source: src/molecule.hpp@ 2a0271

/** \file molecule.hpp
 *
 * Class definitions of atom and molecule, element and periodentafel
 */

#ifndef MOLECULES_HPP_
#define MOLECULES_HPP_

/*********************************************** includes ***********************************/

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

//// STL headers
#include <map>
#include <set>
#include <stack>
#include <deque>
#include <list>
#include <vector>

#include <boost/iterator/transform_iterator.hpp>

#include <string>

#include "Atom/AtomSet.hpp"
#include "CodePatterns/Cacheable.hpp"
#include "CodePatterns/Observer/Observable.hpp"
#include "CodePatterns/Observer/ObservedIterator.hpp"
#include "Descriptors/AtomIdDescriptor.hpp"
#include "Fragmentation/HydrogenSaturation_enum.hpp"
#include "Formula.hpp"
#include "Helpers/defs.hpp"
#include "IdPool_policy.hpp"
#include "IdPool.hpp"
#include "types.hpp"

// TODO: Was is the include of MoleculeDescriptor_impl.hpp doing in molecule.hpp
#include "Descriptors/MoleculeDescriptor_impl.hpp"

/****************************************** forward declarations *****************************/

class atom;
class bond;
class BondedParticle;
class BondGraph;
class DepthFirstSearchAnalysis;
class element;
class ForceMatrix;
class Graph;
class LinkedCell_deprecated;
class molecule;
class MoleculeLeafClass;
class MoleculeListClass;
class periodentafel;
class RealSpaceMatrix;
class Vector;
class Shape;

/******************************** Some definitions for easier reading **********************************/

struct FromIdToAtom :
  public std::unary_function<atom *, atomId_t>
{
    atom * operator()(atomId_t id) const {
     return World::getInstance().getAtom(AtomById(id));
    }
};

/************************************* Class definitions ****************************************/

/** The complete molecule.
 * Class incorporates number of types
 */
class molecule : public Observable
{
  friend molecule *NewMolecule();
  friend void DeleteMolecule(molecule *);

public:
  typedef std::set<atomId_t> atomIdSet;
  typedef boost::transform_iterator<FromIdToAtom, atomIdSet::iterator, atom *, atomId_t> iterator;
  typedef boost::transform_iterator<FromIdToAtom, atomIdSet::const_iterator, const atom *, atomId_t const &> const_iterator;

  const periodentafel * const elemente; //!< periodic table with each element
  int MDSteps; //!< The number of MD steps in Trajectories
  mutable int NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
  mutable int NoNonBonds; //!< number of non-hydrogen bonds in molecule
  mutable int NoCyclicBonds; //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
  bool ActiveFlag; //!< in a MoleculeListClass used to discern active from inactive molecules
  int IndexNr; //!< index of molecule in a MoleculeListClass
  char name[MAXSTRINGSIZE]; //!< arbitrary name

private:
  Formula formula;
  Cacheable<int> AtomCount; //!< number of atoms, brought up-to-date by doCountAtoms()
  Cacheable<int> BondCount; //!< number of atoms, brought up-to-date by doCountBonds()
  moleculeId_t id;
  atomIdSet atomIds; //<!set of atomic ids to check uniqueness of atoms
  IdPool<atomId_t, uniqueId> atomIdPool;  //!< pool of internal ids such that way may guarantee uniqueness

protected:

  molecule(const periodentafel * const teil);
  virtual ~molecule();

public:
  //getter and setter
  const std::string getName() const;
  int getAtomCount() const;
  int doCountAtoms();
  int getBondCount() const;
  int doCountBonds() const;
  moleculeId_t getId() const;
  void setId(moleculeId_t);
  void setName(const std::string);
  const Formula &getFormula() const;
  unsigned int getElementCount() const;
  bool hasElement(const element*) const;
  bool hasElement(atomicNumber_t) const;
  bool hasElement(const std::string&) const;

  virtual bool changeId(atomId_t newId);

