bool OBBond::IsAromatic() const
{
OBMol *mol = ((OBBond*)this)->GetParent();
if (!mol->HasAromaticPerceived())
aromtyper.AssignAromaticFlags(*mol);
if (this->HasFlag(OB_AROMATIC_BOND))
return true;
return false;
}
bool OBBond::IsAromatic() const
{
if (((OBBond*)this)->HasFlag(OB_AROMATIC_BOND))
return(true);
OBMol *mol = (OBMol*)((OBBond*)this)->GetParent();
if (!mol->HasAromaticPerceived())
{
aromtyper.AssignAromaticFlags(*mol);
if (((OBBond*)this)->HasFlag(OB_AROMATIC_BOND))
return(true);
}
return(false);
}
bool OBBond::IsTriple()
{
if (HasFlag(OB_AROMATIC_BOND))
return(false);
if (!((OBMol*)GetParent())->HasAromaticPerceived())
{
aromtyper.AssignAromaticFlags(*((OBMol*)GetParent()));
}
if ((this->GetBondOrder()==3) && !(HasFlag(OB_AROMATIC_BOND)))
return(true);
return(false);
}
namespace OpenBabel
{
class OBBondPrivate
{
public:
OBBondPrivate() {}
};
extern OBAromaticTyper aromtyper;
/** \class OBBond bond.h <openbabel/bond.h>
\brief Bond class
The OBBond class is straightforward in its data access and
modification methods. OBBonds store pointers to the atoms on each end
of the bond. In storing pointers to atoms instead of integer indices,
the necessity of having to reorder bonds when atoms are shuffled,
added, or delete is obviated.
While methods indicate "begin" and "end" atoms in the bond, all methods
are designed to be independent of atom ordering, with the exception of
stereochemically aware properties such as IsUp(), IsDown(), IsWedge, or
IsHash().
*/
// *******************************
// *** OBBond member functions ***
// *******************************
OBBond::OBBond() /*: d(new OBBondPrivate)*/
{
_idx=0;
_order=0;
_flags=0;
_bgn=NULL;
_end=NULL;
_vdata.clear();
}
OBBond::~OBBond()
{
// OBGenericData handled in OBBase parent class.
}
/** Mark the main information for a bond
\param idx The unique bond index for this bond (inside an OBMol)
\param begin The 'beginning' atom for the bond
\param end The 'end' atom for the bond
\param order The bond order (i.e., 1 = single, 2 = double... 5 = aromatic)
\param flags Any initial property flags
**/
void OBBond::Set(int idx,OBAtom *begin,OBAtom *end,int order,int flags)
{
SetIdx(idx);
SetBegin(begin);
SetEnd(end);
SetBondOrder(order);
SetFlag(flags);
}
void OBBond::SetBO(int order)
{
SetBondOrder(order);
}
void OBBond::SetBondOrder(int order)
{
_order = (char)order;
if (order == 5)
{
SetAromatic();
if (_bgn)
_bgn->SetAromatic();
if (_end)
_end->SetAromatic();
}
else
{
if (order == 1)
SetKSingle();
else if (order == 2)
SetKDouble();
else if (order == 3)
SetKTriple();
else
UnsetFlag(OB_KSINGLE_BOND | OB_KDOUBLE_BOND | OB_KTRIPLE_BOND);
UnsetAromatic();
}
}
void OBBond::SetLength(OBAtom *fixed, double length)
{
unsigned int i;
OBMol *mol = (OBMol*)fixed->GetParent();
vector3 v1,v2,v3,v4,v5;
vector<int> children;
obErrorLog.ThrowError(__FUNCTION__,
"Ran OpenBabel::SetBondLength", obAuditMsg);
int a = fixed->GetIdx();
int b = GetNbrAtom(fixed)->GetIdx();
if (a == b)
return; // this would be a problem...
mol->FindChildren(children,a,b);
children.push_back(b);
v1 = GetNbrAtom(fixed)->GetVector();
v2 = fixed->GetVector();
v3 = v1 - v2;
if (IsNearZero(v3.length_2())) { // too small to normalize, move the atoms apart
obErrorLog.ThrowError(__FUNCTION__,
"Atoms are both at the same location, moving out of the way.", obWarning);
v3.randomUnitVector();
} else {
v3.normalize();
}
v3 *= length;
v3 += v2;
v4 = v3 - v1;
cerr << "v3: " << v3 << " v4: " << v4 << endl;
for ( i = 0 ; i < children.size() ; i++ )
{
v1 = mol->GetAtom(children[i])->GetVector();
v1 += v4;
mol->GetAtom(children[i])->SetVector(v1);
}
}
void OBBond::SetLength(double length)
{
OBAtom *atom1 = GetBeginAtom();
OBAtom *atom2 = GetEndAtom();
//split the length difference in half, and modify the bond twice
double firstLength = length + ((GetLength() - length) / 2);
