/**********************************************************************

atom.cpp - Handle OBAtom class.

Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.

Some portions Copyright (C) 2001-2008 by Geoffrey R. Hutchison

Some portions Copyright (C) 2003 by Michael Banck

This file is part of the Open Babel project.

For more information, see <http://openbabel.org/>

This program is free software; you can redistribute it and/or modify

it under the terms of the GNU General Public License as published by

the Free Software Foundation version 2 of the License.

This program is distributed in the hope that it will be useful,

but WITHOUT ANY WARRANTY; without even the implied warranty of

MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the

GNU General Public License for more details.

***********************************************************************/

#include <openbabel/babelconfig.h>

#include <openbabel/atom.h>

#include <openbabel/bond.h>

#include <openbabel/mol.h>

#include <openbabel/obiter.h>

#include <openbabel/generic.h>

#include <openbabel/molchrg.h>

#include <openbabel/ring.h>

#include <openbabel/phmodel.h>

#include <openbabel/builder.h>

#include <openbabel/elements.h>

#include <openbabel/chains.h>

#include <openbabel/obutil.h>

#include <openbabel/residue.h>

#include <openbabel/chains.h>

#include <openbabel/math/matrix3x3.h>

#if !HAVE_STRNCASECMP

extern "C" int strncasecmp(const char *s1, const char *s2, size_t n);

#endif

using namespace std;

namespace OpenBabel

{

OB_EXTERN OBChainsParser chainsparser;

/** \class OBAtom atom.h <openbabel/atom.h>

\brief Atom class

To understand the OBAtom class it is important to state a key

decision on which the design was based. The OBAtom class not only

holds data, but facilitates extraction of data perceived from both

the atom and the molecule. This prevents the OBMol class from

becoming overly large and complicated.

A number of data extraction methods perform what is called

<a href="http://en.wikipedia.org/wiki/Lazy_evaluation">`Lazy Evaluation,'</a>

which is essentially on-the-fly evaluation.

For example, when an atom is queried as to whether it is cyclic

or what it's hybridization state is the information is perceived

automatically. The perception of a particular trait is actually

performed on the entire molecule the first time it is requested of

an atom or bond, and stored for subsequent requests for the same

trait of additional atoms or bonds.The OBAtom class is similar to

OBMol and the whole of Open Babel in that data access and modification

is done through Get and Set methods.

The following code demonstrates how to print out the atom numbers,

element numbers, and coordinates of a molecule:

\code

OBMol mol;

FOR_ATOMS_OF_MOL(atom, mol)

{

cout << atom->GetIdx() << ` `;

cout << atom->GetAtomicNum() << ` `;

cout << atom->GetVector() << endl;

}

\endcode

A number of the property member functions indicate that atoms

have some knowledge of their covalently attached neighbor atoms.

Bonding information is partly redundant within a molecule in

that an OBMol has a complete list of bonds in a molecule, and

an OBAtom has a list bonds of which it is a member. The following

code demonstrates how an OBAtom uses its bond information to loop

over atoms attached to itself:

\code

OBMol mol;

OBAtom *atom;

atom = mol.GetAtom(1);

FOR_NBORS_OF_ATOM(nbr, atom)

{

cout << "atom #" << atom->GetIdx() << " is attached to atom #"

<< nbr->GetIdx() << endl;

}

\endcode

should produce an output like

\code

atom #1 is attached to atom #2

\endcode

*/

extern THREAD_LOCAL OBAromaticTyper aromtyper;

extern THREAD_LOCAL OBAtomTyper atomtyper;

extern THREAD_LOCAL OBPhModel phmodel;

OB_EXTERN OBTypeTable ttab;

//

// OBAtom member functions

//

OBAtom::OBAtom()

{

_parent = nullptr;

Clear();

}

OBAtom::~OBAtom()

{

if (_residue != nullptr)

{

_residue->RemoveAtom(this);

}

/*

if (!_vdata.empty())

{

vector<OBGenericData*>::iterator m;

for (m = _vdata.begin();m != _vdata.end();++m)

delete *m;

