Coordinate
_hDonCalcNormal(OpenBabel::OBAtom* a)
{
int nbrBonds(0);
Coordinate normal;
std::vector<OpenBabel::OBBond*>::iterator bi;
for (OpenBabel::OBBond* b = a->BeginBond(bi); b; b = a->NextBond(bi))
{
OpenBabel::OBAtom* aa = b->GetNbrAtom(a);
if (aa->GetAtomicNum() == 1)
{
continue;
}
++nbrBonds;
normal.x += (aa->x() - a->x());
normal.y += (aa->y() - a->y());
normal.z += (aa->z() - a->z());
}
double length(sqrt(normal.x*normal.x + normal.y*normal.y + normal.z*normal.z));
normal.x /= length;
normal.y /= length;
normal.z /= length;
normal.x = -normal.x;
normal.y = -normal.y;
normal.z = -normal.z;
normal.x += a->x();
normal.y += a->y();
normal.z += a->z();
return normal;
}
void
FilterRings::Calculate(OpenBabel::OBMol* mol)
{
// Are there rings?
bool rings(false);
OpenBabel::OBAtom* atom;
std::vector<OpenBabel::OBAtom*>::iterator i;
for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i))
{
if (atom->IsInRing())
{
rings = true;
break;
}
}
if (rings)
{
std::vector<OpenBabel::OBRing* > nrings = mol->GetSSSR();
_result = nrings.size();
}
else
{
_result = 0;
}
if ((_minLimit && (_result < _min)) || (_maxLimit && (_result > _max)))
{
_passed = false;
}
else
{
_passed = true;
}
}
extern "C" int write_output_(char *out_filename, double *A, int *n)
{
std::ofstream ofs(out_filename);
OpenBabel::OBConversion ob(NULL, &ofs);
OpenBabel::OBAtom atom;
OpenBabel::OBMol mol;
int i;
ob.SetOutFormat("CML");
/* Atom is Iridium */
atom.SetAtomicNum(77);
for (i = 0; i < *n; i++)
{
atom.SetVector(A[i*3], A[i*3+1], A[i*3+2]);
mol.AddAtom(atom);
}
//for (i=0; i < *n; i++)
//{
//for (int j=i; j < *n; j++)
//{
//mol.AddBond(i+1, j+1, 0);
//}
//}
ob.Write(&mol);
ob.CloseOutFile();
}
void
FilterNonaromaticRingFraction::Calculate(OpenBabel::OBMol* mol)
{
// Are there atoms and rings?
unsigned int rings(0);
unsigned int natoms(0);
OpenBabel::OBAtom* atom;
std::vector<OpenBabel::OBAtom*>::iterator i;
for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i))
{
if (atom->IsHydrogen()) continue;
if (atom->IsInRing()) ++rings;
++natoms;
}
if (!natoms)
{
_result = 0.0;
_passed = false;
return;
}
std::set<int> uniqRingIdx;
if (rings)
{
std::vector<OpenBabel::OBRing*> nrings = mol->GetSSSR();
uniqRingIdx.clear();
std::vector<int>::iterator path;
std::vector<OpenBabel::OBRing*>::iterator ri;
for (ri = nrings.begin(); ri != nrings.end(); ++ri)
{
if (!(*ri)->IsAromatic())
{
for (path = (*ri)->_path.begin(); path != (*ri)->_path.end(); ++path)
{
uniqRingIdx.insert(*path);
}
}
}
}
unsigned int ar(uniqRingIdx.size());
if (ar)
{
_result = (double) ar / (double) natoms;
}
else
{
_result = 0.0;
}
if ((_minLimit && (_result < _min)) || (_maxLimit && (_result > _max)))
{
_passed = false;
}
else
{
_passed = true;
}
}
void
FilterCores::Calculate(OpenBabel::OBMol* mol)
{
// Any rings?
OpenBabel::OBAtom* atom;
std::vector<OpenBabel::OBAtom*>::iterator i;
bool rings(false);
for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i))
{
if (atom->IsInRing())
{
rings = true;
break;
}
}
if (rings)
{
// Make workcopy of original mol
OpenBabel::OBMol m = *mol; m.DeleteHydrogens();
// Iteratively remove all endstanding atoms until none are left
OpenBabel::OBAtom* atom;
std::vector<OpenBabel::OBAtom*>::iterator i;
bool endstanding(true);
while (endstanding && m.NumAtoms())
{
endstanding = false;
for (atom = m.BeginAtom(i); atom; atom = m.NextAtom(i))
{
if (atom->GetValence() < 2)
{
if (m.DeleteAtom(atom))
{
endstanding = true;
break;
}
}
}
}
if (m.NumAtoms()) _result = 1;
else _result = 0;
}
else
{
_result = 0;
}
if ((_minLimit && (_result < _min)) || (_maxLimit && (_result > _max)))
{
_passed = false;
}
else
{
_passed = true;
}
}
void ReadFileThread::detectConformers(unsigned int c,
const OpenBabel::OBMol &first,
const OpenBabel::OBMol ¤t)
{
if (!c) {
// this is the first molecule read
m_moleculeFile->setConformerFile(true);
addConformer(current);
return;
}
if (!m_moleculeFile->isConformerFile())
return;
