int main(int argc,char **argv)
{
// Create a test molecule
OpenBabel::OBMol mol;
OpenBabel::OBAtom* a[5];
a[0] = mol.NewAtom(); a[0]->SetAtomicNum(6); a[0]->SetVector(-0.013, 1.086, 0.008);
a[1] = mol.NewAtom(); a[1]->SetAtomicNum(1); a[1]->SetVector( 0.002, -0.004, 0.002);
a[2] = mol.NewAtom(); a[2]->SetAtomicNum(9); a[2]->SetVector( 1.300, 1.570, -0.002);
a[3] = mol.NewAtom(); a[3]->SetAtomicNum(35); a[3]->SetVector(-0.964, 1.737, -1.585);
a[4] = mol.NewAtom(); a[4]->SetAtomicNum(17); a[4]->SetVector(-0.857, 1.667, 1.491);
OpenBabel::OBBond* b;
for (int i(1); i < 5; ++i)
{
b = mol.NewBond();
b->SetBegin(a[0]); b->SetEnd(a[i]); b->SetBondOrder(1);
}
// Run the tests
test01(&mol);
test02(&mol);
test03(&mol);
test04(&mol);
test05(&mol);
test06(&mol);
test07(&mol);
test08(&mol);
test09(&mol);
// End
return 0;
}
int spectrophoretest(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;
}
}
// Create a test molecule
OpenBabel::OBMol mol;
OpenBabel::OBAtom* a[5];
a[0] = mol.NewAtom(); a[0]->SetAtomicNum(6); a[0]->SetVector(-0.013, 1.086, 0.008);
a[1] = mol.NewAtom(); a[1]->SetAtomicNum(1); a[1]->SetVector( 0.002, -0.004, 0.002);
a[2] = mol.NewAtom(); a[2]->SetAtomicNum(9); a[2]->SetVector( 1.300, 1.570, -0.002);
a[3] = mol.NewAtom(); a[3]->SetAtomicNum(35); a[3]->SetVector(-0.964, 1.737, -1.585);
a[4] = mol.NewAtom(); a[4]->SetAtomicNum(17); a[4]->SetVector(-0.857, 1.667, 1.491);
OpenBabel::OBBond* b;
for (int i(1); i < 5; ++i)
{
b = mol.NewBond();
b->SetBegin(a[0]); b->SetEnd(a[i]); b->SetBondOrder(1);
}
switch(choice) {
case 1:
test01(&mol);
test02(&mol);
break;
case 2:
test03(&mol);
test04(&mol);
break;
case 3:
test05(&mol);
test06(&mol);
break;
case 4:
test07(&mol);
test08(&mol);
break;
case 5:
test09(&mol);
break;
default:
std::cout << "Test number " << choice << " does not exist!\n";
return -1;
}
return 0;
}
bool
Oprea_1::CalculateScaffold(const OpenBabel::OBMol& mol, Options* o)
{
OpenBabel::OBMol m(mol);
OpenBabel::OBAtom* atom;
OpenBabel::OBAtom* nbrAtom[2];
OpenBabel::OBBondIterator bi;
std::vector<OpenBabel::OBAtom*>::iterator avi;
OpenBabel::OBBond* bond;
std::vector<OpenBabel::OBBond*>::iterator bvi;
bool removed(true);
while (removed)
{
removed = false;
for (atom = m.BeginAtom(avi); atom; atom = m.NextAtom(avi))
{
if (IsEndStanding(atom, false, false))
{
m.DeleteAtom(atom);
removed = true;
break;
}
}
}
// Make all atoms as neutral C and all bond orders equal to 1
m.BeginModify();
for (atom = m.BeginAtom(avi); atom; atom = m.NextAtom(avi))
{
atom->SetAtomicNum(6);
atom->SetFormalCharge(0);
}
for (bond = m.BeginBond(bvi); bond; bond = m.NextBond(bvi))
{
bond->SetBondOrder(1);
}
m.EndModify();
// Transform all neighbouring linker atoms into a single bond
removed = true;
while (removed)
{
removed = false;
for (atom = m.BeginAtom(avi); atom; atom = m.NextAtom(avi))
{
if (!atom->IsInRing() && (atom->GetValence() == 2))
{
nbrAtom[0] = atom->BeginNbrAtom(bi);