_vdata.clear();

}

*/

}

bool OBAtom::Clear()

{

_c = nullptr;

_cidx = 0;

_flags=0;

_idx = 0;

_hyb = 0;

_ele = (char)0;

_isotope = 0;

_spinmultiplicity=0; // CM 18 Sept 2003

_imph = 0;

_fcharge = 0;

_type[0] = '\0';

_pcharge = 0.0;

_vbond.clear();

_vbond.reserve(4);

_residue = nullptr;

_id = NoId;

return(OBBase::Clear());

}

OBAtom &OBAtom::operator=(OBAtom &src)

//copy atom information

//bond info is not copied here as ptrs may be invalid

{

if (this != &src) {

_idx = src.GetIdx();

Duplicate(&src);

}

return(*this);

}

void OBAtom::Duplicate(OBAtom *src)

{

if (!src)

return;

_hyb = src->_hyb;

_ele = src->_ele;

_imph = src->_imph;

_isotope = src->_isotope;

_fcharge = src->_fcharge;

_spinmultiplicity = src->_spinmultiplicity;

strncpy(_type,src->_type, sizeof(_type) - 1);

_type[sizeof(_type) - 1] = '\0';

_pcharge = src->_pcharge;

_v = src->GetVector();

_flags = src->_flags;

_residue = nullptr;

_id = src->_id;

_vdata.clear();

//Copy all the OBGenericData, providing the new atom

vector<OBGenericData*>::iterator itr;

for(itr=src->BeginData();itr!=src->EndData();++itr)

{

OBGenericData* pCopiedData = (*itr)->Clone(this);

SetData(pCopiedData);

}

}

bool OBAtom::IsConnected(OBAtom *a1)

{

OBBondIterator i;

OBBond *bond;

for (bond = BeginBond(i);bond;bond = NextBond(i))

if (bond->GetBeginAtom() == a1 || bond->GetEndAtom() == a1)

return(true);

return(false);

}

bool OBAtom::IsOneThree(OBAtom *a1)

{

OBAtom *atom1,*atom2;

OBBond *bond1,*bond2;

OBBondIterator i,j;

atom1 = this;

atom2 = a1;

for (bond1 = atom1->BeginBond(i);bond1;bond1 = atom1->NextBond(i))

for (bond2 = atom2->BeginBond(j);bond2;bond2 = atom2->NextBond(j))

if (bond1->GetNbrAtom(atom1) == bond2->GetNbrAtom(atom2))

return(true);

return(false);

}

bool OBAtom::IsOneFour(OBAtom *a1)

{

OBAtom *atom1,*atom2;

OBBond *bond1,*bond2;

OBBondIterator i,j;

atom1 = this;

atom2 = a1;

for (bond1 = atom1->BeginBond(i);bond1;bond1 = atom1->NextBond(i))

for (bond2 = atom2->BeginBond(j);bond2;bond2 = atom2->NextBond(j))

if ((bond1->GetNbrAtom(atom1))->IsConnected(bond2->GetNbrAtom(atom2)))

return(true);

return(false);

}

bool OBAtom::IsAxial()

{

double tor;

OBAtom *a,*b,*c;

OBBondIterator i,j,k;

for (a = BeginNbrAtom(i);a;a = NextNbrAtom(i))

if (a->GetHyb() == 3 && a->IsInRing() && !(*i)->IsInRing())

for (b = a->BeginNbrAtom(j);b;b = a->NextNbrAtom(j))

if (b != this && b->IsInRing() && b->GetHyb() == 3)

for (c = b->BeginNbrAtom(k);c;c = b->NextNbrAtom(k))

if (c != a && c->IsInRing())

{

tor = fabs(((OBMol*)GetParent())->GetTorsion(this,a,b,c));

return(tor > 55.0 && tor < 75.0);

}

return(false);

}

/** This can be sketched as follows

\code

'*'

\

a=b

\endcode

where a and b are the 'apha' and 'beta' atoms, respectively and '*'

indicates the current atom.