// as long as we are not sure if this really is a
// conformer/trajectory file, add the conformers
addConformer(current);
// performance: check only certain molecule 1-10,20,50
switch (c) {
case 1:
case 2:
case 3:
case 4:
case 5:
case 6:
case 7:
case 8:
case 9:
case 10:
case 20:
case 50:
break;
default:
return;
}
if (first.NumAtoms() != current.NumAtoms()) {
m_moleculeFile->setConformerFile(false);
m_moleculeFile->m_conformers.clear();
return;
}
for (unsigned int i = 0; i < first.NumAtoms(); ++i) {
OpenBabel::OBAtom *firstAtom = first.GetAtom(i+1);
OpenBabel::OBAtom *currentAtom = current.GetAtom(i+1);
if (firstAtom->GetAtomicNum() != currentAtom->GetAtomicNum()) {
m_moleculeFile->setConformerFile(false);
m_moleculeFile->m_conformers.clear();
return;
}
}
}
void StereoCenterItem::paint(QPainter *painter, const QStyleOptionGraphicsItem *option, QWidget *widget)
{
Molecule *mol = molecule();
painter->save();
painter->setPen(Qt::green);
if (!mol) {
// not connected: default behaviour (draw connectable box)
MolInputItem::paint(painter, option, widget);
painter->restore();
return;
}
const QList<Atom*> &atoms = mol->atoms();
OpenBabel::OBMol *obmol = mol->OBMol();
QPointF offset(-5.0, 5.0);
#ifdef OPENBABEL2_TRUNK
// need to calculate symmetry first
std::vector<unsigned int> symmetry_classes;
OpenBabel::OBGraphSym graphsym(obmol);
graphsym.GetSymmetry(symmetry_classes);
//std::vector<unsigned long> atomIds = FindTetrahedralAtoms(obmol, symmetry_classes);
std::vector<OpenBabel::StereogenicUnit> units = FindStereogenicUnits(obmol, symmetry_classes);
for (unsigned int i = 0; i < units.size(); ++i) {
if (units.at(i).type == OpenBabel::OBStereo::Tetrahedral) {
OpenBabel::OBAtom *obatom = obmol->GetAtomById(units.at(i).id);
painter->drawEllipse(mapFromItem(mol, atoms[obatom->GetIndex()]->pos()), 10, 10);
} else
if (units.at(i).type == OpenBabel::OBStereo::CisTrans) {
OpenBabel::OBBond *obbond = obmol->GetBondById(units.at(i).id);
OpenBabel::OBAtom *obatom1 = obbond->GetBeginAtom();
OpenBabel::OBAtom *obatom2 = obbond->GetEndAtom();
painter->drawEllipse(mapFromItem(mol, atoms[obatom1->GetIndex()]->pos()), 10, 10);
painter->drawEllipse(mapFromItem(mol, atoms[obatom2->GetIndex()]->pos()), 10, 10);
}
}
#else
using OpenBabel::OBMolAtomIter;
FOR_ATOMS_OF_MOL(atom, obmol)
if (atom->IsChiral())
painter->drawEllipse(mapFromItem(mol, atoms[atom->GetIdx()-1]->pos()), 10, 10);
#endif
// default behavious (draw the label())
MolInputItem::paint(painter, option, widget);
painter->restore();
}
std::list<OpenBabel::OBAtom*>
_hAccGetNeighbors(OpenBabel::OBAtom* a)
{
std::list<OpenBabel::OBAtom*> aList;
OpenBabel::OBMol* parent(a->GetParent());
double r;
OpenBabel::OBElementTable et;
std::vector<OpenBabel::OBAtom*>::iterator ai;
for (OpenBabel::OBAtom* aa = parent->BeginAtom(ai); aa; aa = parent->NextAtom(ai))
{
if (*aa == a)
{
continue;
}
r = et.GetVdwRad(aa->GetAtomicNum());
double delta(H_BOND_DIST + H_RADIUS + r);
double maxDistSq(delta*delta);
double distSq((a->x() - aa->x()) * (a->x() - aa->x()) +
(a->y() - aa->y()) * (a->y() - aa->y()) +
(a->z() - aa->z()) * (a->z() - aa->z()));
if (distSq <= maxDistSq)
{
aList.push_back(aa);
}
}
return aList;
}
OpenBabel::OBMol
Schuffenhauer::Rule_1(OpenBabel::OBMol& oldMol)
{
if (oldMol.GetSSSR().size() <= _ringsToBeRetained)
{
return oldMol;
}
OpenBabel::OBMol newMol(oldMol);
std::vector<OpenBabel::OBAtom*>::iterator avi;
OpenBabel::OBBondIterator bi;
OpenBabel::OBAtom* atom;
OpenBabel::OBAtom* nbrAtom[2];
for (atom = newMol.BeginAtom(avi); atom; atom = newMol.NextAtom(avi))
{
if ((atom->MemberOfRingSize() == 3) &&
(atom->IsNitrogen() || atom->IsOxygen()) &&
(atom->MemberOfRingCount() == 1) &&
(atom->GetHvyValence() == 2))
{
nbrAtom[0] = atom->BeginNbrAtom(bi);
nbrAtom[1] = atom->NextNbrAtom(bi);
if (nbrAtom[0] && nbrAtom[1])
{
newMol.DeleteAtom(atom);
newMol.GetBond(nbrAtom[0], nbrAtom[1])->SetBondOrder(2);
}
}
}
return newMol;
}
