source: molecuilder/src/bondgraph.cpp@ 7e4dc3f

/*
 * bondgraph.cpp
 *
 *  Created on: Oct 29, 2009
 *      Author: heber
 */

#include <iostream>

#include "atom.hpp"
#include "bond.hpp"
#include "bondgraph.hpp"
#include "element.hpp"
#include "info.hpp"
#include "log.hpp"
#include "molecule.hpp"
#include "parser.hpp"
#include "periodentafel.hpp"
#include "vector.hpp"

/** Constructor of class BondGraph.
 * This classes contains typical bond lengths and thus may be used to construct a bond graph for a given molecule.
 */
BondGraph::BondGraph(bool IsA) : BondLengthMatrix(NULL), max_distance(0), IsAngstroem(IsA)
{
};

/** Destructor of class BondGraph.
 */
BondGraph::~BondGraph()
{
  if (BondLengthMatrix != NULL) {
    delete(BondLengthMatrix);
  }
};

/** Parses the bond lengths in a given file and puts them int a matrix form.
 * Allocates \a MatrixContainer for BondGraph::BondLengthMatrix, using MatrixContainer::ParseMatrix(),
 * but only if parsing is successful. Otherwise variable is left as NULL.
 * \param *out output stream for debugging
 * \param filename file with bond lengths to parse
 * \return true - success in parsing file, false - failed to parse the file
 */
bool BondGraph::LoadBondLengthTable(const string &filename)
{
  Info FunctionInfo(__func__);
  bool status = true;
  MatrixContainer *TempContainer = NULL;

  // allocate MatrixContainer
  if (BondLengthMatrix != NULL) {
    Log() << Verbose(1) << "MatrixContainer for Bond length already present, removing." << endl;
    delete(BondLengthMatrix);
  }
  TempContainer = new MatrixContainer;

  // parse in matrix
  if (status = TempContainer->ParseMatrix(filename.c_str(), 0, 1, 0)) {
    Log() << Verbose(1) << "Parsing bond length matrix successful." << endl;
  } else {
    DoeLog(1) && (eLog()<< Verbose(1) << "Parsing bond length matrix failed." << endl);
  }

  // find greatest distance
  max_distance=0;
  if (status) {
    for(int i=0;i<TempContainer->RowCounter[0];i++)
      for(int j=i;j<TempContainer->ColumnCounter[0];j++)
        if (TempContainer->Matrix[0][i][j] > max_distance)
          max_distance = TempContainer->Matrix[0][i][j];
  }

  if (status) // set to not NULL only if matrix was parsed
    BondLengthMatrix = TempContainer;
  else {
    BondLengthMatrix = NULL;
    delete(TempContainer);
  }
  return status;
};

/** Parses the bond lengths in a given file and puts them int a matrix form.
 * \param *out output stream for debugging
 * \param *mol molecule with atoms
 * \return true - success, false - failed to construct bond structure
 */
bool BondGraph::ConstructBondGraph(molecule * const mol)
{
  Info FunctionInfo(__func__);
bool status = true;

  if (mol->start->next == mol->end) // only construct if molecule is not empty
    return false;

  if (BondLengthMatrix == NULL) { // no bond length matrix parsed?
    SetMaxDistanceToMaxOfCovalentRadii(mol);
    mol->CreateAdjacencyList(max_distance, IsAngstroem, &BondGraph::CovalentMinMaxDistance, this);
  } else
    mol->CreateAdjacencyList(max_distance, IsAngstroem, &BondGraph::BondLengthMatrixMinMaxDistance, this);

  return status;
};

/** Returns the entry for a given index pair.
 * \param firstelement index/atom number of first element (row index)
 * \param secondelement index/atom number of second element (column index)
 * \note matrix is of course symmetric.
 */
double BondGraph::GetBondLength(int firstZ, int secondZ)
{
  if (BondLengthMatrix == NULL)
    return( -1. );
  else
    return (BondLengthMatrix->Matrix[0][firstZ][secondZ]);
};

/** Determines the maximum of all element::CovalentRadius for elements present in \a *mol.
 * \param *out output stream for debugging
 * \param *mol molecule with all atoms and their respective elements.
 */
double BondGraph::SetMaxDistanceToMaxOfCovalentRadii(const molecule * const mol)
{
  Info FunctionInfo(__func__);
  max_distance = 0.;

  atom *Runner = mol->start;
  while (Runner->next != mol->end) {
    Runner = Runner->next;
    if (Runner->type->CovalentRadius > max_distance)
      max_distance = Runner->type->CovalentRadius;
  }
  max_distance *= 2.;

  return max_distance;
};