**/

bool OBAtom::HasAlphaBetaUnsat(bool includePandS)

{

OBAtom *a1,*a2;

OBBondIterator i,j;

for (a1 = BeginNbrAtom(i);a1;a1 = NextNbrAtom(i))

if (includePandS || (a1->GetAtomicNum() != OBElements::Phosphorus && a1->GetAtomicNum() != OBElements::Sulfur))

for (a2 = a1->BeginNbrAtom(j);a2;a2 = a1->NextNbrAtom(j))

if (a2 != this && ((*j)->GetBondOrder() == 2 || (*j)->GetBondOrder() == 3 || (*j)->GetBondOrder() == 5))

return(true);

return(false);

}

bool OBAtom::HasBondOfOrder(unsigned int order)

{

OBBond *bond;

OBBondIterator i;

for (bond = BeginBond(i);bond;bond = NextBond(i))

if (bond->GetBondOrder() == order)

return(true);

return(false);

}

int OBAtom::CountBondsOfOrder(unsigned int order)

{

int count = 0;

OBBond *bond;

OBBondIterator i;

for (bond = BeginBond(i);bond;bond = NextBond(i))

if (bond->GetBondOrder() == order)

count++;

return(count);

}

int OBAtom::HighestBondOrder()

{

unsigned int highest = 0;

OBBond *bond;

OBBondIterator i;

for(bond = BeginBond(i); bond; bond = NextBond(i))

if(bond->GetBondOrder() > highest)

highest = bond->GetBondOrder();

return(highest);

}

bool OBAtom::HasNonSingleBond()

{

OBBond *bond;

OBBondIterator i;

for (bond = BeginBond(i);bond;bond = NextBond(i))

if (bond->GetBondOrder() != 1)

return(true);

return(false);

}

bool OBAtom::IsPolarHydrogen()

{

if (GetAtomicNum() != OBElements::Hydrogen)

return(false);

OBAtom *atom;

OBBond *bond;

OBBondIterator i;

for (bond = BeginBond(i);bond;bond = NextBond(i))

{

atom = bond->GetNbrAtom(this);

if (atom->GetAtomicNum() == 7)

return(true);

if (atom->GetAtomicNum() == 8)

return(true);

if (atom->GetAtomicNum() == 15)

return(true);

if (atom->GetAtomicNum() == 16)

return(true);

}

return(false);

}

bool OBAtom::IsNonPolarHydrogen()

{

if (GetAtomicNum() != OBElements::Hydrogen)

return(false);

OBAtom *atom;

OBBond *bond;

OBBondIterator i;

for (bond = BeginBond(i);bond;bond = NextBond(i))

{

atom = bond->GetNbrAtom(this);

if (atom->GetAtomicNum() == 6)

return(true);

}

return(false);

}

vector3 &OBAtom::GetVector()

{

if (!_c)

return(_v);

_v.Set((*_c)[_cidx],(*_c)[_cidx+1],(*_c)[_cidx+2]);

return(_v);

}

const vector3 &OBAtom::GetVector() const

{

if (!_c)

return(_v);

_v.Set((*_c)[_cidx],(*_c)[_cidx+1],(*_c)[_cidx+2]);

return(_v);

}

void OBAtom::SetVector()

{

// obAssert(_c);

if (_c)

_v.Set((*_c)[_cidx],(*_c)[_cidx+1],(*_c)[_cidx+2]);

}

void OBAtom::SetVector(const vector3 &v)

{

if (!_c)

_v = v;

else

{

(*_c)[_cidx ] = v.x();

(*_c)[_cidx+1] = v.y();

(*_c)[_cidx+2] = v.z();

}

}

void OBAtom::SetVector(const double v_x,const double v_y,const double v_z)

{

if (!_c)

_v.Set(v_x,v_y,v_z);

else

{

(*_c)[_cidx ] = v_x;

(*_c)[_cidx+1] = v_y;

(*_c)[_cidx+2] = v_z;

}

}

void OBAtom::SetType(const char *type)

{

strncpy(_type,type, sizeof(_type) - 1);