void
Fingerprint::_getFragments(std::vector<int> levels, std::vector<int>curfrag,
int level, OpenBabel::OBAtom* patom, OpenBabel::OBBond* pbond)
{
const int MaxFragSize = 7;
int bo(0);
if (pbond) bo = pbond->IsAromatic() ? 5 : pbond->GetBondOrder();
curfrag.push_back(bo);
curfrag.push_back(patom->GetAtomicNum());
levels[patom->GetIdx()] = level;
std::vector<OpenBabel::OBBond*>::iterator i;
OpenBabel::OBBond* pnewbond;
for (pnewbond = patom->BeginBond(i); pnewbond; pnewbond = patom->NextBond(i))
{
if (pnewbond == pbond)
{
continue;
}
OpenBabel::OBAtom* pnxtat = pnewbond->GetNbrAtom(patom);
int atlevel = levels[pnxtat->GetIdx()];
if (atlevel)
{
if (atlevel == 1)
{
curfrag[0] = bo;
_ringset.insert(curfrag);
}
}
else
{
if (level < MaxFragSize)
{
_getFragments(levels, curfrag, level + 1, pnxtat, pnewbond);
}
}
}
if ((curfrag[0] == 0) &&
((level > 1) || (patom->GetAtomicNum() > 8) || (patom->GetAtomicNum() < 6)))
{
_fragset.insert(curfrag);
}
}
void
hAccFuncCalc(OpenBabel::OBMol* mol, Pharmacophore* pharmacophore)
{
// Create for every hydrogen acceptor a pharmacophore point
std::vector<OpenBabel::OBAtom*>::iterator ai;
for (OpenBabel::OBAtom* atom = mol->BeginAtom(ai); atom; atom = mol->NextAtom(ai))
{
if (atom->GetAtomicNum() == 7 || atom->GetAtomicNum() == 8)
{
if (atom->GetFormalCharge() <= 0)
{
if(_hAccDelocalized(atom) || (_hAccCalcAccSurf(atom) < 0.02))
{
continue;
}
PharmacophorePoint p;
p.func = HACC;
p.point.x = atom->x();
p.point.y = atom->y();
p.point.z = atom->z();
p.hasNormal = true;
p.alpha = funcSigma[HACC];
p.normal = _hAccCalcNormal(atom);
pharmacophore->push_back(p);
}
}
}
}
//--
// [rad] generate path and ident for bond
void RelationBond::GetPathAndIdentBond(const std::string& refMoleculeId, std::string& refPath, std::string& refIdent)
{
refPath = m_vecSatisfiedClasses.front()->GetPrefix() + ":" + m_vecSatisfiedClasses.front()->GetName();
std::stringstream ssConv;
OpenBabel::OBBond* pBond = m_pBond;
OpenBabel::OBAtom* pAtomStart = pBond->GetBeginAtom();
OpenBabel::OBAtom* pAtomEnd = pBond->GetEndAtom();
ssConv << m_vecSatisfiedClasses.front()->GetName() << "_" << refMoleculeId << "_" <<
pAtomStart->GetIdx() << "_" << pAtomEnd->GetIdx();
refIdent = "";
ssConv >> refIdent;
}
void
FilterAtomsInLargestNonaromaticRing::Calculate(OpenBabel::OBMol* mol)
{
// Are there rings?
bool rings(false);
OpenBabel::OBAtom* atom;
std::vector<OpenBabel::OBAtom*>::iterator i;
for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i))
{
if (atom->IsInRing())
{
rings = true;
break;
}
}
if (rings)
{
std::vector<OpenBabel::OBRing*> nrings = mol->GetSSSR();
_result = 0;
std::vector<OpenBabel::OBRing*>::iterator ri;
for (ri = nrings.begin(); ri != nrings.end(); ++ri)
{
if ( !(*ri)->IsAromatic() && ((*ri)->Size() > _result))
{
_result = (*ri)->Size();
}
}
if ((_minLimit && (_result < _min)) || (_maxLimit && (_result > _max)))
{
_passed = false;
}
else
{
_passed = true;
}
}
else
{
_result = 0;
_passed = true;
}
}
// [rad] generate path and ident for bond
void RelationBond::GetObjectPropertyPathAndIdentBond(int iPosition,
const std::string& refMoleculeId,
std::string& refPath,
std::string& refIdent)
{
refPath = m_vecSatisfiedObjectPropertiesBond[iPosition].first->GetPrefix() + ":" +
m_vecSatisfiedObjectPropertiesBond[iPosition].first->GetName();
std::stringstream ssConv;
OpenBabel::OBAtom* pAtomStart = m_vecSatisfiedObjectPropertiesBond[iPosition].second->m_pBond->GetBeginAtom();
OpenBabel::OBAtom* pAtomEnd = m_vecSatisfiedObjectPropertiesBond[iPosition].second->m_pBond->GetEndAtom();
ssConv << m_vecSatisfiedObjectPropertiesBond[iPosition].second->m_vecSatisfiedClasses.front()->GetName() << "_" << refMoleculeId << "_" <<
pAtomStart->GetIdx() << "_" << pAtomEnd->GetIdx();
refIdent = "";
ssConv >> refIdent;
}
unsigned int
Schuffenhauer::CalculateHeteroAtoms(OpenBabel::OBMol& mol, OpenBabel::OBRing* ring, int a = 0)
{
unsigned int n(0);
OpenBabel::OBAtom* atom;
