source: src/molecule_graph.cpp@ 5f61dde

/*
 * Project: MoleCuilder
 * Description: creates and alters molecular systems
 * Copyright (C)  2010 University of Bonn. All rights reserved.
 * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
 */

/*
 * molecule_graph.cpp
 *
 *  Created on: Oct 5, 2009
 *      Author: heber
 */

// include config.h
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include "CodePatterns/MemDebug.hpp"

#include <stack>

#include "atom.hpp"
#include "Bond/bond.hpp"
#include "Box.hpp"
#include "CodePatterns/Assert.hpp"
#include "CodePatterns/Info.hpp"
#include "CodePatterns/Log.hpp"
#include "CodePatterns/Verbose.hpp"
#include "config.hpp"
#include "Graph/DepthFirstSearchAnalysis.hpp"
#include "Element/element.hpp"
#include "Graph/BondGraph.hpp"
#include "Helpers/defs.hpp"
#include "LinearAlgebra/RealSpaceMatrix.hpp"
#include "linkedcell.hpp"
#include "molecule.hpp"
#include "PointCloudAdaptor.hpp"
#include "World.hpp"
#include "WorldTime.hpp"


/** Fills the bond structure of this chain list subgraphs that are derived from a complete \a *reference molecule.
 * Calls this routine in each MoleculeLeafClass::next subgraph if it's not NULL.
 * \param *reference reference molecule with the bond structure to be copied
 * \param **&ListOfLocalAtoms Lookup table for this subgraph and index of each atom in \a *reference, may be NULL on start, then it is filled
 * \param FreeList true - ***ListOfLocalAtoms is free'd before return, false - it is not
 * \return true - success, false - failure
 */
bool molecule::FillBondStructureFromReference(const molecule * const reference, atom **&ListOfLocalAtoms, bool FreeList)
{
  atom *OtherWalker = NULL;
  atom *Father = NULL;
  bool status = true;
  int AtomNo;

  DoLog(1) && (Log() << Verbose(1) << "Begin of FillBondStructureFromReference." << endl);
  // fill ListOfLocalAtoms if NULL was given
  if (!FillListOfLocalAtoms(ListOfLocalAtoms, reference->getAtomCount())) {
    DoLog(1) && (Log() << Verbose(1) << "Filling of ListOfLocalAtoms failed." << endl);
    return false;
  }

  if (status) {
    DoLog(1) && (Log() << Verbose(1) << "Creating adjacency list for molecule " << getName() << "." << endl);
    // remove every bond from the list
    for_each(begin(), end(),
        boost::bind(&BondedParticle::ClearBondsAtStep,_1,WorldTime::getTime()));


    for(molecule::const_iterator iter = begin(); iter != end(); ++iter) {
      Father = (*iter)->GetTrueFather();
      AtomNo = Father->getNr(); // global id of the current walker
      const BondList& ListOfBonds = Father->getListOfBonds();
      for (BondList::const_iterator Runner = ListOfBonds.begin();
          Runner != ListOfBonds.end();
          ++Runner) {
        OtherWalker = ListOfLocalAtoms[(*Runner)->GetOtherAtom((*iter)->GetTrueFather())->getNr()]; // local copy of current bond partner of walker
        if (OtherWalker != NULL) {
          if (OtherWalker->getNr() > (*iter)->getNr())
            AddBond((*iter), OtherWalker, (*Runner)->BondDegree);
        } else {
          DoLog(1) && (Log() << Verbose(1) << "OtherWalker = ListOfLocalAtoms[" << (*Runner)->GetOtherAtom((*iter)->GetTrueFather())->getNr() << "] is NULL!" << endl);
          status = false;
        }
      }
    }
  }

  if ((FreeList) && (ListOfLocalAtoms != NULL)) {
    // free the index lookup list
    delete[](ListOfLocalAtoms);
  }
  DoLog(1) && (Log() << Verbose(1) << "End of FillBondStructureFromReference." << endl);
  return status;
};

/** Checks for presence of bonds within atom list.
 * TODO: more sophisticated check for bond structure (e.g. connected subgraph, ...)
 * \return true - bonds present, false - no bonds
 */
bool molecule::hasBondStructure() const
{
  for(molecule::const_iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner) {
    //LOG(0, "molecule::hasBondStructure() - checking bond list of atom " << (*AtomRunner)->getId() << ".");
    const BondList& ListOfBonds = (*AtomRunner)->getListOfBonds();
    if (!ListOfBonds.empty())
      return true;
  }
  return false;
}