SetLength(atom1, firstLength);
SetLength(atom2, length);
}
bool OBBond::IsRotor()
{
return(_bgn->GetHvyValence() > 1 && _end->GetHvyValence() > 1 &&
_order == 1 && !IsInRing() && _bgn->GetHyb() != 1 &&
_end->GetHyb() != 1);
}
bool OBBond::IsAmide()
{
OBAtom *c,*n;
c = n = NULL;
// Look for C-N bond
if (_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 7)
{
c = (OBAtom*)_bgn;
n = (OBAtom*)_end;
}
if (_bgn->GetAtomicNum() == 7 && _end->GetAtomicNum() == 6)
{
c = (OBAtom*)_end;
n = (OBAtom*)_bgn;
}
if (!c || !n) return(false);
if (GetBondOrder() != 1) return(false);
if (n->GetImplicitValence() != 3) return(false);
// Make sure C is attached to =O
OBBond *bond;
vector<OBBond*>::iterator i;
for (bond = c->BeginBond(i); bond; bond = c->NextBond(i))
{
if (bond->IsCarbonyl()) return(true);
}
// Return
return(false);
}
bool OBBond::IsPrimaryAmide()
{
OBAtom *c,*n;
c = n = NULL;
// Look for C-N bond
if (_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 7)
{
c = (OBAtom*)_bgn;
n = (OBAtom*)_end;
}
if (_bgn->GetAtomicNum() == 7 && _end->GetAtomicNum() == 6)
{
c = (OBAtom*)_end;
n = (OBAtom*)_bgn;
}
if (!c || !n) return(false);
if (GetBondOrder() != 1) return(false);
if (n->GetImplicitValence() != 3) return(false);
// Make sure that N is connected to one non-H
if (n->GetHvyValence() != 1) return(false);
// Make sure C is attached to =O
OBBond *bond;
vector<OBBond*>::iterator i;
for (bond = c->BeginBond(i); bond; bond = c->NextBond(i))
{
if (bond->IsCarbonyl()) return(true);
}
return(false);
}
bool OBBond::IsSecondaryAmide()
{
OBAtom *c,*n;
c = n = NULL;
// Look for C-N bond
if (_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 7)
{
c = (OBAtom*)_bgn;
n = (OBAtom*)_end;
}
if (_bgn->GetAtomicNum() == 7 && _end->GetAtomicNum() == 6)
{
c = (OBAtom*)_end;
n = (OBAtom*)_bgn;
}
if (!c || !n) return(false);
if (GetBondOrder() != 1) return(false);
if (n->GetImplicitValence() != 3) return(false);
// Make sure that N is connected to two non-H atoms
if (n->GetHvyValence() != 2) return(false);
// Make sure C is attached to =O
OBBond *bond;
vector<OBBond*>::iterator i;
for (bond = c->BeginBond(i); bond; bond = c->NextBond(i))
{
if (bond->IsCarbonyl()) return(true);
}
return(false);
}
bool OBBond::IsTertiaryAmide()
{
OBAtom *c,*n;
c = n = NULL;
// Look for C-N bond
if (_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 7)
{
c = (OBAtom*)_bgn;
n = (OBAtom*)_end;
}
if (_bgn->GetAtomicNum() == 7 && _end->GetAtomicNum() == 6)
{
c = (OBAtom*)_end;
n = (OBAtom*)_bgn;
}
if (!c || !n) return(false);
if (GetBondOrder() != 1) return(false);
if (n->GetImplicitValence() != 3) return(false);
// Make sure that N is connected to three non-H atoms
if (n->GetHvyValence() != 3) return(false);
// Make sure C is attached to =O
OBBond *bond;
vector<OBBond*>::iterator i;
for (bond = c->BeginBond(i); bond; bond = c->NextBond(i))
{
if (bond->IsCarbonyl()) return(true);
}
return(false);
}
bool OBBond::IsAmidine()
{
OBAtom *c,*n;
c = n = NULL;
// Look for C-N bond
if (_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 7)
{
c = (OBAtom*)_bgn;
n = (OBAtom*)_end;
}
if (_bgn->GetAtomicNum() == 7 && _end->GetAtomicNum() == 6)
{
c = (OBAtom*)_end;
n = (OBAtom*)_bgn;
}
if (!c || !n) return(false);
if (GetBondOrder() != 1) return(false);
if (n->GetImplicitValence() != 3) return(false);
// Make sure C is attached to =N
OBBond *bond;
vector<OBBond*>::iterator i;
for (bond = c->BeginBond(i); bond; bond = c->NextBond(i))
{
if (bond->IsImide()) return(true);
}
// Return
return(false);
}
/*
bool OBBond::IsAmide()
{
OBAtom *a1,*a2;
a1 = a2 = NULL;
if (_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 7)
{
a1 = (OBAtom*)_bgn;
a2 = (OBAtom*)_end;
}
if (_bgn->GetAtomicNum() == 7 && _end->GetAtomicNum() == 6)
{
a1 = (OBAtom*)_end;
a2 = (OBAtom*)_bgn;
}
