void WriteTorsions(ostream &ofs,OBMol &mol)
{
vector<OBEdgeBase*>::iterator bi1,bi2,bi3;
OBBond* bond;
OBAtom *a,*b,*c,*d;
char buffer[BUFF_SIZE];
//loop through all bonds generating torsions
for(bond = mol.BeginBond(bi1); bond; bond = mol.NextBond(bi1))
{
b = bond->GetBeginAtom();
c = bond->GetEndAtom();
for(a = b->BeginNbrAtom(bi2);a;a = b->NextNbrAtom(bi2))
{
if(a == c)
continue;
for(d = c->BeginNbrAtom(bi3);d;d = c->NextNbrAtom(bi3))
{
if(d == b)
continue;
sprintf(buffer,"%4d %4d %4d %4d %10.3f",
a->GetIdx(), b->GetIdx(),c->GetIdx(),d->GetIdx(),
CalcTorsionAngle(a->GetVector(), b->GetVector(),
c->GetVector(), d->GetVector()));
ofs << buffer << endl;
}
}
}
}
/*! 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);
}