_type[sizeof(_type) - 1] = '\0';

if (_ele == 1 && type[0] == 'D')

_isotope = 2;

}

void OBAtom::SetType(const string &type)

{

strncpy(_type,type.c_str(), sizeof(_type) - 1);

_type[sizeof(_type) - 1] = '\0';

if (_ele == 1 && type[0] == 'D')

_isotope = 2;

}

void OBAtom::SetIsotope(unsigned int iso)

{

_isotope = iso;

}

OBResidue *OBAtom::GetResidue()

{

OBMol *mol = this->GetParent();

if (!mol->HasChainsPerceived())

chainsparser.PerceiveChains(*mol);

return _residue;

}

double OBAtom::GetAtomicMass() const

{

if (_isotope == 0)

return OBElements::GetMass(_ele);

else

return OBElements::GetExactMass(_ele, _isotope);

}

double OBAtom::GetExactMass() const

{

return OBElements::GetExactMass(_ele, _isotope);

}

char *OBAtom::GetType()

{

OBMol *mol = (OBMol*)GetParent();

if (mol)

if (!mol->HasAtomTypesPerceived())

atomtyper.AssignTypes(*((OBMol*)GetParent()));

if (strlen(_type) == 0) // Somehow we still don't have a type!

{

char num[6];

string fromType = ttab.GetFromType(); // save previous types

string toType = ttab.GetToType();

ttab.SetFromType("ATN");

ttab.SetToType("INT");

snprintf(num, 6, "%d", GetAtomicNum());

ttab.Translate(_type, num);

ttab.SetFromType(fromType.c_str());

ttab.SetToType(toType.c_str());

}

if (_ele == 1 && _isotope == 2)

snprintf(_type, 6, "%s", "D");

return(_type);

}

unsigned int OBAtom::GetHyb() const

{

//hybridization is assigned when atoms are typed

OBMol *mol = (OBMol*)((OBAtom*)this)->GetParent();

if (mol && !mol->HasHybridizationPerceived())

atomtyper.AssignHyb(*mol);

return(_hyb);

}

unsigned int OBAtom::GetHvyDegree() const

{

unsigned int count=0;

OBBond *bond;

OBBondIterator i;

for (bond = ((OBAtom*)this)->BeginBond(i); bond; bond = ((OBAtom*)this)->NextBond(i))

if (bond->GetNbrAtom((OBAtom*)this)->GetAtomicNum() != OBElements::Hydrogen)

count++;

return(count);

}

unsigned int OBAtom::GetHeteroDegree() const

{

unsigned int count=0;

OBBond *bond;

OBBondIterator i;

for (bond = ((OBAtom*)this)->BeginBond(i);bond;bond = ((OBAtom*)this)->NextBond(i))

if (bond->GetNbrAtom((OBAtom*)this)->IsHeteroatom())

count++;

return((unsigned int)count);

}

double OBAtom::GetPartialCharge()

{

if (!GetParent())

return(_pcharge);

if (!((OBMol*)GetParent())->AutomaticPartialCharge())

return(_pcharge);

if (!((OBMol*)GetParent())->HasPartialChargesPerceived())

{

//seed partial charges are set in the atom typing procedure

OBAtom *atom;

OBMol *mol = (OBMol*)GetParent();

vector<OBAtom*>::iterator i;

for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i))

atom->SetPartialCharge(0.0);

phmodel.AssignSeedPartialCharge(*((OBMol*)GetParent()));

OBGastChrg gc;

gc.AssignPartialCharges(*((OBMol*)GetParent()));

}

return(_pcharge);

}

//! Returns true if nitrogen is part of an amide

bool OBAtom::IsAmideNitrogen()

{

if (GetAtomicNum() != OBElements::Nitrogen)

return(false);

OBAtom *nbratom,*atom;

OBBond *abbond,*bond;

OBBondIterator i,j;

atom = this;

for (bond = BeginBond(i);bond;bond = NextBond(i))