nbrAtom[1] = atom->NextNbrAtom(bi);
if (nbrAtom[0] && nbrAtom[1])
{
m.BeginModify();
m.AddBond(nbrAtom[0]->GetIdx(), nbrAtom[1]->GetIdx(), 1);
m.DeleteAtom(atom);
m.EndModify();
removed = true;
break;
}
}
}
}
// Shrink all rings to their minimum size
removed = true;
while (removed)
{
removed = false;
for (atom = m.BeginAtom(avi); atom; atom = m.NextAtom(avi))
{
if ((atom->MemberOfRingSize() > 3) &&
(atom->GetValence() == 2))
{
nbrAtom[0] = atom->BeginNbrAtom(bi);
nbrAtom[1] = atom->NextNbrAtom(bi);
if (nbrAtom[0] && nbrAtom[1])
{
m.BeginModify();
m.AddBond(nbrAtom[0]->GetIdx(), nbrAtom[1]->GetIdx(), 1);
m.DeleteAtom(atom);
m.EndModify();
removed = true;
break;
}
}
}
}
if (!m.Empty())
{
_smiles = _mol2can.WriteString(&m, true);
}
else
{
_smiles = "-";
return false;
}
return true;
}
bool
Oprea_2::CalculateScaffold(const OpenBabel::OBMol& mol, Options* o)
{
OpenBabel::OBMol m(mol);
// Tag all HBD
std::vector<bool> hbd(m.NumAtoms() + 1);
for (OpenBabel::OBMolAtomIter atom(m); atom; ++atom)
{
if (atom->MatchesSMARTS("[NH,NH2,NH3,OH,nH]"))
{
hbd[atom->GetIdx()] = true;
}
else
{
hbd[atom->GetIdx()] = false;
}
}
// Tag all HBA
std::vector<bool> hba(m.NumAtoms() + 1);
for (OpenBabel::OBMolAtomIter atom(m); atom; ++atom)
{
if (!atom->IsAmideNitrogen() && // No amide nitrogen
!atom->IsAromatic() && // Not aromatic
(atom->GetFormalCharge() <= 0) && // No + charge
atom->MatchesSMARTS("[NH0]")) // No hydrogens
{
hba[atom->GetIdx()] = true;
}
else
if (atom->IsNitrogen() && // Nitrogen
atom->IsAromatic() && // Aromatic
atom->MatchesSMARTS("[nH0]") && // No hydrogens
(atom->GetHvyValence() <= 2) && // Maximal two non-H atoms connected
(atom->GetFormalCharge() <= 0)) // No + charge
{
hba[atom->GetIdx()] = true;
}
else
if (atom->IsOxygen() && // Oxygen
(atom->GetFormalCharge() <= 0)) // No + charge
{
hba[atom->GetIdx()] = true;
}
else
{
hba[atom->GetIdx()] = false;
}
}
// Mark the C(=O) or S(=O) also as HBA
for (OpenBabel::OBMolAtomIter atom(m); atom; ++atom)
{
if (atom->MatchesSMARTS("C=O"))
{
hba[atom->GetIdx()] = true;
}
else
if (atom->MatchesSMARTS("S=O"))
{
hba[atom->GetIdx()] = true;
}
}
// Make all atoms as neutral C, N (HBD), or O (HBA)
m.BeginModify();
std::vector<OpenBabel::OBAtom*>::iterator avi;
OpenBabel::OBAtom* atom;
for (atom = m.BeginAtom(avi); atom; atom = m.NextAtom(avi))
{
if (hba[atom->GetIdx()])
{
atom->SetAtomicNum(8);
}
else
if (hbd[atom->GetIdx()])
{
atom->SetAtomicNum(7);
}
else
{
atom->SetAtomicNum(6);
}
atom->SetFormalCharge(0);
}
m.EndModify();
// Remove all endstanding atoms
OpenBabel::OBBondIterator bi;
OpenBabel::OBBond* bond;
std::vector<OpenBabel::OBBond*>::iterator bvi;
bool removed(true);
while (removed)
{
removed = false;
for (atom = m.BeginAtom(avi); atom; atom = m.NextAtom(avi))
{
if (IsEndStanding(atom, false, false))
{
m.DeleteAtom(atom);
removed = true;
break;
}
}
}
// Set all bond orders equal to 1
m.BeginModify();
