++k)
mol.GetAtom((*i)[k->first])->SetAtomicNum(k->second);
}
//make sure same atom isn't deleted twice
vector<bool> vda;
vector<OBAtom*> vdel;
vda.resize(mol.NumAtoms()+1,false);
for (i = mlist.begin();i != mlist.end();++i)
for (j = _vadel.begin();j != _vadel.end();++j)
if (!vda[(*i)[*j]])
{
vda[(*i)[*j]] = true;
vdel.push_back(mol.GetAtom((*i)[*j]));
}
vector<OBAtom*>::iterator k;
for (k = vdel.begin();k != vdel.end();++k)
mol.DeleteAtom((OBAtom*)*k);
}
mol.EndModify();
return(true);
}
int mol(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
cout << "# Unit tests for OBMol \n";
cout << "ok 1\n"; // for loading tests
OBMol emptyMol, testMol1;
cout << "ok 2\n"; // ctor works
testMol1.ReserveAtoms(-1);
testMol1.ReserveAtoms(0);
testMol1.ReserveAtoms(2);
cout << "ok 3\n";
// atom component tests
if (testMol1.NumAtoms() == 0) {
cout << "ok 4\n";
} else {
cout << "not ok 4\n";
}
testMol1.NewAtom();
if (testMol1.NumAtoms() == 1) {
cout << "ok 5\n";
} else {
cout << "not ok 5\n";
}
testMol1.NewAtom();
testMol1.AddBond(1, 2, 1);
if (testMol1.NumBonds() == 1) {
cout << "ok 6\n";
} else {
cout << "not ok 6\n";
}
testMol1.Clear();
if (testMol1.NumAtoms() == 0) {
cout << "ok 7\n";
} else {
cout << "not ok 7\n";
}
ifstream ifs1(kd3file.c_str());
if (!ifs1)
{
cout << "Bail out! Cannot read input file!" << endl;
return(-1);
}
OBConversion conv(&ifs1, &cout);
OBFormat* pFormat;
pFormat = conv.FindFormat("XYZ");
if ( pFormat == NULL )
{
cout << "Bail out! Cannot read file format!" << endl;
return(-1);
}
if (! conv.SetInAndOutFormats(pFormat, pFormat))
{
cout << "Bail out! File format isn't loaded" << endl;
return (-1);
}
OBMol testMol2D, testMol3D;
if (conv.Read(&testMol3D))
cout << "ok 8\n";
else
cout << "not ok 8\n";
testMol3D.Center();
// test bond insertion (PR#1665649)
OBMol doubleBondMol;
OBAtom *a1, *a2;
OBBond *b;
doubleBondMol.BeginModify();
a1 = doubleBondMol.NewAtom();
a1->SetVector(0.0, 0.0, 0.0);
a1->SetAtomicNum(6);
a2 = doubleBondMol.NewAtom();
a2->SetVector(1.6, 0.0, 0.0);
a2->SetAtomicNum(6);
b = doubleBondMol.NewBond();
b->SetBegin(a1);
b->SetEnd(a2);
a1->AddBond(b);
a2->AddBond(b);
doubleBondMol.EndModify();
cout << "ok 9" << endl;
// test AddHydrogens
OBMol testMolH;
testMolH.BeginModify();
OBAtom *testAtom = testMolH.NewAtom();
testAtom->SetVector(0.5f, 0.5f, 0.5f);
testAtom->SetAtomicNum(6);
testAtom->SetImplicitHCount(4);
testMolH.EndModify();
testMolH.AddHydrogens();
if (testMolH.NumAtoms() == 5) {
cout << "ok 10" << endl;
} else {
cout << "not ok 10" << endl;
}
// test AddHydrogens (pr #1665519)
OBMol testMolH2;
OBAtom *testAtom2 = testMolH2.NewAtom();
testAtom2->SetVector(0.5f, 0.5f, 0.5f);
testAtom2->SetAtomicNum(6);
testAtom2->SetImplicitHCount(4);
testMolH2.AddHydrogens();
if (testMolH2.NumAtoms() == 5) {
cout << "ok 11" << endl;
} else {
cout << "not ok 11 # hydrogen additions" << endl;
}
// Attempt to write an empty InChI (PR#2864334)
pFormat = conv.FindFormat("InChI");
if ( pFormat != NULL && conv.SetOutFormat(pFormat))
{
if (conv.Write(&emptyMol))
cout << "ok 12" << endl;
else
cout << "not ok 12 # failed empty InChI" << endl;
}
OBMol testMolFormula;
string formula("C6");
testMolFormula.SetFormula(formula);
if ( testMolFormula.GetFormula() == formula ) {
cout << "ok 13" << endl;
} else {
cout << "not ok 13 # SetFormula "<< endl;
}
// Reset the formula to test for a double delete error
testMolFormula.SetFormula(formula);
// Test molecular formulas with large atomic numbers
OBMol testLgAtNo;
testLgAtNo.BeginModify();
OBAtom *lgAtom = testLgAtNo.NewAtom();
lgAtom->SetAtomicNum(118);
// Undefined atomic numbers should be ignored with an obWarning instead of segfault
lgAtom = testLgAtNo.NewAtom();
lgAtom->SetAtomicNum(200);
lgAtom = testLgAtNo.NewAtom();
lgAtom->SetAtomicNum(1);
lgAtom->SetIsotope(2);
testLgAtNo.EndModify();
if ( testLgAtNo.GetFormula() == "DOg" ) {
cout << "ok 14" << endl;
} else {
cout << "not ok 14" << endl;
}
double dihedral = CalcTorsionAngle(vector3(-1., -1., 0.),
vector3(-1., 0., 0.),
vector3( 1., 0., 0.),
vector3( 1., 1., 0.));
double dihedral_error = fabs(dihedral) - 180.0;
if (fabs(dihedral_error) < 0.001) {
std::cout << "ok 15 " << dihedral_error << std::endl;
} else {
std::cout << "not ok 15 # CalcTorsionAngle " << dihedral << "!= 180.0" << std::endl;
}
cout << "1..15\n"; // total number of tests for Perl's "prove" tool
return(0);
}