{

nbratom = bond->GetNbrAtom(atom);

for (abbond = nbratom->BeginBond(j);abbond;abbond = nbratom->NextBond(j))

if (abbond->GetBondOrder() == 2 &&

(((abbond->GetNbrAtom(nbratom))->GetAtomicNum() == 8) ||

((abbond->GetNbrAtom(nbratom))->GetAtomicNum() == 16)))

return(true);

}

return(false);

}

bool OBAtom::IsAromaticNOxide()

{

if (GetAtomicNum() != OBElements::Nitrogen || !IsAromatic())

return(false);

OBAtom *atom;

OBBondIterator i;

for (atom = BeginNbrAtom(i);atom;atom = NextNbrAtom(i))

if (atom->GetAtomicNum() == OBElements::Oxygen && !(*i)->IsInRing() && (*i)->GetBondOrder() == 2)

return(true);

return(false);

}

bool OBAtom::IsCarboxylOxygen()

{

if (GetAtomicNum() != OBElements::Oxygen)

return(false);

if (GetHvyDegree() != 1)

return(false);

OBAtom *atom;

OBBond *bond;

OBBondIterator i;

atom = nullptr;

for (bond = BeginBond(i);bond;bond = NextBond(i))

if ((bond->GetNbrAtom(this))->GetAtomicNum() == OBElements::Carbon)

{

atom = bond->GetNbrAtom(this);

break;

}

if (!atom)

return(false);

if (!(atom->CountFreeOxygens() == 2)

&& !(atom->CountFreeOxygens() == 1 && atom->CountFreeSulfurs() == 1))

return(false);

//atom is connected to a carbon that has a total

//of 2 attached free oxygens or 1 free oxygen and 1 free sulfur

return(true);

}

bool OBAtom::IsPhosphateOxygen()

{

if (GetAtomicNum() != OBElements::Oxygen)

return(false);

if (GetHvyDegree() != 1)

return(false);

OBAtom *atom;

OBBond *bond;

OBBondIterator i;

atom = nullptr;

for (bond = BeginBond(i);bond;bond = NextBond(i))

if ((bond->GetNbrAtom(this))->GetAtomicNum() == OBElements::Phosphorus)

{

atom = bond->GetNbrAtom(this);

break;

}

if (!atom)

return(false);

if (atom->CountFreeOxygens() > 2)

return(true);

//atom is connected to a carbon that has a total

//of 2 attached free oxygens

return(false);

}

bool OBAtom::IsSulfateOxygen()

{

if (GetAtomicNum() != OBElements::Oxygen)

return(false);

if (GetHvyDegree() != 1)

return(false);

OBAtom *atom;

OBBond *bond;

OBBondIterator i;

atom = nullptr;

for (bond = BeginBond(i);bond;bond = NextBond(i))

if ((bond->GetNbrAtom(this))->GetAtomicNum() == OBElements::Sulfur)

{

atom = bond->GetNbrAtom(this);

break;

}

if (!atom)

return(false);

if (atom->CountFreeOxygens() < 3)

return(false);

//atom is connected to a carbon that has a total

//of 2 attached free oxygens

return(true);

}

// Helper function for IsHBondAcceptor

static bool IsSulfoneOxygen(OBAtom* atm)

// Stefano Forli

//atom is connected to a sulfur that has a total

//of 2 attached free oxygens, and it's not a sulfonamide

//e.g. C-SO2-C

// Is this atom an oxygen in a sulfone(R1 - SO2 - R2) group ?

{

if (atm->GetAtomicNum() != OBElements::Oxygen)

return(false);

if (atm->GetHvyDegree() != 1){

//cerr << "sulfone> O valence is not 1\n";

return(false);

}

OBAtom *nbr = nullptr;

OBBond *bond1,*bond2;

OBBondIterator i,j;

// searching for attached sulfur

for (bond1 = atm->BeginBond(i); bond1; bond1 = atm->NextBond(i))

if ((bond1->GetNbrAtom(atm))->GetAtomicNum() == OBElements::Sulfur)