std::vector<OpenBabel::OBAtom*>::iterator avi;
for (atom = mol.BeginAtom(avi); atom; atom = mol.NextAtom(avi))
{
if (ring->IsMember(atom) && (atom->GetAtomicNum() == a))
{
++n;
}
if (!a && ring->IsMember(atom))
{
if ((atom->GetAtomicNum() == 7) ||
(atom->GetAtomicNum() == 8) ||
(atom->GetAtomicNum() == 16))
{
++n;
}
}
}
return n;
}
void
hDonFuncCalc(OpenBabel::OBMol* mol, Pharmacophore* pharmacophore)
{
// Create for every hydrogen donor a pharmacophore point
std::vector<OpenBabel::OBAtom*>::iterator ai;
for (OpenBabel::OBAtom* a = mol->BeginAtom(ai); a; a = mol->NextAtom(ai))
{
if (a->GetAtomicNum() == 7 || a->GetAtomicNum() == 8)
{
if (a->GetFormalCharge() >= 0 && ((a->GetImplicitValence() - a->GetHvyValence()) !=0))
{
PharmacophorePoint p;
p.func = HDON;
p.point.x = a->x();
p.point.y = a->y();
p.point.z = a->z();
p.hasNormal = true;
p.alpha = funcSigma[HDON];
p.normal = _hDonCalcNormal(a);
pharmacophore->push_back(p);
}
}
}
}
static int extract_thermo(OpenBabel::OBMol *mol,string method,double temperature,
double ezpe,double Hcorr,double Gcorr,double E0,double CV,
int RotSymNum,std::vector<double> Scomponents)
{
// Initiate correction database
OpenBabel::OBAtomicHeatOfFormationTable *ahof = new OpenBabel::OBAtomicHeatOfFormationTable();
OpenBabel::OBAtomIterator OBai;
OpenBabel::OBAtom *OBa;
OpenBabel::OBElementTable *OBet;
char valbuf[128];
int ii,atomid,atomicnumber,found,foundall;
double dhofM0, dhofMT, S0MT, DeltaSMT;
double eFactor = HARTEE_TO_KCALPERMOL;
OBet = new OpenBabel::OBElementTable();
// Now loop over atoms in order to correct the Delta H formation
OBai = mol->BeginAtoms();
atomid = 0;
foundall = 0;
dhofM0 = E0*eFactor;
dhofMT = dhofM0+(Hcorr-ezpe)*eFactor;
S0MT = 0;
if (temperature > 0)
{
// Multiply by 1000 to make the unit cal/mol K
S0MT += 1000*eFactor*(Hcorr-Gcorr)/temperature;
}
// Check for symmetry
OBPointGroup obPG;
obPG.Setup(mol);
const char *pg = obPG.IdentifyPointGroup();
double Rgas = 1.9872041; // cal/mol K http://en.wikipedia.org/wiki/Gas_constant
double Srot = -Rgas * log(RotSymNum);
//printf("DHf(M,0) = %g, DHf(M,T) = %g, S0(M,T) = %g\nPoint group = %s RotSymNum = %d Srot = %g\n",
// dhofM0, dhofMT, S0MT, pg, RotSymNum, Srot);
if (RotSymNum > 1)
{
// We assume Gaussian has done this correctly!
Srot = 0;
}
S0MT += Srot;
DeltaSMT = S0MT;
for (OBa = mol->BeginAtom(OBai); (NULL != OBa); OBa = mol->NextAtom(OBai))
{
double dhfx0, dhfxT, S0xT;
atomicnumber = OBa->GetAtomicNum();
found = ahof->GetHeatOfFormation(OBet->GetSymbol(atomicnumber),
0,
method,
temperature,
&dhfx0, &dhfxT, &S0xT);
if (1 == found)
{
dhofM0 += dhfx0;
dhofMT += dhfxT;
DeltaSMT += S0xT;
foundall ++;
}
atomid++;
}
if (foundall == atomid)
{
std::string attr[5];
double result[5];
char buf[32];
attr[0].assign("DeltaHform(0K)");
result[0] = dhofM0;
snprintf(buf, sizeof(buf), "DeltaHform(%gK)", temperature);
attr[1].assign(buf);
result[1] = dhofMT;
snprintf(buf, sizeof(buf), "DeltaSform(%gK)", temperature);
attr[2].assign(buf);
result[2] = DeltaSMT;
snprintf(buf, sizeof(buf), "DeltaGform(%gK)", temperature);
attr[3].assign(buf);
result[3] = dhofMT - temperature*result[2]/1000;
snprintf(buf, sizeof(buf), "S0(%gK)", temperature);
attr[4].assign(buf);
result[4] = S0MT;
add_unique_pairdata_to_mol(mol, "method", method, 0);
for(ii=0; (ii<5); ii++)
{
// Add to molecule properties
sprintf(valbuf,"%f", result[ii]);
add_unique_pairdata_to_mol(mol, attr[ii], valbuf, 0);
}
sprintf(valbuf, "%f", CV);
add_unique_pairdata_to_mol(mol, "cv", valbuf, 0);
sprintf(valbuf, "%f", CV+Rgas);
add_unique_pairdata_to_mol(mol, "cp", valbuf, 0);
// Entropy components
if (Scomponents.size() == 3)
{
const char *comps[3] = { "Strans", "Srot", "Svib" };
for(int i=0; (i<3); i++)
{
sprintf(valbuf, "%f", Scomponents[i]);
add_unique_pairdata_to_mol(mol, comps[i], valbuf, 0);
}
}
// Finally store the energy in internal data structures as well.
mol->SetEnergy(dhofMT);
}
else
{
// Debug message?