if (!a1 || !a2)
return(false);
if (GetBO() != 1)
return(false);
OBBond *bond;
vector<OBBond*>::iterator i;
for (bond = a1->BeginBond(i);bond;bond = a1->NextBond(i))
if (bond->IsCarbonyl())
return(true);
return(false);
}
bool OBBond::IsPrimaryAmide()
{
OBAtom *a1,*a2;
a1 = a2 = NULL;
if (_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 7)
{
a1 = (OBAtom*)_bgn;
a2 = (OBAtom*)_end;
}
if (_bgn->GetAtomicNum() == 7 && _end->GetAtomicNum() == 6)
{
a1 = (OBAtom*)_end;
a2 = (OBAtom*)_bgn;
}
if (!a1 || !a2)
return(false);
if (GetBO() != 1)
return(false);
OBBond *bond;
vector<OBBond*>::iterator i;
for (bond = a1->BeginBond(i);bond;bond = a1->NextBond(i))
if (bond->IsCarbonyl())
if (a2->GetHvyValence() == 2)
return(true);
return(false);
}
bool OBBond::IsSecondaryAmide()
{
OBAtom *a1,*a2;
a1 = a2 = NULL;
if (_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 7)
{
a1 = (OBAtom*)_bgn;
a2 = (OBAtom*)_end;
}
if (_bgn->GetAtomicNum() == 7 && _end->GetAtomicNum() == 6)
{
a1 = (OBAtom*)_end;
a2 = (OBAtom*)_bgn;
}
if (!a1 || !a2)
return(false);
if (GetBO() != 1)
return(false);
OBBond *bond;
vector<OBBond*>::iterator i;
for (bond = a1->BeginBond(i);bond;bond = a1->NextBond(i))
if (bond->IsCarbonyl())
if (a2->GetHvyValence() == 3)
return(true);
return(false);
}
*/
bool OBBond::IsEster()
{
OBAtom *a1,*a2;
a1 = a2 = NULL;
if (_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 8)
{
a1 = (OBAtom*)_bgn;
a2 = (OBAtom*)_end;
}
if (_bgn->GetAtomicNum() == 8 && _end->GetAtomicNum() == 6)
{
a1 = (OBAtom*)_end;
a2 = (OBAtom*)_bgn;
}
if (!a1 || !a2)
return(false);
if (GetBO() != 1)
return(false);
OBBond *bond;
vector<OBBond*>::iterator i;
for (bond = a1->BeginBond(i);bond;bond = a1->NextBond(i))
if (bond->IsCarbonyl())
return(true);
return(false);
}
bool OBBond::IsCarbonyl()
{
if (GetBO() != 2)
return(false);
if ((_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 8) ||
(_bgn->GetAtomicNum() == 8 && _end->GetAtomicNum() == 6))
return(true);
return(false);
}
bool OBBond::IsImide()
{
if (GetBO() != 2)
return(false);
if ((_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 7) ||
(_bgn->GetAtomicNum() == 7 && _end->GetAtomicNum() == 6))
return(true);
return(false);
}
bool OBBond::IsSingle()
{
if (HasFlag(OB_AROMATIC_BOND))
return(false);
if (!((OBMol*)GetParent())->HasAromaticPerceived())
{
aromtyper.AssignAromaticFlags(*((OBMol*)GetParent()));
}
if ((this->GetBondOrder()==1) && !(HasFlag(OB_AROMATIC_BOND)))
return(true);
return(false);
}
bool OBBond::IsDouble()
{
if (HasFlag(OB_AROMATIC_BOND))
return(false);
if (!((OBMol*)GetParent())->HasAromaticPerceived())
{
aromtyper.AssignAromaticFlags(*((OBMol*)GetParent()));
}
if ((this->GetBondOrder()==2) && !(HasFlag(OB_AROMATIC_BOND)))
return(true);
return(false);
}
bool OBBond::IsTriple()
{
if (HasFlag(OB_AROMATIC_BOND))
return(false);
if (!((OBMol*)GetParent())->HasAromaticPerceived())
{
aromtyper.AssignAromaticFlags(*((OBMol*)GetParent()));
}
if ((this->GetBondOrder()==3) && !(HasFlag(OB_AROMATIC_BOND)))
return(true);
return(false);
}
bool OBBond::IsAromatic() const
{
if (((OBBond*)this)->HasFlag(OB_AROMATIC_BOND))
return(true);
OBMol *mol = (OBMol*)((OBBond*)this)->GetParent();
if (!mol->HasAromaticPerceived())
{
aromtyper.AssignAromaticFlags(*mol);
if (((OBBond*)this)->HasFlag(OB_AROMATIC_BOND))
return(true);
}
return(false);
}
/*! This method checks if the geometry around this bond looks unsaturated
by measuring the torsion angles formed by all connected atoms X-start=end-Y
and checking that they are close to 0 or 180 degrees */
bool OBBond::IsDoubleBondGeometry()
{
double torsion;
OBAtom *nbrStart,*nbrEnd;
vector<OBBond*>::iterator i,j;
// We concentrate on sp2 atoms with valence up to 3 and ignore the rest (like sp1 or S,P)
// As this is called from PerceiveBondOrders, GetHyb() may still be undefined.