{ nbr = bond1->GetNbrAtom(atm);

break; }

if (!nbr){

//cerr << "sulfone> atom null\n" ;

return(false); }

// check for sulfate

//cerr << "sulfone> If we're here... " << atom->GetAtomicNum() <<"\n" << atom->GetAtomicNum() == OBElements::Sulfur << "\n";

//cerr << "sulfone> number of free oxygens:" << atom->CountFreeOxygens() << "\n";

if (nbr->CountFreeOxygens() != 2){

//cerr << "sulfone> count of free oxygens not 2" << atom->CountFreeOxygens() << '\n' ;

return(false); }

// check for sulfonamide

for (bond2 = nbr->BeginBond(j);bond2;bond2 = nbr->NextBond(j)){

//cerr<<"NEIGH: " << (bond2->GetNbrAtom(atom))->GetAtomicNum()<<"\n";

if ((bond2->GetNbrAtom(nbr))->GetAtomicNum() == OBElements::Nitrogen){

//cerr << "sulfone> sulfonamide null\n" ;

return(false);}}

//cerr << "sulfone> none of the above\n";

return(true); // true sulfone

}

bool OBAtom::IsNitroOxygen()

{

if (GetAtomicNum() != OBElements::Oxygen)

return(false);

if (GetHvyDegree() != 1)

return(false);

OBAtom *atom;

OBBond *bond;

OBBondIterator i;

atom = nullptr;

for (bond = BeginBond(i);bond;bond = NextBond(i))

if ((bond->GetNbrAtom(this))->GetAtomicNum() == OBElements::Nitrogen)

{

atom = bond->GetNbrAtom(this);

break;

}

if (!atom)

return(false);

if (atom->CountFreeOxygens() != 2)

return(false);

//atom is connected to a nitrogen that has a total

//of 2 attached free oxygens

return(true);

}

bool OBAtom::IsHeteroatom()

{

switch(GetAtomicNum())

{

case 7:

case 8:

case 15:

case 16:

case 33:

case 34:

case 51:

case 52:

case 83:

case 84:

return(true);

}

return(false);

}

bool OBAtom::IsAromatic() const

{

OBMol *mol = ((OBAtom*)this)->GetParent();

if (!mol->HasAromaticPerceived())

aromtyper.AssignAromaticFlags(*mol);

if (((OBAtom*)this)->HasFlag(OB_AROMATIC_ATOM))

return true;

return false;

}

bool OBAtom::IsInRing() const

{

OBMol *mol = ((OBAtom*)this)->GetParent();

if (!mol->HasRingAtomsAndBondsPerceived())

mol->FindRingAtomsAndBonds();

if (((OBAtom*)this)->HasFlag(OB_RING_ATOM))

return true;

return false;

}

//! @todo

bool OBAtom::IsChiral()

{

OBMol *mol = (OBMol*) GetParent();

OBStereoFacade stereoFacade(mol);

return stereoFacade.HasTetrahedralStereo(_id);

}

bool OBAtom::IsPeriodic() const

{

OBMol *mol = (OBMol*)((OBAtom*)this)->GetParent();

if (mol == nullptr)

return false;

return mol->IsPeriodic();

}

bool OBAtom::IsInRingSize(int size) const

{

vector<OBRing*> rlist;

vector<OBRing*>::iterator i;

OBMol *mol = (OBMol*)((OBAtom*)this)->GetParent();

if (!mol->HasSSSRPerceived())

mol->FindSSSR();

if (!((OBAtom*)this)->HasFlag(OB_RING_ATOM))

return(false);

rlist = mol->GetSSSR();

for (i = rlist.begin();i != rlist.end();++i)

if ((*i)->IsInRing(GetIdx()) && static_cast<int>((*i)->Size()) == size)

return(true);

return(false);

}

unsigned int OBAtom::MemberOfRingCount() const

{

vector<OBRing*> rlist;

vector<OBRing*>::iterator i;

unsigned int count=0;