}
// Clean up
delete OBet;
delete ahof;
if (foundall == atomid)
return 1;
else
return 0;
}
OpenBabel::OBMol
Schuffenhauer::Rule_4(OpenBabel::OBMol& oldMol)
{
std::vector<OpenBabel::OBRing*> allrings(oldMol.GetSSSR());
if (allrings.size() <= _ringsToBeRetained)
{
return oldMol;
}
// Only focus on ringsystems with more than one ring
std::vector<OpenBabel::OBAtom*>::iterator avi;
std::vector<OpenBabel::OBMol> mols;
OpenBabel::OBAtom* atom;
std::vector<int> fusedRings;
for (unsigned int i(0); i < allrings.size(); ++i)
{
for (atom = oldMol.BeginAtom(avi); atom; atom = oldMol.NextAtom(avi))
{
if (allrings[i]->IsMember(atom) && (atom->MemberOfRingCount() > 1))
{
fusedRings.push_back(i);
mols.push_back(oldMol);
break;
}
}
}
if (fusedRings.empty())
{
return oldMol;
}
std::vector<OpenBabel::OBMol> validMols;
for (unsigned int i(0); i < fusedRings.size(); ++i)
{
mols[i] = RemoveRing(mols[i], allrings, fusedRings[i]);
if (!mols[i].Empty())
{
validMols.push_back(mols[i]);
}
}
if (validMols.empty())
{
return oldMol;
}
int delta;
int absdelta;
std::vector<int> score;
for (unsigned int i(0); i < validMols.size(); ++i)
{
delta = CalculateDelta(validMols[i]);
absdelta = abs(delta);
score.push_back(1000 * absdelta + delta);
}
int maximum = score[0];
for (unsigned int i(1); i < validMols.size(); ++i)
{
if (score[i] > maximum)
{
maximum = score[i];
}
}
unsigned int oldMolecules = validMols.size();
std::vector<OpenBabel::OBMol> remainingMols;
for (unsigned int i(0); i < validMols.size(); ++i)
{
if (score[i] == maximum)
{
remainingMols.push_back(validMols[i]);
}
}
if (remainingMols.size() == 1)
{
return remainingMols[0];
}
return oldMol;
}
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::Rule_6(OpenBabel::OBMol& oldMol)
{
std::vector<OpenBabel::OBRing*> allrings(oldMol.GetSSSR());
if (allrings.size() <= _ringsToBeRetained)
{
return oldMol;
}
std::vector<OpenBabel::OBMol> mols;
std::vector<int> rings;
int size;
for (unsigned int i(0); i < allrings.size(); ++i)
{
size = allrings[i]->Size();
if ((size == 3) || (size == 5) || (size == 6))
{
mols.push_back(oldMol);
rings.push_back(i);
}
}
if (mols.empty())
{
return oldMol;
}
// Only focus on ringsystems with more than one ring
std::vector<OpenBabel::OBAtom*>::iterator avi;
OpenBabel::OBAtom* atom;
std::vector<int> fusedRings;
for (unsigned int i(0); i < rings.size(); ++i)
{
for (atom = oldMol.BeginAtom(avi); atom; atom = oldMol.NextAtom(avi))
{
if (allrings[rings[i]]->IsMember(atom) && (atom->MemberOfRingCount() > 1))
{
fusedRings.push_back(rings[i]);
break;
}
}
}
if (fusedRings.empty())
{
return oldMol;
}
std::vector<OpenBabel::OBMol> validMols;
for (unsigned int i(0); i < fusedRings.size(); ++i)
{
mols[i] = RemoveRing(mols[i], allrings, fusedRings[i]);
if (!mols[i].Empty())
{
validMols.push_back(mols[i]);
}
}
if (validMols.size() == 1)
{
return validMols[0];
}
return oldMol;
}
bool
_hAccDelocalized(OpenBabel::OBAtom* a)
{
if (a->GetAtomicNum() != 7)
{
return false;
}
if (a->IsAromatic() && a->GetImplicitValence() == 3)
{
return true;
}
std::vector<OpenBabel::OBBond*>::iterator bi1;
for (OpenBabel::OBBond* b1 = a->BeginBond(bi1); b1; b1 = a->NextBond(bi1))
{
OpenBabel::OBAtom* aa = b1->GetNbrAtom(a);
if (aa->IsAromatic() && a->GetImplicitValence() == 3)
{
return true;
}
if (aa->GetAtomicNum() == 6)
{
std::vector<OpenBabel::OBBond*>::iterator bi2;
for (OpenBabel::OBBond* b2 = aa->BeginBond(bi2); b2; b2 = aa->NextBond(bi2))
{
OpenBabel::OBAtom* aaa = b2->GetNbrAtom(aa);
if (aaa == a)
{
continue;
}
if (b2->GetBO() == 2)
{
if (aaa->GetAtomicNum() == 8) return true;
if (aaa->GetAtomicNum() == 7) return true;
if (aaa->GetAtomicNum() == 16) return true;
}
}
}
else if (aa->GetAtomicNum() == 16)
{
std::vector<OpenBabel::OBBond*>::iterator bi2;
for (OpenBabel::OBBond* b2 = aa->BeginBond(bi2); b2; b2 = aa->NextBond(bi2))
{
OpenBabel::OBAtom* aaa = b2->GetNbrAtom(aa);
if (aaa == a)
{
continue;
}
if ((b2->GetBO() == 2) && (aaa->GetAtomicNum() == 8))
{
return true;
}
}
}
}
return false;
}
OpenBabel::OBMol
Schuffenhauer::Rule_7(OpenBabel::OBMol& oldMol)
{
std::vector<OpenBabel::OBRing*> allrings(oldMol.GetSSSR());
if (allrings.size() <= _ringsToBeRetained)
{
return oldMol;
}
// Are all atoms and bonds aromatic?