/** Prints a list of all bonds to \a *out.
 */
void molecule::OutputBondsList() const
{
  DoLog(1) && (Log() << Verbose(1) << endl << "From contents of bond chain list:");
  for(molecule::const_iterator AtomRunner = molecule::begin(); AtomRunner != molecule::end(); ++AtomRunner) {
    const BondList& ListOfBonds = (*AtomRunner)->getListOfBonds();
    for(BondList::const_iterator BondRunner = ListOfBonds.begin();
        BondRunner != ListOfBonds.end();
        ++BondRunner)
      if ((*BondRunner)->leftatom == *AtomRunner) {
        DoLog(0) && (Log() << Verbose(0) << *(*BondRunner) << "\t" << endl);
      }
  }
  DoLog(0) && (Log() << Verbose(0) << endl);
}
;


/** Storing the bond structure of a molecule to file.
 * Simply stores Atom::Nr and then the Atom::Nr of all bond partners per line.
 * \param &filename name of file
 * \param path path to file, defaults to empty
 * \return true - file written successfully, false - writing failed
 */
bool molecule::StoreAdjacencyToFile(std::string filename, std::string path)
{
  ofstream AdjacencyFile;
  string line;
  bool status = true;

  if (path != "")
    line = path + "/" + filename;
  else
    line = filename;
  AdjacencyFile.open(line.c_str(), ios::out);
  DoLog(1) && (Log() << Verbose(1) << "Saving adjacency list ... " << endl);
  if (AdjacencyFile.good()) {
    AdjacencyFile << "m\tn" << endl;
    for_each(atoms.begin(),atoms.end(),bind2nd(mem_fun(&atom::OutputAdjacency),&AdjacencyFile));
    AdjacencyFile.close();
    DoLog(1) && (Log() << Verbose(1) << "\t... done." << endl);
  } else {
    DoLog(1) && (Log() << Verbose(1) << "\t... failed to open file " << line << "." << endl);
    status = false;
  }

  return status;
}
;

/** Storing the bond structure of a molecule to file.
 * Simply stores Atom::Nr and then the Atom::Nr of all bond partners, one per line.
 * \param &filename name of file
 * \param path path to file, defaults to empty
 * \return true - file written successfully, false - writing failed
 */
bool molecule::StoreBondsToFile(std::string filename, std::string path)
{
  ofstream BondFile;
  string line;
  bool status = true;

  if (path != "")
    line = path + "/" + filename;
  else
    line = filename;
  BondFile.open(line.c_str(), ios::out);
  DoLog(1) && (Log() << Verbose(1) << "Saving adjacency list ... " << endl);
  if (BondFile.good()) {
    BondFile << "m\tn" << endl;
    for_each(atoms.begin(),atoms.end(),bind2nd(mem_fun(&atom::OutputBonds),&BondFile));
    BondFile.close();
    DoLog(1) && (Log() << Verbose(1) << "\t... done." << endl);
  } else {
    DoLog(1) && (Log() << Verbose(1) << "\t... failed to open file " << line << "." << endl);
    status = false;
  }

  return status;
}
;

/** Adds a bond as a copy to a given one
 * \param *left leftatom of new bond
 * \param *right rightatom of new bond
 * \param *CopyBond rest of fields in bond are copied from this
 * \return pointer to new bond
 */
bond * molecule::CopyBond(atom *left, atom *right, bond *CopyBond)
{
  bond *Binder = AddBond(left, right, CopyBond->BondDegree);
  Binder->Cyclic = CopyBond->Cyclic;
  Binder->Type = CopyBond->Type;
  return Binder;
}
;

/** Fills a lookup list of father's Atom::nr -> atom for each subgraph.
 * \param **&ListOfLocalAtoms Lookup table for each subgraph and index of each atom in global molecule, may be NULL on start, then it is filled
 * \param GlobalAtomCount number of atoms in the complete molecule
 * \return true - success, false - failure (ListOfLocalAtoms != NULL)
 */
bool molecule::FillListOfLocalAtoms(atom **&ListOfLocalAtoms, const int GlobalAtomCount)
{
  bool status = true;

  if (ListOfLocalAtoms == NULL) { // allocate and fill list of this fragment/subgraph
    status = status && CreateFatherLookupTable(ListOfLocalAtoms, GlobalAtomCount);
  } else
    return false;

  return status;
}