OBMol *mol = (OBMol*)((OBAtom*)this)->GetParent();

if (!mol->HasSSSRPerceived())

mol->FindSSSR();

if (!((OBAtom*)this)->IsInRing())

return(0);

rlist = mol->GetSSSR();

for (i = rlist.begin();i != rlist.end();++i)

if ((*i)->IsInRing(GetIdx()))

count++;

return((unsigned int)count);

}

unsigned int OBAtom::MemberOfRingSize() const

{

vector<OBRing*> rlist;

vector<OBRing*>::iterator i;

OBMol *mol = (OBMol*)((OBAtom*)this)->GetParent();

if (!mol->HasSSSRPerceived())

mol->FindSSSR();

if (!((OBAtom*)this)->IsInRing())

return(0);

rlist = mol->GetSSSR();

for (i = rlist.begin();i != rlist.end();++i)

if ((*i)->IsInRing(GetIdx()))

return((*i)->Size());

return(0);

}

unsigned int OBAtom::CountRingBonds() const

{

unsigned int count = 0;

OBBond *bond;

OBBondIterator i;

for (bond = ((OBAtom*)this)->BeginBond(i);

bond;

bond = ((OBAtom*)this)->NextBond(i))

{

if (bond->IsInRing())

count++;

}

return count;

}

double OBAtom::SmallestBondAngle()

{

OBAtom *b, *c;

vector3 v1, v2;

double degrees, minDegrees;

// vector<OBAtom*>::iterator i;

OBBondIterator j,k;

minDegrees = 360.0;

for (b = BeginNbrAtom(j); b; b = NextNbrAtom(j))

{

k = j;

for (c = NextNbrAtom(k); c; c = NextNbrAtom(k))

{

degrees = b->GetAngle((OBAtom*)this, c);

if (degrees < minDegrees)

minDegrees = degrees;

}

}

return minDegrees;

}

double OBAtom::AverageBondAngle()

{

OBAtom *b, *c;

vector3 v1, v2;

double degrees, avgDegrees;

// vector<OBAtom*>::iterator i;

OBBondIterator j,k;

int n=0;

avgDegrees = 0.0;

for (b = BeginNbrAtom(j); b; b = NextNbrAtom(j))

{

k = j;

for (c = NextNbrAtom(k); c; c = NextNbrAtom(k))

{

degrees = b->GetAngle((OBAtom*)this, c);

avgDegrees += degrees;

n++;

}

}

if (n >=1)

avgDegrees /= n;

return avgDegrees;

}

unsigned int OBAtom::CountFreeOxygens() const

{

unsigned int count = 0;

OBAtom *atom;

OBBond *bond;

OBBondIterator i;

for (bond = ((OBAtom*)this)->BeginBond(i);bond;bond = ((OBAtom*)this)->NextBond(i))

{

atom = bond->GetNbrAtom((OBAtom*)this);

if (atom->GetAtomicNum() == OBElements::Oxygen && atom->GetHvyDegree() == 1)

count++;

}

return(count);

}

unsigned int OBAtom::CountFreeSulfurs() const

{

unsigned int count = 0;

OBAtom *atom;

OBBond *bond;

OBBondIterator i;

for (bond = ((OBAtom*)this)->BeginBond(i);bond;bond = ((OBAtom*)this)->NextBond(i))

{

atom = bond->GetNbrAtom((OBAtom*)this);

if (atom->GetAtomicNum() == OBElements::Sulfur && atom->GetHvyDegree() == 1)

count++;

}

return(count);

}

unsigned int OBAtom::GetExplicitValence() const

{

unsigned int bosum = 0;

OBBondIterator i;

for (OBBond *bond = ((OBAtom*)this)->BeginBond(i); bond; bond = ((OBAtom*)this)->NextBond(i))

bosum += bond->GetBondOrder();

return bosum;

}

unsigned int OBAtom::GetTotalValence() const

{

return GetExplicitValence() + _imph;

}

unsigned int OBAtom::ExplicitHydrogenCount(bool ExcludeIsotopes) const

{

//If ExcludeIsotopes is true, H atoms with _isotope!=0 are not included.

//This excludes D, T and H when _isotope exlicitly set to 1 rather than the default 0.

int numH=0;