std::vector<OpenBabel::OBAtom*>::iterator avi;
OpenBabel::OBAtom* atom;
for (atom = oldMol.BeginAtom(avi); atom; atom = oldMol.NextAtom(avi))
{
if (!atom->IsAromatic())
{
return oldMol;
}
}
std::vector<OpenBabel::OBBond*>::iterator bvi;
OpenBabel::OBBond* bond;
for (bond = oldMol.BeginBond(bvi); bond; bond = oldMol.NextBond(bvi))
{
if (!bond->IsAromatic())
{
return oldMol;
}
}
std::vector<OpenBabel::OBMol> mols;
for (unsigned int i(0); i < allrings.size(); ++i)
{
mols.push_back(oldMol);
}
std::vector<OpenBabel::OBMol> validMols;
for (unsigned int i(0); i < mols.size(); ++i)
{
mols[i] = RemoveRing(mols[i], allrings, i);
if (!mols[i].Empty())
{
// Has aromaticity been broken?
bool broken(false);
for (atom = mols[i].BeginAtom(avi); atom; atom = mols[i].NextAtom(avi))
{
if (atom->IsInRing() && !atom->IsAromatic())
{
broken = true;
break;
}
}
if (!broken)
{
validMols.push_back(mols[i]);
}
}
}
if (validMols.size() == 1)
{
return validMols[0];
}
return oldMol;
}
//--
bool DataProperty::Satisfy(OpenBabel::OBMol* pMolecule,
const std::string& refTo,
std::vector<Class*>& vecSatisfiedClasses,
std::string& refValue)
{
//bool bSatisfied = false;
int iPosition = -1;
// [rad] if we are default, we automatically satisfy
if(!IsDefault())
{
if(!SatisfyCommon(vecSatisfiedClasses, iPosition))
{
// [rad] this property does not apply
refValue = "";
return(false);
}
}
// [rad] go through possible data types..
if(!refTo.compare("MOLECULE_ATOM_COUNT"))
{
ConvertInt(pMolecule->NumAtoms(), refValue);
}
else if(!refTo.compare("MOLECULE_BOND_COUNT"))
{
ConvertInt(pMolecule->NumBonds(), refValue);
}
else if(!refTo.compare("MOLECULE_RING_COUNT"))
{
std::vector<OpenBabel::OBRing*>& refSSSR = pMolecule->GetSSSR();
ConvertInt(refSSSR.size(), refValue);
}
else if(!refTo.compare("MOLECULE_HEAVY_HYDROGEN_COUNT"))
{
ConvertInt(pMolecule->NumHvyAtoms(), refValue);
}
else if(!refTo.compare("MOLECULE_RESIDUE_COUNT"))
{
ConvertInt(pMolecule->NumResidues(), refValue);
}
else if(!refTo.compare("MOLECULE_ROTOR_COUNT"))
{
ConvertInt(pMolecule->NumRotors(), refValue);
}
else if(!refTo.compare("MOLECULE_FORMULA"))
{
refValue = pMolecule->GetFormula();
}
else if(!refTo.compare("MOLECULE_FORMATION_HEAT"))
{
ConvertDouble(pMolecule->GetEnergy(), refValue);
}
else if(!refTo.compare("MOLECULE_STANDARD_MOLAR_MASS"))
{
ConvertDouble(pMolecule->GetMolWt(), refValue);
}
else if(!refTo.compare("MOLECULE_EXACT_MASS"))
{
ConvertDouble(pMolecule->GetExactMass(), refValue);
}
else if(!refTo.compare("MOLECULE_TOTAL_CHARGE"))
{
ConvertInt(pMolecule->GetTotalCharge(), refValue);
}
else if(!refTo.compare("MOLECULE_SPIN_MULTIPLICITY"))
{
ConvertInt(pMolecule->GetTotalSpinMultiplicity(), refValue);
}
else if(!refTo.compare("MOLECULE_IS_CHIRAL"))
{
ConvertBool(pMolecule->IsChiral(), refValue);
}
else if(!refTo.compare("MOLECULE_HAS_AROMATIC_RING"))
{
std::vector<OpenBabel::OBRing*>& refSSSR = pMolecule->GetSSSR();
bool bAromatic = false;
std::vector<OpenBabel::OBRing*>::iterator iter_rings = refSSSR.begin();
while(iter_rings != refSSSR.end())
{
if((*iter_rings)->IsAromatic())
{
bAromatic = true;
break;
}
iter_rings++;
}
ConvertBool(bAromatic, refValue);
}
else if(!refTo.compare("MOLECULE_HAS_HOMOCYCLIC_RING"))
{
std::vector<OpenBabel::OBRing*>& refSSSR = pMolecule->GetSSSR();
std::vector<OpenBabel::OBRing*>::iterator iter_rings = refSSSR.begin();
OpenBabel::OBAtom* pAtom;
bool bHomoCyclic = true;
while(iter_rings != refSSSR.end())
{
std::vector<int>::iterator iter_path = (*iter_rings)->_path.begin();
while(iter_path != (*iter_rings)->_path.end())
{
pAtom = pMolecule->GetAtom((*iter_path));
if(pAtom)
{
if(6 != pAtom->GetAtomicNum())
{
bHomoCyclic = false;
break;
}
}
iter_path++;
}
if(!bHomoCyclic) break;
iter_rings++;
}
ConvertBool(bHomoCyclic, refValue);
}
else if(!refTo.compare("MOLECULE_HAS_HETEROCYCLIC_RING"))
{
std::vector<OpenBabel::OBRing*>& refSSSR = pMolecule->GetSSSR();
std::vector<OpenBabel::OBRing*>::iterator iter_rings = refSSSR.begin();
OpenBabel::OBAtom* pAtom;
bool bHeteroCyclic = false;
while(iter_rings != refSSSR.end())
{
std::vector<int>::iterator iter_path = (*iter_rings)->_path.begin();
while(iter_path != (*iter_rings)->_path.end())
{
pAtom = pMolecule->GetAtom((*iter_path));
if(pAtom)
{
if(6 != pAtom->GetAtomicNum())
{
bHeteroCyclic = true;
break;
}
}
iter_path++;
}
if(bHeteroCyclic) break;
iter_rings++;
}
ConvertBool(bHeteroCyclic, refValue);
}
else
{
// [rad] maybe it's a descriptor?