if (_bgn->GetHyb()==1 || _bgn->GetValence()>3||
_end->GetHyb()==1 || _end->GetValence()>3)
return(true);
for (nbrStart = static_cast<OBAtom*>(_bgn)->BeginNbrAtom(i); nbrStart;
nbrStart = static_cast<OBAtom*>(_bgn)->NextNbrAtom(i))
{
if (nbrStart != _end)
{
for (nbrEnd = static_cast<OBAtom*>(_end)->BeginNbrAtom(j);
nbrEnd; nbrEnd = static_cast<OBAtom*>(_end)->NextNbrAtom(j))
{
if (nbrEnd != _bgn)
{
torsion=fabs(CalcTorsionAngle(nbrStart->GetVector(),
static_cast<OBAtom*>(_bgn)->GetVector(),
static_cast<OBAtom*>(_end)->GetVector(),
nbrEnd->GetVector()));
// >12&&<168 not enough
if (torsion > 15.0 && torsion < 160.0)
{
// Geometry does not match a double bond
return(false);
}
}
} // end loop for neighbors of end
}
} // end loop for neighbors of start
return(true);
}
void OBBond::SetKSingle()
{
_flags &= (~(OB_KSINGLE_BOND|OB_KDOUBLE_BOND|OB_KTRIPLE_BOND));
_flags |= OB_KSINGLE_BOND;
}
void OBBond::SetKDouble()
{
_flags &= (~(OB_KSINGLE_BOND|OB_KDOUBLE_BOND|OB_KTRIPLE_BOND));
_flags |= OB_KDOUBLE_BOND;
}
void OBBond::SetKTriple()
{
_flags &= (~(OB_KSINGLE_BOND|OB_KDOUBLE_BOND|OB_KTRIPLE_BOND));
_flags |= OB_KTRIPLE_BOND;
}
bool OBBond::IsKSingle()
{
if (_flags & OB_KSINGLE_BOND)
return(true);
if (!((OBMol*)GetParent())->HasKekulePerceived())
((OBMol*)GetParent())->NewPerceiveKekuleBonds();
return((_flags & OB_KSINGLE_BOND) != 0) ? true : false;
}
bool OBBond::IsKDouble()
{
if (_flags & OB_KDOUBLE_BOND)
return(true);
if (!((OBMol*)GetParent())->HasKekulePerceived())
((OBMol*)GetParent())->NewPerceiveKekuleBonds();
return((_flags & OB_KDOUBLE_BOND) != 0) ? true : false;
}
bool OBBond::IsKTriple()
{
if (_flags & OB_KTRIPLE_BOND)
return(true);
if (!((OBMol*)GetParent())->HasKekulePerceived())
((OBMol*)GetParent())->NewPerceiveKekuleBonds();
return((_flags & OB_KTRIPLE_BOND) != 0) ? true : false;
}
bool OBBond::IsInRing() const
{
if (((OBBond*)this)->HasFlag(OB_RING_BOND))
return(true);
OBMol *mol = (OBMol*)((OBBond*)this)->GetParent();
if (!mol->HasRingAtomsAndBondsPerceived())
{
mol->FindRingAtomsAndBonds();
if (((OBBond*)this)->HasFlag(OB_RING_BOND))
return(true);
}
return(false);
}
// Adapted from OBAtom::IsInRingSize()
OBRing* OBBond::FindSmallestRing() const
{
vector<OBRing*> rlist;
vector<OBRing*>::iterator i;
OBMol *mol = (OBMol*)((OBBond*)this)->GetParent();
rlist = mol->GetSSSR();
OBRing* result = (OBRing*) NULL;
size_t min_size = UINT_MAX;
for (i = rlist.begin();i != rlist.end();++i) {
if ((*i)->IsMember((OBBond*)this) && (*i)->Size() < min_size) {
min_size = (*i)->Size();
result = *i;
}
}
return result;
}
bool OBBond::IsClosure()
{
OBMol *mol = (OBMol*)GetParent();
if (!mol)
return(false);
if (mol->HasClosureBondsPerceived())
return(HasFlag(OB_CLOSURE_BOND));
mol->SetClosureBondsPerceived();
obErrorLog.ThrowError(__FUNCTION__,
"Ran OpenBabel::PerceiveClosureBonds", obAuditMsg);
OBBond *bond;
OBAtom *atom,*nbr;
OBBitVec uatoms,ubonds;
vector<OBAtom*> curr,next;
vector<OBAtom*>::iterator i;
vector<OBBond*>::iterator j;
uatoms.Resize(mol->NumAtoms()+1);
ubonds.Resize(mol->NumAtoms()+1);
for (;static_cast<unsigned int>(uatoms.CountBits()) < mol->NumAtoms();)
{
if (curr.empty())
for (atom = mol->BeginAtom(i);atom;atom = mol->NextAtom(i))
if (!uatoms[atom->GetIdx()])
{
uatoms |= atom->GetIdx();
curr.push_back(atom);
break;
}
for (;!curr.empty();)
{
for (i = curr.begin();i != curr.end();++i)
for (nbr = ((OBAtom*)*i)->BeginNbrAtom(j);nbr;nbr = ((OBAtom*)*i)->NextNbrAtom(j))
if (!uatoms[nbr->GetIdx()])
{
uatoms |= nbr->GetIdx();
ubonds |= (*j)->GetIdx();
next.push_back(nbr);
}
curr = next;
next.clear();
}
}
for (bond = mol->BeginBond(j);bond;bond = mol->NextBond(j))
if (!ubonds[bond->GetIdx()])
bond->SetClosure();
return(HasFlag(OB_CLOSURE_BOND));
}
double OBBond::GetEquibLength() const
{
double length;
const OBAtom *begin, *end;
// CorrectedBondRad will always return a # now
// if (!CorrectedBondRad(GetBeginAtom(),rad1)) return(0.0);
// if (!CorrectedBondRad(GetEndAtom(),rad2)) return(0.0);
begin = GetBeginAtom();
end = GetEndAtom();
length = etab.CorrectedBondRad(begin->GetAtomicNum(), begin->GetHyb())
+ etab.CorrectedBondRad(end->GetAtomicNum(), end->GetHyb());
if (IsAromatic())
length *= 0.93;
else if (GetBO() == 2)
length *= 0.91;
else if (GetBO() == 3)
length *= 0.87;
return(length);
}
double OBBond::GetLength() const
{
double d2;
const OBAtom *begin, *end;
begin = GetBeginAtom();
end = GetEndAtom();