for (bond = m.BeginBond(bvi); bond; bond = m.NextBond(bvi))
{
bond->SetBondOrder(1);
}
m.EndModify();
// Transform all neighbouring linker atoms into a single bond
removed = true;
OpenBabel::OBAtom* nbrAtom[2];
while (removed)
{
removed = false;
for (atom = m.BeginAtom(avi); atom; atom = m.NextAtom(avi))
{
if (!atom->IsInRing() && (atom->GetValence() == 2))
{
m.BeginModify();
nbrAtom[0] = atom->BeginNbrAtom(bi);
nbrAtom[1] = atom->NextNbrAtom(bi);
if (nbrAtom[0] && nbrAtom[1])
{
m.AddBond(nbrAtom[0]->GetIdx(), nbrAtom[1]->GetIdx(), 1);
m.DeleteAtom(atom);
m.EndModify();
removed = true;
break;
}
}
}
}
// Shrink all rings to their minimum size
removed = true;
while (removed)
{
removed = false;
for (atom = m.BeginAtom(avi); atom; atom = m.NextAtom(avi))
{
if ((atom->MemberOfRingSize() > 3) && (atom->GetValence() == 2))
{
nbrAtom[0] = atom->BeginNbrAtom(bi);
nbrAtom[1] = atom->NextNbrAtom(bi);
if (nbrAtom[0] && nbrAtom[1])
{
if (nbrAtom[0]->GetAtomicNum() == atom->GetAtomicNum())
{
m.BeginModify();
m.AddBond(nbrAtom[0]->GetIdx(), nbrAtom[1]->GetIdx(), 1);
m.DeleteAtom(atom);
m.EndModify();
removed = true;
break;
}
else
if (nbrAtom[1]->GetAtomicNum() == atom->GetAtomicNum())
{
m.BeginModify();
m.AddBond(nbrAtom[0]->GetIdx(), nbrAtom[1]->GetIdx(), 1);
m.DeleteAtom(atom);
m.EndModify();
removed = true;
break;
}
}
}
}
}
if (!m.Empty())
{
_smiles = _mol2can.WriteString(&m, true);
}
else
{
_smiles = "-";
return false;
}
return true;
}
OpenBabel::OBMol
Schuffenhauer::RemoveRing(OpenBabel::OBMol& oldMol,
std::vector<OpenBabel::OBRing*>& rings, unsigned int ringIdx)
{
OpenBabel::OBMol newMol(oldMol);
// Make list of the ring bonds
std::set<OpenBabel::OBBond*> ringBonds;
OpenBabel::OBBond* bond;
std::vector<OpenBabel::OBBond*>::iterator bvi;
for (bond = newMol.BeginBond(bvi); bond; bond = newMol.NextBond(bvi))
{
if (rings[ringIdx]->IsMember(bond))
{
ringBonds.insert(bond);
}
}
// Make list of delocalizable bonds (aromatic, single and flanked by two double bonds)
std::set<OpenBabel::OBBond*> delocalizableBonds;
std::set<OpenBabel::OBBond*>::iterator bli;
OpenBabel::OBBondIterator bi;
OpenBabel::OBAtom* atom;
OpenBabel::OBBond* nbrBond;
unsigned int n;
for (bli = ringBonds.begin(); bli != ringBonds.end(); ++bli)
{
bond = *bli;
if ((bond->GetBondOrder() == 1) &&
bond->IsAromatic())
{
n = 0;
atom = bond->GetBeginAtom();
for (nbrBond = atom->BeginBond(bi); nbrBond; nbrBond = atom->NextBond(bi))
{
if ((nbrBond != bond) &&
ringBonds.count(nbrBond) &&
(nbrBond->GetBondOrder() == 2))
{
++n;
}
}
atom = bond->GetEndAtom();
for (nbrBond = atom->BeginBond(bi); nbrBond; nbrBond = atom->NextBond(bi))
{
if ((nbrBond != bond) &&
ringBonds.count(nbrBond) &&
(nbrBond->GetBondOrder() == 2))
{
++n;
}
}
}
if (n == 2)
{
delocalizableBonds.insert(bond);
}
}
// Make list of bonds which form the fusion with other rings
std::set<OpenBabel::OBBond*> fusionBonds;
for (bli = ringBonds.begin(); bli != ringBonds.end(); ++bli)