/** Returns bond criterion for given pair based on covalent radius.
 * \param *Walker first BondedParticle
 * \param *OtherWalker second BondedParticle
 * \param &MinDistance lower bond bound on return
 * \param &MaxDistance upper bond bound on return
 * \param IsAngstroem whether units are in angstroem or bohr radii
 */
void BondGraph::CovalentMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem)
{
  MinDistance = OtherWalker->type->CovalentRadius + Walker->type->CovalentRadius;
  MinDistance *= (IsAngstroem) ? 1. : 1. / AtomicLengthToAngstroem;
  MaxDistance = MinDistance + BONDTHRESHOLD;
  MinDistance -= BONDTHRESHOLD;
};

/** Returns bond criterion for given pair based on a bond length matrix.
 * The matrix should be contained in \a this BondGraph and contain an element-
 * to-element length.
 * \param *Walker first BondedParticle
 * \param *OtherWalker second BondedParticle
 * \param &MinDistance lower bond bound on return
 * \param &MaxDistance upper bond bound on return
 * \param IsAngstroem whether units are in angstroem or bohr radii
 */
void BondGraph::BondLengthMatrixMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem)
{
  if (BondLengthMatrix == NULL) {// safety measure if no matrix has been parsed yet
    DoeLog(2) && (eLog()<< Verbose(2) << "BondLengthMatrixMinMaxDistance() called without having parsed the bond length matrix yet!" << endl);
    CovalentMinMaxDistance(Walker, OtherWalker, MinDistance, MaxDistance, IsAngstroem);
  } else {
    MinDistance = GetBondLength(Walker->type->Z-1, OtherWalker->type->Z-1);
    MinDistance *= (IsAngstroem) ? 1. : 1. / AtomicLengthToAngstroem;
    MaxDistance = MinDistance + BONDTHRESHOLD;
    MinDistance -= BONDTHRESHOLD;
  }
};

/** Counts the number of hydrogen bridge bonds.
 * With \a *InterfaceElement an extra element can be specified that identifies some boundary.
 * Then, counting is for the h-bridges that connect to interface only.
 * \param *molecules molecules to count bonds
 * \param *InterfaceElement or NULL
 */
int CountHydrogenBridgeBonds(MoleculeListClass *molecules, element * InterfaceElement = NULL)
{
  Info FunctionInfo(__func__);
  atom *Walker = NULL;
  atom *Runner = NULL;
  atom *Hydrogen = NULL;
  atom *OtherHydrogen = NULL;
  Vector OHBond;
  Vector OOBond;
  int count = 0;
  bool HydrogenFlag = false;
  bool OtherHydrogenFlag = false;
  bool InterfaceFlag = false;
  for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin();MolWalker != molecules->ListOfMolecules.end(); MolWalker++) {
    Walker = (*MolWalker)->start;
    while (Walker->next != (*MolWalker)->end) {
      Walker = Walker->next;
      for (MoleculeList::const_iterator MolRunner = molecules->ListOfMolecules.begin();MolRunner != molecules->ListOfMolecules.end(); MolRunner++) {
        Runner = (*MolRunner)->start;
        while (Runner->next != (*MolRunner)->end) {
          Runner = Runner->next;
          if ((Runner != Walker) && (Walker->type->Z  == 8) && (Runner->type->Z  == 8)) {
            // check distance
            const double distance = Runner->x.DistanceSquared(&Walker->x);
            if (distance < HBRIDGEDISTANCE*HBRIDGEDISTANCE) {
              // get hydrogen, check for InterfaceElement
              HydrogenFlag = false;
              OtherHydrogenFlag = false;
              InterfaceFlag = (InterfaceElement == NULL);
              // on other atom(Runner) we check for bond to interface element
              for (BondList::const_iterator BondRunner = Runner->ListOfBonds.begin(); BondRunner != Runner->ListOfBonds.end(); BondRunner++) {
                atom * const OtherAtom = (*BondRunner)->GetOtherAtom(Runner);
                if (!OtherHydrogenFlag && (OtherAtom->type->Z == 1)) {
                  OtherHydrogen = OtherAtom;
                  OtherHydrogenFlag = true;
                }
                InterfaceFlag = InterfaceFlag || (OtherAtom->type == InterfaceElement);
              }
              // on this element (Walker) we check for bond to hydrogen, i.e. part of water molecule
              for (BondList::const_iterator BondRunner = Walker->ListOfBonds.begin(); BondRunner != Walker->ListOfBonds.end(); BondRunner++) {
                atom * const OtherAtom = (*BondRunner)->GetOtherAtom(Walker);
                if (!HydrogenFlag && (OtherAtom->type->Z == 1)) {
                  Hydrogen = OtherAtom;
                  HydrogenFlag = true;
                }
              }
              if (InterfaceFlag && HydrogenFlag) {
                if ((Walker->nr < Runner->nr) || (!OtherHydrogenFlag)) {
                  // check angle
                  OHBond.CopyVector(&Hydrogen->x);
                  OHBond.SubtractVector(&Walker->x);
                  OOBond.CopyVector(&Runner->x);
                  OOBond.SubtractVector(&Walker->x);
                  const double angle = OHBond.Angle(&OOBond);
                  if (angle < M_PI*(30./180.)) {
                    DoLog(1) && (Log() << Verbose(1) << Walker->Name << ", " << Hydrogen->Name << " and " << Runner->Name << " have a hydrogen bridge bond with " << sqrt(distance) << " and at angle " << (180./M_PI)*angle << " degrees." << endl);
                    count++;
                  }
                }
              }
            }
          }
        }
      }
    }
  }
  return count;
}