d2 = SQUARE(begin->GetX() - end->GetX());
d2 += SQUARE(begin->GetY() - end->GetY());
d2 += SQUARE(begin->GetZ() - end->GetZ());
return(sqrt(d2));
}
/*Now in OBBase
// OBGenericData methods
bool OBBond::HasData(string &s)
//returns true if the generic attribute/value pair exists
{
if (_vdata.empty())
return(false);
vector<OBGenericData*>::iterator i;
for (i = _vdata.begin();i != _vdata.end();++i)
if ((*i)->GetAttribute() == s)
return(true);
return(false);
}
bool OBBond::HasData(const char *s)
//returns true if the generic attribute/value pair exists
{
if (_vdata.empty())
return(false);
vector<OBGenericData*>::iterator i;
for (i = _vdata.begin();i != _vdata.end();++i)
if ((*i)->GetAttribute() == s)
return(true);
return(false);
}
bool OBBond::HasData(unsigned int dt)
//returns true if the generic attribute/value pair exists
{
if (_vdata.empty())
return(false);
vector<OBGenericData*>::iterator i;
for (i = _vdata.begin();i != _vdata.end();++i)
if ((*i)->GetDataType() == dt)
return(true);
return(false);
}
OBGenericData *OBBond::GetData(string &s)
//returns the value given an attribute
{
vector<OBGenericData*>::iterator i;
for (i = _vdata.begin();i != _vdata.end();++i)
if ((*i)->GetAttribute() == s)
return(*i);
return(NULL);
}
OBGenericData *OBBond::GetData(const char *s)
//returns the value given an attribute
{
vector<OBGenericData*>::iterator i;
for (i = _vdata.begin();i != _vdata.end();++i)
if ((*i)->GetAttribute() == s)
return(*i);
return(NULL);
}
OBGenericData *OBBond::GetData(unsigned int dt)
{
vector<OBGenericData*>::iterator i;
for (i = _vdata.begin();i != _vdata.end();++i)
if ((*i)->GetDataType() == dt)
return(*i);
return(NULL);
}
void OBBond::DeleteData(unsigned int dt)
{
vector<OBGenericData*> vdata;
vector<OBGenericData*>::iterator i;
for (i = _vdata.begin();i != _vdata.end();++i)
if ((*i)->GetDataType() == dt)
delete *i;
else
vdata.push_back(*i);
_vdata = vdata;
}
void OBBond::DeleteData(vector<OBGenericData*> &vg)
{
vector<OBGenericData*> vdata;
vector<OBGenericData*>::iterator i,j;
bool del;
for (i = _vdata.begin();i != _vdata.end();++i)
{
del = false;
for (j = vg.begin();j != vg.end();++j)
if (*i == *j)
{
del = true;
break;
}
if (del)
delete *i;
else
vdata.push_back(*i);
}
_vdata = vdata;
}
void OBBond::DeleteData(OBGenericData *gd)
{
vector<OBGenericData*>::iterator i;
for (i = _vdata.begin();i != _vdata.end();++i)
if (*i == gd)
{
delete *i;
_vdata.erase(i);
}
}
*/
} // end namespace OpenBabel
namespace OpenBabel
{
class OBBondPrivate
{
public:
OBBondPrivate() {}
};
extern OBAromaticTyper aromtyper;
/** \class OBBond bond.h <openbabel/bond.h>
\brief Bond class
The OBBond class is straightforward in its data access and
modification methods. OBBonds store pointers to the atoms on each end
of the bond. In storing pointers to atoms instead of integer indices,
the necessity of having to reorder bonds when atoms are shuffled,
added, or delete is obviated.
While methods indicate "begin" and "end" atoms in the bond, all methods
are designed to be independent of atom ordering, with the exception of
stereochemically aware properties such as IsUp(), IsDown(), IsWedge, or
IsHash().
*/
// *******************************
// *** OBBond member functions ***
// *******************************
OBBond::OBBond() /*: d(new OBBondPrivate)*/
{
_idx=0;
_order=0;
_flags=0;
_bgn=NULL;
_end=NULL;
_vdata.clear();
_parent=(OBMol*)NULL;
}
OBBond::~OBBond()
{
// OBGenericData handled in OBBase parent class.
}
/** Mark the main information for a bond
\param idx The unique bond index for this bond (inside an OBMol)
\param begin The 'beginning' atom for the bond
\param end The 'end' atom for the bond
\param order The bond order (i.e., 1 = single, 2 = double... 5 = aromatic)
\param flags Any initial property flags
**/
void OBBond::Set(int idx,OBAtom *begin,OBAtom *end,int order,int flags)
{
SetIdx(idx);
SetBegin(begin);
SetEnd(end);
SetBondOrder(order);
SetFlag(flags);
}
void OBBond::SetBO(int order)
{
SetBondOrder(order);
}
void OBBond::SetBondOrder(int order)
{
_order = (char)order;
}
void OBBond::SetLength(OBAtom *fixed, double length)
{
unsigned int i;
OBMol *mol = (OBMol*)fixed->GetParent();
vector3 v1,v2,v3,v4,v5;
vector<int> children;
obErrorLog.ThrowError(__FUNCTION__,
"Ran OpenBabel::SetBondLength", obAuditMsg);
int a = fixed->GetIdx();
int b = GetNbrAtom(fixed)->GetIdx();
if (a == b)
return; // this would be a problem...