if(SatisfyDescriptor(pMolecule, refTo, refValue))
{
return(true);
}
// [rad] unknown datatype?
refValue = "";
return(false);
}
return(true);
}
//--
bool DataProperty::Satisfy(OpenBabel::OBRing* pRing,
const std::string& refTo,
std::vector<Class*>& vecSatisfiedClasses,
std::string& refValue)
{
//bool bSatisfied = false;
int iPosition = -1;
// [rad] if we are default, we automatically satisfy
if(!IsDefault())
{
if(!SatisfyCommon(vecSatisfiedClasses, iPosition))
{
// [rad] this property does not apply
refValue = "";
return(false);
}
}
// [rad] go through possible data types..
if(!refTo.compare("RING_SIZE"))
{
ConvertInt(pRing->Size(), refValue);
}
else if(!refTo.compare("RING_IS_AROMATIC"))
{
ConvertBool(pRing->IsAromatic(), refValue);
}
else if(!refTo.compare("RING_IS_HOMOCYCLIC"))
{
OpenBabel::OBMol* pMolecule = pRing->GetParent();
OpenBabel::OBAtom* pAtom;
bool bHomoCyclic = true;
std::vector<int>::iterator iter_path = pRing->_path.begin();
while(iter_path != pRing->_path.end())
{
pAtom = pMolecule->GetAtom((*iter_path));
if(pAtom)
{
if(6 != pAtom->GetAtomicNum())
{
bHomoCyclic = false;
break;
}
}
iter_path++;
}
ConvertBool(bHomoCyclic, refValue);
}
else if(!refTo.compare("RING_IS_HETEROCYCLIC"))
{
OpenBabel::OBMol* pMolecule = pRing->GetParent();
OpenBabel::OBAtom* pAtom;
bool bHeteroCyclic = false;
std::vector<int>::iterator iter_path = pRing->_path.begin();
while(iter_path != pRing->_path.end())
{
pAtom = pMolecule->GetAtom((*iter_path));
if(pAtom)
{
if(6 != pAtom->GetAtomicNum())
{
bHeteroCyclic = true;
break;
}
}
iter_path++;
}
ConvertBool(bHeteroCyclic, refValue);
}
else
{
// [rad] unknown datatype?
refValue = "";
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;
}
OpenBabel::OBMol
Schuffenhauer::Rule_11(OpenBabel::OBMol& oldMol)
{
// Return if the molecule contains an acyclic linker
std::vector<OpenBabel::OBAtom*>::iterator avi;
OpenBabel::OBAtom* atom;
for (atom = oldMol.BeginAtom(avi); atom; atom = oldMol.NextAtom(avi))
{
if (!atom->IsInRing() && atom->GetValence() >= 2)
{
return oldMol;
}
}
// Make sure we are dealing with a mixed aromatic/nonaromatic system
bool notaromatic(false);
bool aromatic(false);
for (atom = oldMol.BeginAtom(avi); atom; atom = oldMol.NextAtom(avi))
{
if (atom->IsAromatic())
{
aromatic = true;
}
else
{
notaromatic = true;
}
}
if (aromatic && notaromatic)
{
std::vector<OpenBabel::OBRing*> allrings(oldMol.GetSSSR());
if (allrings.size() <= _ringsToBeRetained)
{
return oldMol;
}
std::vector<OpenBabel::OBMol> mols;
std::vector<unsigned int> aromaticRings;
for (unsigned int i(0); i < allrings.size(); ++i)
{
if (allrings[i]->IsAromatic())
{
mols.push_back(oldMol);
aromaticRings.push_back(i);
}
}
std::vector<OpenBabel::OBMol> validMols;
for (unsigned int i(0); i < aromaticRings.size(); ++i)
{
mols[i] = RemoveRing(mols[i], allrings, aromaticRings[i]);
if (!mols[i].Empty())
{
validMols.push_back(mols[i]);
}
}
if (validMols.size() == 1)
{
return validMols[0];
}
}
return oldMol;
}
void Molecule::addHydrogens(Atom *a,
const QList<unsigned long> &atomIds,
const QList<unsigned long> &bondIds)
{
if (atomIds.size() != bondIds.size()) {
qDebug() << "Error, addHydrogens called with atom & bond id lists of different size!";
}
// Construct an OBMol, call AddHydrogens and translate the changes
OpenBabel::OBMol obmol = OBMol();
if (a) {
OpenBabel::OBAtom *obatom = obmol.GetAtom(a->index()+1);
// Set implicit valence for unusual elements not handled by OpenBabel
// PR#2803076
switch (obatom->GetAtomicNum()) {
case 3:
case 11:
case 19:
case 37:
case 55:
case 85:
case 87:
obatom->SetImplicitValence(1);
obatom->SetHyb(1);
obmol.SetImplicitValencePerceived();
break;
case 4:
case 12:
case 20:
case 38:
case 56:
case 88:
obatom->SetImplicitValence(2);
obatom->SetHyb(2);
obmol.SetImplicitValencePerceived();
break;
case 84: // Po
obatom->SetImplicitValence(2);