  World::AtomComposite getAtomSet() const;

  iterator begin();
  const_iterator begin() const;
  iterator end();
  const_iterator end() const;
  bool empty() const;
  size_t size() const;
  const_iterator find(atom * key) const;
  pair<iterator, bool> insert(atom * const key);
  bool containsAtom(atom* key);

private:
  friend void atom::removeFromMolecule();
  /** Erase an atom from the list.
   * \note This should only be called by atom::removeFromMolecule(),
   * otherwise it is not assured that the atom knows about it.
   *
   * @param loc locator to atom in list
   * @return iterator to just after removed item (compliant with standard)
   */
  const_iterator erase(const_iterator loc);
  /** Erase an atom from the list.
   * \note This should only be called by atom::removeFromMolecule(),
   * otherwise it is not assured that the atom knows about it.
   *
   * @param *key key to atom in list
   * @return iterator to just after removed item (compliant with standard)
   */
  const_iterator erase(atom * key);

private:
  friend bool atom::changeNr(int newId);
  /**
   * used when changing an ParticleInfo::Nr.
   * Note that this number is local with this molecule.
   * Unless you are calling this method from inside an atom don't fiddle with the third parameter.
   *
   * @param oldNr old Nr
   * @param newNr new Nr to set
   * @param *target ref to atom
   * @return indicates wether the change could be done or not.
   */
  bool changeAtomNr(int oldNr, int newNr, atom* target=0);

  /** Sets the name of the atom.
   *
   * The name is set via its element symbol and its internal ParticleInfo::Nr.
   *
   * @param _atom atom whose name to set
   */
  void setAtomName(atom *_atom) const;

public:

  /// remove atoms from molecule.
  bool AddAtom(atom *pointer);
  bool RemoveAtom(atom *pointer);
  bool UnlinkAtom(atom *pointer);
  bool CleanupMolecule();
  void removeAtomsinMolecule();

  /// Add/remove atoms to/from molecule.
  atom * AddCopyAtom(atom *pointer);
  bool AddXYZFile(string filename);
  bool AddHydrogenReplacementAtom(bond *Bond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bool IsAngstroem);
  bond * AddBond(atom *first, atom *second, int degree = 1);
  bool RemoveBond(bond *pointer);
  bool RemoveBonds(atom *BondPartner);
  bool hasBondStructure() const;

  /// Find atoms.
  atom * FindAtom(int Nr) const;
  atom * AskAtom(string text);
  bool isInMolecule(const atom * const _atom);

  /// Count and change present atoms' coordination.
  bool CenterInBox();
  bool BoundInBox();
  void CenterEdge(Vector *max);
  void CenterOrigin();
  void CenterPeriodic();
  void CenterAtVector(Vector *newcenter);
  void Translate(const Vector *x);
  void TranslatePeriodically(const Vector *trans);
  void Mirror(const Vector *x);
  void Align(Vector *n);
  void Scale(const double ** const factor);
  void DeterminePeriodicCenter(Vector &center, const enum HydrogenSaturation _saturation = DoSaturate);
  Vector * DetermineCenterOfGravity() const;
  Vector * DetermineCenterOfAll() const;
  Vector * DetermineCenterOfBox() const;
  void SetNameFromFilename(const char *filename);
  void SetBoxDimension(Vector *dim);
  bool ScanForPeriodicCorrection();
  double VolumeOfConvexEnvelope(bool IsAngstroem);
  RealSpaceMatrix getInertiaTensor() const;
  void RotateToPrincipalAxisSystem(Vector &Axis);

  bool CheckBounds(const Vector *x) const;
  void GetAlignvector(struct lsq_params * par) const;

  /// Initialising routines in fragmentation
  void OutputBondsList() const;

  bond * CopyBond(atom *left, atom *right, bond *CopyBond);

  molecule *CopyMolecule() const;
  molecule* CopyMoleculeFromSubRegion(const Shape&) const;

  /// Fragment molecule by two different approaches:
  bool StoreBondsToFile(std::string filename, std::string path = "");
  bool StoreAdjacencyToFile(std::string filename, std::string path = "");
  bool CreateFatherLookupTable(atom **&LookupTable, int count = 0);

  // Recognize doubly appearing molecules in a list of them
  int * GetFatherSonAtomicMap(molecule *OtherMolecule);
  bool FillBondStructureFromReference(const molecule * const reference, atom **&ListOfLocalAtoms, bool FreeList = false);
  bool FillListOfLocalAtoms(atom **&ListOfLocalAtoms, const int GlobalAtomCount);

  // Output routines.
  bool Output(std::ostream * const output) const;
  bool OutputTrajectories(ofstream * const output) const;
  void OutputListOfBonds() const;
  bool OutputXYZ(ofstream * const output) const;
  bool OutputTrajectoriesXYZ(ofstream * const output);
  bool Checkout(ofstream * const output) const;

  // Manipulation routines
  void flipActiveFlag();

private:
  int last_atom; //!< number given to last atom
};

molecule *NewMolecule();
void DeleteMolecule(molecule* mol);



#endif /*MOLECULES_HPP_*/