mol->FindChildren(children,a,b);
children.push_back(b);
v1 = GetNbrAtom(fixed)->GetVector();
v2 = fixed->GetVector();
v3 = v1 - v2;
if (IsNearZero(v3.length_2())) { // too small to normalize, move the atoms apart
obErrorLog.ThrowError(__FUNCTION__,
"Atoms are both at the same location, moving out of the way.", obWarning);
v3.randomUnitVector();
} else {
v3.normalize();
}
v3 *= length;
v3 += v2;
v4 = v3 - v1;
cerr << "v3: " << v3 << " v4: " << v4 << endl;
for ( i = 0 ; i < children.size() ; i++ )
{
v1 = mol->GetAtom(children[i])->GetVector();
v1 += v4;
mol->GetAtom(children[i])->SetVector(v1);
}
}
void OBBond::SetLength(double length)
{
OBAtom *atom1 = GetBeginAtom();
OBAtom *atom2 = GetEndAtom();
//split the length difference in half, and modify the bond twice
double firstLength = length + ((GetLength() - length) / 2);
SetLength(atom1, firstLength);
SetLength(atom2, length);
}
bool OBBond::IsRotor(bool includeRingBonds)
{
// This could be one hellish conditional, but let's break it down
// .. the bond is a single bond
if (_order != 1)
return false;
// not in a ring, or in a large ring
// and if it's a ring, not sp2
OBRing *ring = FindSmallestRing();
if (ring != NULL) {
if(!includeRingBonds)
return false;
if (ring->Size() <= 3)
return false;
if (_bgn->GetHyb() == 2 || _end->GetHyb() == 2)
return false;
}
// atoms are not sp hybrids
if (_bgn->GetHyb() == 1 || _end->GetHyb() == 1)
return false;
// not just an -OH or -NH2, etc.
// maybe we want to add this as an option
// rotatable = rotatable && ((_bgn->IsHeteroatom() || _bgn->GetHvyValence() > 1)
// && (_end->IsHeteroatom() || _end->GetHvyValence() > 1) );
return (_bgn->GetHvyValence() > 1 && _end->GetHvyValence() > 1);
}
static unsigned int TotalNumberOfBonds(OBAtom* atom)
{
return atom->GetImplicitHCount() + atom->GetValence();
}
bool OBBond::IsAmide()
{
OBAtom *c,*n;
c = n = NULL;
// Look for C-N bond
if (_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 7)
{
c = (OBAtom*)_bgn;
n = (OBAtom*)_end;
}
if (_bgn->GetAtomicNum() == 7 && _end->GetAtomicNum() == 6)
{
c = (OBAtom*)_end;
n = (OBAtom*)_bgn;
}
if (!c || !n) return(false);
if (GetBondOrder() != 1) return(false);
if (TotalNumberOfBonds(n) != 3) return false; // must be a degree 3 nitrogen
// Make sure C is attached to =O
OBBond *bond;
vector<OBBond*>::iterator i;
for (bond = c->BeginBond(i); bond; bond = c->NextBond(i))
{
if (bond->IsCarbonyl()) return(true);
}
// Return
return(false);
}
bool OBBond::IsPrimaryAmide()
{
OBAtom *c,*n;
c = n = NULL;
// Look for C-N bond
if (_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 7)
{
c = (OBAtom*)_bgn;
n = (OBAtom*)_end;
}
if (_bgn->GetAtomicNum() == 7 && _end->GetAtomicNum() == 6)
{
c = (OBAtom*)_end;
n = (OBAtom*)_bgn;
}
if (!c || !n) return(false);
if (GetBondOrder() != 1) return(false);
if (TotalNumberOfBonds(n) != 3) return false; // must be a degree 3 nitrogen
// Make sure that N is connected to one non-H
if (n->GetHvyValence() != 1) return(false);
// Make sure C is attached to =O
OBBond *bond;
vector<OBBond*>::iterator i;
for (bond = c->BeginBond(i); bond; bond = c->NextBond(i))
{
if (bond->IsCarbonyl()) return(true);
}
return(false);
}
bool OBBond::IsSecondaryAmide()
{
OBAtom *c,*n;
c = n = NULL;
// Look for C-N bond
if (_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 7)
{
c = (OBAtom*)_bgn;
n = (OBAtom*)_end;
}
if (_bgn->GetAtomicNum() == 7 && _end->GetAtomicNum() == 6)
{
c = (OBAtom*)_end;
n = (OBAtom*)_bgn;
}
if (!c || !n) return(false);
if (GetBondOrder() != 1) return(false);
if (TotalNumberOfBonds(n) != 3) return false; // must be a degree 3 nitrogen
// Make sure that N is connected to two non-H atoms
if (n->GetHvyValence() != 2) return(false);
// Make sure C is attached to =O
OBBond *bond;
vector<OBBond*>::iterator i;