/** Counts the number of bonds between two given elements.
 * \param *molecules list of molecules with all atoms
 * \param *first pointer to first element
 * \param *second pointer to second element
 * \return number of found bonds (\a *first-\a *second)
 */
int CountBondsOfTwo(MoleculeListClass * const molecules, const element * const first, const element * const second)
{
  atom *Walker = NULL;
  int count = 0;

  for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin();MolWalker != molecules->ListOfMolecules.end(); MolWalker++) {
    Walker = (*MolWalker)->start;
    while (Walker->next != (*MolWalker)->end) {
      Walker = Walker->next;
      if ((Walker->type == first) || (Walker->type == second)) {  // first element matches
        for (BondList::const_iterator BondRunner = Walker->ListOfBonds.begin(); BondRunner != Walker->ListOfBonds.end(); BondRunner++) {
          atom * const OtherAtom = (*BondRunner)->GetOtherAtom(Walker);
          if (((OtherAtom->type == first) || (OtherAtom->type == second)) && (Walker->nr < OtherAtom->nr)) {
            count++;
            DoLog(1) && (Log() << Verbose(1) << first->name << "-" << second->name << " bond found between " << *Walker << " and " << *OtherAtom << "." << endl);
          }
        }
      }
    }
  }
  return count;
};

/** Counts the number of bonds between three given elements.
 * Note that we do not look for arbitrary sequence of given bonds, but \a *second will be the central atom and we check
 * whether it has bonds to both \a *first and \a *third.
 * \param *molecules list of molecules with all atoms
 * \param *first pointer to first element
 * \param *second pointer to second element
 * \param *third pointer to third element
 * \return number of found bonds (\a *first-\a *second-\a *third, \a *third-\a *second-\a *first, respectively)
 */
int CountBondsOfThree(MoleculeListClass * const molecules, const element * const first, const element * const second, const element * const third)
{
  int count = 0;
  bool MatchFlag[2];
  bool result = false;
  atom *Walker = NULL;
  const element * ElementArray[2];
  ElementArray[0] = first;
  ElementArray[1] = third;

  for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin();MolWalker != molecules->ListOfMolecules.end(); MolWalker++) {
    Walker = (*MolWalker)->start;
    while (Walker->next != (*MolWalker)->end) {
      Walker = Walker->next;
      if (Walker->type == second) {  // first element matches
        for (int i=0;i<2;i++)
          MatchFlag[i] = false;
        for (BondList::const_iterator BondRunner = Walker->ListOfBonds.begin(); BondRunner != Walker->ListOfBonds.end(); BondRunner++) {
          atom * const OtherAtom = (*BondRunner)->GetOtherAtom(Walker);
          for (int i=0;i<2;i++)
            MatchFlag[i] = MatchFlag[i] || (OtherAtom->type == ElementArray[i]);
        }
        result = true;
        for (int i=0;i<2;i++)
          result = result && MatchFlag[i];
        if (result) {
          count++;
          DoLog(1) && (Log() << Verbose(1) << first->name << "-" << second->name << "-" << third->name << " bond found at " << *Walker << "." << endl);
        }
      }
    }
  }
  return count;
};