obatom->SetHyb(3);
obmol.SetImplicitValencePerceived();
break;
default: // do nothing
break;
}
obmol.AddHydrogens(obatom);
}
else
obmol.AddHydrogens();
// All new atoms in the OBMol must be the additional hydrogens
unsigned int numberAtoms = numAtoms();
int j = 0;
for (unsigned int i = numberAtoms+1; i <= obmol.NumAtoms(); ++i, ++j) {
if (obmol.GetAtom(i)->IsHydrogen()) {
OpenBabel::OBAtom *obatom = obmol.GetAtom(i);
Atom *atom;
if (atomIds.isEmpty())
atom = addAtom();
else if (j < atomIds.size())
atom = addAtom(atomIds.at(j));
else {
qDebug() << "Error - not enough unique ids in addHydrogens.";
break;
}
atom->setOBAtom(obatom);
// Get the neighbor atom
OpenBabel::OBBondIterator iter;
OpenBabel::OBAtom *next = obatom->BeginNbrAtom(iter);
Bond *bond;
if (bondIds.isEmpty())
bond = addBond();
else // Already confirmed by atom ids
bond = addBond(bondIds.at(j));
bond->setEnd(Molecule::atom(atom->index()));
bond->setBegin(Molecule::atom(next->GetIdx()-1));
}
}
for (unsigned int i = 1; i <= numberAtoms; ++i) {
// Warning -- OB atom index off-by-one here
atom(i-1)->setPartialCharge(obmol.GetAtom(i)->GetPartialCharge());
}
}
void
FilterAtomsInSmallestBridge::Calculate(OpenBabel::OBMol* mol)
{
// Are there rings?
OpenBabel::OBAtom* atom;
std::vector<OpenBabel::OBAtom*>::iterator i;
bool rings(false);
for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i))
{
if (atom->IsInRing())
{
rings = true;
break;
}
}
if (rings)
{
// Make workcopy of original mol
OpenBabel::OBMol m = *mol; m.DeleteHydrogens();
// Iteratively remove all endstanding atoms until none are left
OpenBabel::OBAtom* atom;
std::vector<OpenBabel::OBAtom*>::iterator i;
bool endstanding(true);
while (endstanding && m.NumAtoms())
{
endstanding = false;
for (atom = m.BeginAtom(i); atom; atom = m.NextAtom(i))
{
if (atom->GetValence() < 2)
{
if (m.DeleteAtom(atom))
{
endstanding = true;
break;
}
}
}
}
// Now remove all ring atoms
rings = true;
while (rings && m.NumAtoms())
{
rings = false;
for (atom = m.BeginAtom(i); atom; atom = m.NextAtom(i))
{
if (atom->IsInRing())
{
if (m.DeleteAtom(atom))
{
rings = true;
break;
}
}
}
}
// Separate into fragments
if (m.NumAtoms())
{
std::vector<std::vector<int> > bridges;
m.ContigFragList(bridges);
_result = bridges[0].size();
for (unsigned int i(1); i < bridges.size(); ++i)
{
if (bridges[i].size() < _result) _result = bridges[i].size();
}
}
if ((_minLimit && (_result < _min)) || (_maxLimit && (_result > _max)))
{
_passed = false;
}
else
{
_passed = true;
}
}
else
{
_result = 0;
_passed = true;
}
}
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;
}
void
FilterBridgeFraction::Calculate(OpenBabel::OBMol* mol)
{
// Are there rings?
OpenBabel::OBAtom* atom;
std::vector<OpenBabel::OBAtom*>::iterator i;
bool rings(false);
for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i))
{
if (atom->IsInRing())
{
rings = true;
break;
}
}
if (rings)
{
// Make workcopy of original mol
OpenBabel::OBMol m = *mol; m.DeleteHydrogens();
unsigned int natoms(m.NumAtoms());
if (!natoms)
{
_result = 0.0;
_passed = false;
return;
}
// Iteratively remove all endstanding atoms until none are left
OpenBabel::OBAtom* atom;
std::vector<OpenBabel::OBAtom*>::iterator i;
bool endstanding(true);
while (endstanding && m.NumAtoms())
{
endstanding = false;
for (atom = m.BeginAtom(i); atom; atom = m.NextAtom(i))
{
if (atom->GetValence() < 2)
{
if (m.DeleteAtom(atom))
{
endstanding = true;
break;
}
}
}
}
// Now remove all ring atoms
rings = true;
while (rings && m.NumAtoms())
{
rings = false;
for (atom = m.BeginAtom(i); atom; atom = m.NextAtom(i))
{
if (atom->IsInRing())
{
if (m.DeleteAtom(atom))
{
rings = true;
break;
}
}
}
}
_result = (double) m.NumAtoms() / (double) natoms;
}
else
{
_result = 0.0;
}
if ((_minLimit && (_result < _min)) || (_maxLimit && (_result > _max)))
{
_passed = false;
}
else
{
_passed = true;
}
}