for (bond = c->BeginBond(i); bond; bond = c->NextBond(i))
{
if (bond->IsCarbonyl()) return(true);
}
return(false);
}
bool OBBond::IsTertiaryAmide()
{
OBAtom *c,*n;
c = n = NULL;
// Look for C-N bond
if (_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 7)
{
c = (OBAtom*)_bgn;
n = (OBAtom*)_end;
}
if (_bgn->GetAtomicNum() == 7 && _end->GetAtomicNum() == 6)
{
c = (OBAtom*)_end;
n = (OBAtom*)_bgn;
}
if (!c || !n) return(false);
if (GetBondOrder() != 1) return(false);
if (TotalNumberOfBonds(n) != 3) return false; // must be a degree 3 nitrogen
// Make sure that N is connected to three non-H atoms
if (n->GetHvyValence() != 3) return(false);
// Make sure C is attached to =O
OBBond *bond;
vector<OBBond*>::iterator i;
for (bond = c->BeginBond(i); bond; bond = c->NextBond(i))
{
if (bond->IsCarbonyl()) return(true);
}
return(false);
}
/*
bool OBBond::IsAmide()
{
OBAtom *a1,*a2;
a1 = a2 = NULL;
if (_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 7)
{
a1 = (OBAtom*)_bgn;
a2 = (OBAtom*)_end;
}
if (_bgn->GetAtomicNum() == 7 && _end->GetAtomicNum() == 6)
{
a1 = (OBAtom*)_end;
a2 = (OBAtom*)_bgn;
}
if (!a1 || !a2)
return(false);
if (GetBO() != 1)
return(false);
OBBond *bond;
vector<OBBond*>::iterator i;
for (bond = a1->BeginBond(i);bond;bond = a1->NextBond(i))
if (bond->IsCarbonyl())
return(true);
return(false);
}
bool OBBond::IsPrimaryAmide()
{
OBAtom *a1,*a2;
a1 = a2 = NULL;
if (_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 7)
{
a1 = (OBAtom*)_bgn;
a2 = (OBAtom*)_end;
}
if (_bgn->GetAtomicNum() == 7 && _end->GetAtomicNum() == 6)
{
a1 = (OBAtom*)_end;
a2 = (OBAtom*)_bgn;
}
if (!a1 || !a2)
return(false);
if (GetBO() != 1)
return(false);
OBBond *bond;
vector<OBBond*>::iterator i;
for (bond = a1->BeginBond(i);bond;bond = a1->NextBond(i))
if (bond->IsCarbonyl())
if (a2->GetHvyValence() == 2)
return(true);
return(false);
}
bool OBBond::IsSecondaryAmide()
{
OBAtom *a1,*a2;
a1 = a2 = NULL;
if (_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 7)
{
a1 = (OBAtom*)_bgn;
a2 = (OBAtom*)_end;
}
if (_bgn->GetAtomicNum() == 7 && _end->GetAtomicNum() == 6)
{
a1 = (OBAtom*)_end;
a2 = (OBAtom*)_bgn;
}
if (!a1 || !a2)
return(false);
if (GetBO() != 1)
return(false);
OBBond *bond;
vector<OBBond*>::iterator i;
for (bond = a1->BeginBond(i);bond;bond = a1->NextBond(i))
if (bond->IsCarbonyl())
if (a2->GetHvyValence() == 3)
return(true);
return(false);
}
*/
bool OBBond::IsEster()
{
OBAtom *a1,*a2;
a1 = a2 = NULL;
if (_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 8)
{
a1 = (OBAtom*)_bgn;
a2 = (OBAtom*)_end;
}
if (_bgn->GetAtomicNum() == 8 && _end->GetAtomicNum() == 6)
{
a1 = (OBAtom*)_end;
a2 = (OBAtom*)_bgn;
}
if (!a1 || !a2)
return(false);
if (GetBO() != 1)
return(false);
OBBond *bond;
vector<OBBond*>::iterator i;
for (bond = a1->BeginBond(i);bond;bond = a1->NextBond(i))
if (bond->IsCarbonyl())
return(true);
return(false);
}
bool OBBond::IsCarbonyl()
{
if (GetBO() != 2)
return(false);
if ((_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 8) ||
(_bgn->GetAtomicNum() == 8 && _end->GetAtomicNum() == 6))
return(true);
return(false);
}
bool OBBond::IsAromatic() const
{
OBMol *mol = ((OBBond*)this)->GetParent();
if (!mol->HasAromaticPerceived())
aromtyper.AssignAromaticFlags(*mol);
if (this->HasFlag(OB_AROMATIC_BOND))
return true;
return false;
}
/*! This method checks if the geometry around this bond looks unsaturated
by measuring the torsion angles formed by all connected atoms X-start=end-Y
and checking that they are close to 0 or 180 degrees */
bool OBBond::IsDoubleBondGeometry()
{
double torsion;
OBAtom *nbrStart,*nbrEnd;
vector<OBBond*>::iterator i,j;
// We concentrate on sp2 atoms with valence up to 3 and ignore the rest (like sp1 or S,P)
// As this is called from PerceiveBondOrders, GetHyb() may still be undefined.