{
bond = *bli;
for (unsigned int i(0); i < rings.size(); ++i)
{
if (i != ringIdx)
{
if (rings[i]->IsMember(bond))
{
fusionBonds.insert(bond);
}
}
}
}
// Make list of bonds which are the fusion between aromatic and non-aromatic
std::set<OpenBabel::OBBond*> aromaticNonaromaticFusionBonds;
if (rings[ringIdx]->IsAromatic())
{
for (bli = fusionBonds.begin(); bli != fusionBonds.end(); ++bli)
{
bond = *bli;
for (unsigned int i(0); i < rings.size(); ++i)
{
if (i != ringIdx)
{
if (rings[i]->IsMember(bond) &&
!rings[i]->IsAromatic())
{
aromaticNonaromaticFusionBonds.insert(bond);
}
}
}
}
}
// Make list of bonds which are the fusion between aromatic and aromatic
std::set<OpenBabel::OBBond*> aromaticAromaticFusionBonds;
if (rings[ringIdx]->IsAromatic())
{
for (bli = fusionBonds.begin(); bli != fusionBonds.end(); ++bli)
{
bond = *bli;
for (unsigned int i(0); i < rings.size(); ++i)
{
if (i != ringIdx)
{
if (rings[i]->IsMember(bond) &&
rings[i]->IsAromatic())
{
aromaticAromaticFusionBonds.insert(bond);
}
}
}
}
}
// Remove ring
std::set<OpenBabel::OBBond*> bondsToBeDeleted;
std::set<OpenBabel::OBAtom*> atomsToBeDeleted;
OpenBabel::OBAtom* nbrAtom[2];
for (bli = ringBonds.begin(); bli != ringBonds.end(); ++bli)
{
bond = *bli;
if (fusionBonds.count(bond))
{
continue;
}
else
{
bondsToBeDeleted.insert(bond);
nbrAtom[0] = bond->GetBeginAtom();
nbrAtom[1] = bond->GetEndAtom();
if (nbrAtom[0] && nbrAtom[1])
{
if (nbrAtom[0]->MemberOfRingCount() == 1)
{
atomsToBeDeleted.insert(nbrAtom[0]);
}
if (nbrAtom[1]->MemberOfRingCount() == 1)
{
atomsToBeDeleted.insert(nbrAtom[1]);
}
}
}
}
newMol.BeginModify();
for (bli = bondsToBeDeleted.begin(); bli != bondsToBeDeleted.end(); ++bli)
{
newMol.DeleteBond(*bli);
}
newMol.EndModify();
newMol.BeginModify();
std::set<OpenBabel::OBAtom*>::iterator ali;
for (ali = atomsToBeDeleted.begin(); ali != atomsToBeDeleted.end(); ++ali)
{
newMol.DeleteAtom(*ali);
}
newMol.EndModify();
// Correct the bond orders of the ex-fusion bond(s)
newMol.BeginModify();
for (bond = newMol.BeginBond(bvi); bond; bond = newMol.NextBond(bvi))
{
if (aromaticNonaromaticFusionBonds.count(bond))
{
bond->SetBondOrder(2);
}
else
if (aromaticAromaticFusionBonds.count(bond) &&
delocalizableBonds.count(bond))
{
bond->SetBondOrder(2);
}
}
newMol.EndModify();
// Remove single atoms that originate from exocyclic bonds at ring
(void) RemoveSidechains(&newMol);
// Check if there are atoms with valences that are not allowed
std::vector<OpenBabel::OBAtom*>::iterator avi;
for (atom = newMol.BeginAtom(avi); atom; atom = newMol.NextAtom(avi))
{
if (atom->IsCarbon() &&
(atom->BOSum() > 4))
{
newMol.Clear();
break;
}
else
if (atom->IsNitrogen() &&
(atom->BOSum() > 3))
{
newMol.Clear();
break;
}
else
if (atom->IsOxygen() &&
(atom->BOSum() > 2))
{
newMol.Clear();
break;
}
}
// Check if there are no discontinuous fragments
if (newMol.Separate().size() > 1)
{
newMol.Clear();
}
return newMol;
}