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

bond.cpp - Handle OBBond class

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

Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison

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/elements.h>

#include <openbabel/oberror.h>

#include <openbabel/obutil.h>

#include <openbabel/ring.h>

#include <openbabel/bond.h>

#include <openbabel/mol.h>

#include <openbabel/generic.h>

#include <climits>

using namespace std;

namespace OpenBabel

{

  class OBBondPrivate

  {

    public:

      OBBondPrivate() {}

  };

  extern THREAD_LOCAL OBAromaticTyper  aromtyper;

  extern OBMessageHandler obErrorLog;

  /** \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=nullptr;

    _end=nullptr;

    _vdata.clear();

    _parent=nullptr;

  }

  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::SetBondOrder(int order)

  {

    _order = (char)order;

  }

  // TODO: Figure out how to consider periodicity, etc.

  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 (fabs(v3.length_2()) < 2e-6) { // 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;

    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 != nullptr) {

      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->GetHvyDegree() > 1)

    //                               && (_end->IsHeteroatom() || _end->GetHvyDegree() > 1) );

    return (_bgn->GetHvyDegree() > 1 && _end->GetHvyDegree() > 1);

  }

  bool OBBond::IsPeriodic() const

  {

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

    return mol->IsPeriodic();

  }

   bool OBBond::IsAmide()

   {

      OBAtom *c,*n;

      c = n = nullptr;

      // 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->GetTotalDegree() != 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 = nullptr;

      // 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->GetTotalDegree() != 3) return false; // must be a degree 3 nitrogen

      // Make sure that N is connected to one non-H

      if (n->GetHvyDegree() != 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 = nullptr;

      // 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->GetTotalDegree() != 3) return false; // must be a degree 3 nitrogen

      // Make sure that N is connected to two non-H atoms

      if (n->GetHvyDegree() != 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 = nullptr;

      // 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->GetTotalDegree() != 3) return false; // must be a degree 3 nitrogen

      // Make sure that N is connected to three non-H atoms

      if (n->GetHvyDegree() != 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 (GetBondOrder() != 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 (GetBondOrder() != 1)

      return(false);

    OBBond *bond;

    vector<OBBond*>::iterator i;

    for (bond = a1->BeginBond(i);bond;bond = a1->NextBond(i))

      if (bond->IsCarbonyl())

        if (a2->GetHvyDegree() == 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 (GetBondOrder() != 1)

      return(false);

    OBBond *bond;

    vector<OBBond*>::iterator i;

    for (bond = a1->BeginBond(i);bond;bond = a1->NextBond(i))

      if (bond->IsCarbonyl())

        if (a2->GetHvyDegree() == 3)

          return(true);

    return(false);

  }

*/

  bool OBBond::IsEster()

  {

    OBAtom *a1,*a2;

    a1 = a2 = nullptr;

    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 (GetBondOrder() != 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 (GetBondOrder() != 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->GetExplicitDegree()>3||

        _end->GetHyb()==1 || _end->GetExplicitDegree()>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(_parent->GetTorsion(nbrStart, _bgn, _end, nbrEnd));

                    // >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

  {

    OBMol *mol = ((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 = nullptr;

    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();

    if (!IsPeriodic())

      {

        d2 = SQUARE(begin->GetX() - end->GetX());

        d2 += SQUARE(begin->GetY() - end->GetY());

        d2 += SQUARE(begin->GetZ() - end->GetZ());

        return(sqrt(d2));

      }

    else

      {

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

        OBUnitCell *box = (OBUnitCell*)mol->GetData(OBGenericDataType::UnitCell);

        return (box->MinimumImageCartesian(begin->GetVector() - end->GetVector())).length();

      }

  }

  /*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

//! \file bond.cpp

//! \brief Handle OBBond class