if (_bgn->GetHyb()==1 || _bgn->GetValence()>3||
_end->GetHyb()==1 || _end->GetValence()>3)
return(true);
for (nbrStart = static_cast<OBAtom*>(_bgn)->BeginNbrAtom(i); nbrStart;
nbrStart = static_cast<OBAtom*>(_bgn)->NextNbrAtom(i))
{
if (nbrStart != _end)
{
for (nbrEnd = static_cast<OBAtom*>(_end)->BeginNbrAtom(j);
nbrEnd; nbrEnd = static_cast<OBAtom*>(_end)->NextNbrAtom(j))
{
if (nbrEnd != _bgn)
{
torsion=fabs(CalcTorsionAngle(nbrStart->GetVector(),
static_cast<OBAtom*>(_bgn)->GetVector(),
static_cast<OBAtom*>(_end)->GetVector(),
nbrEnd->GetVector()));
// >12&&<168 not enough
if (torsion > 15.0 && torsion < 160.0)
{
// Geometry does not match a double bond
return(false);
}
}
} // end loop for neighbors of end
}
} // end loop for neighbors of start
return(true);
}
bool OBBond::IsInRing() const
{
if (((OBBond*)this)->HasFlag(OB_RING_BOND))
return(true);
OBMol *mol = (OBMol*)((OBBond*)this)->GetParent();
if (!mol->HasRingAtomsAndBondsPerceived())
{
mol->FindRingAtomsAndBonds();
if (((OBBond*)this)->HasFlag(OB_RING_BOND))
return(true);
}
return(false);
}
// Adapted from OBAtom::IsInRingSize()
OBRing* OBBond::FindSmallestRing() const
{
vector<OBRing*> rlist;
vector<OBRing*>::iterator i;
OBMol *mol = (OBMol*)((OBBond*)this)->GetParent();
rlist = mol->GetSSSR();
OBRing* result = (OBRing*) NULL;
size_t min_size = UINT_MAX;
for (i = rlist.begin();i != rlist.end();++i) {
if ((*i)->IsMember((OBBond*)this) && (*i)->Size() < min_size) {
min_size = (*i)->Size();
result = *i;
}
}
return result;
}
bool OBBond::IsClosure()
{
OBMol *mol = (OBMol*)GetParent();
if (!mol)
return false;
if (!mol->HasClosureBondsPerceived())
mol->FindRingAtomsAndBonds();
return HasFlag(OB_CLOSURE_BOND);
}
//! \return a "corrected" bonding radius based on the hybridization.
//! Scales the covalent radius by 0.95 for sp2 and 0.90 for sp hybrids
static double CorrectedBondRad(unsigned int elem, unsigned int hyb)
{
double rad = OBElements::GetCovalentRad(elem);
switch (hyb) {
case 2:
return rad * 0.95;
case 1:
return rad * 0.90;
default:
return rad;
}
}
double OBBond::GetEquibLength() const
{
const OBAtom *begin, *end;
begin = GetBeginAtom();
end = GetEndAtom();
double length = CorrectedBondRad(begin->GetAtomicNum(), begin->GetHyb())
+ CorrectedBondRad(end->GetAtomicNum(), end->GetHyb());
if (IsAromatic())
return length * 0.93;
switch (_order) {
case 3:
return length * 0.87;
case 2:
return length * 0.91;
}
return length;
}
double OBBond::GetLength() const
{
double d2;
const OBAtom *begin, *end;
begin = GetBeginAtom();
end = GetEndAtom();
d2 = SQUARE(begin->GetX() - end->GetX());
d2 += SQUARE(begin->GetY() - end->GetY());
d2 += SQUARE(begin->GetZ() - end->GetZ());
return(sqrt(d2));
}
/*Now in OBBase
// OBGenericData methods
bool OBBond::HasData(string &s)
//returns true if the generic attribute/value pair exists
{
if (_vdata.empty())
return(false);
vector<OBGenericData*>::iterator i;
for (i = _vdata.begin();i != _vdata.end();++i)
if ((*i)->GetAttribute() == s)
return(true);
return(false);
}
bool OBBond::HasData(const char *s)
//returns true if the generic attribute/value pair exists
{
if (_vdata.empty())
return(false);
vector<OBGenericData*>::iterator i;
for (i = _vdata.begin();i != _vdata.end();++i)
if ((*i)->GetAttribute() == s)
return(true);
return(false);
}
bool OBBond::HasData(unsigned int dt)
//returns true if the generic attribute/value pair exists
{
if (_vdata.empty())
return(false);
vector<OBGenericData*>::iterator i;
for (i = _vdata.begin();i != _vdata.end();++i)
if ((*i)->GetDataType() == dt)
return(true);
return(false);
}
OBGenericData *OBBond::GetData(string &s)
//returns the value given an attribute
{
vector<OBGenericData*>::iterator i;
for (i = _vdata.begin();i != _vdata.end();++i)
if ((*i)->GetAttribute() == s)
return(*i);
return(NULL);
}
OBGenericData *OBBond::GetData(const char *s)
//returns the value given an attribute
{
vector<OBGenericData*>::iterator i;
for (i = _vdata.begin();i != _vdata.end();++i)
if ((*i)->GetAttribute() == s)
return(*i);
return(NULL);
}
OBGenericData *OBBond::GetData(unsigned int dt)
{
vector<OBGenericData*>::iterator i;
for (i = _vdata.begin();i != _vdata.end();++i)
if ((*i)->GetDataType() == dt)
return(*i);
return(NULL);
}
void OBBond::DeleteData(unsigned int dt)
{
vector<OBGenericData*> vdata;
vector<OBGenericData*>::iterator i;
for (i = _vdata.begin();i != _vdata.end();++i)
if ((*i)->GetDataType() == dt)
delete *i;
else
vdata.push_back(*i);
_vdata = vdata;
}
void OBBond::DeleteData(vector<OBGenericData*> &vg)
{
vector<OBGenericData*> vdata;
vector<OBGenericData*>::iterator i,j;
bool del;
for (i = _vdata.begin();i != _vdata.end();++i)
{
del = false;
for (j = vg.begin();j != vg.end();++j)
if (*i == *j)
{
del = true;
break;
}
if (del)
delete *i;
else
vdata.push_back(*i);
}
_vdata = vdata;
}
void OBBond::DeleteData(OBGenericData *gd)
{
vector<OBGenericData*>::iterator i;
for (i = _vdata.begin();i != _vdata.end();++i)
if (*i == gd)
{
delete *i;
_vdata.erase(i);
}
}
*/
} // end namespace OpenBabel
