| 1 | /** \file molecule.hpp
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| 2 | *
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| 3 | * Class definitions of atom and molecule, element and periodentafel
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| 4 | */
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| 5 |
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| 6 | #ifndef MOLECULES_HPP_
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| 7 | #define MOLECULES_HPP_
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| 8 |
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| 9 | /*********************************************** includes ***********************************/
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| 10 |
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| 11 | #ifdef HAVE_CONFIG_H
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| 12 | #include <config.h>
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| 13 | #endif
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| 14 |
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| 15 | //// STL headers
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| 16 | #include <map>
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| 17 | #include <set>
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| 18 | #include <deque>
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| 19 | #include <list>
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| 20 | #include <vector>
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| 21 |
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| 22 | #include <string>
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| 23 |
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| 24 | #include "types.hpp"
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| 25 | #include "graph.hpp"
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| 26 | #include "tesselation.hpp"
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| 27 | #include "Patterns/Observer.hpp"
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| 28 | #include "Patterns/ObservedIterator.hpp"
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| 29 | #include "Patterns/Cacheable.hpp"
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| 30 | #include "Formula.hpp"
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| 31 | #include "AtomSet.hpp"
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| 32 |
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| 33 | #include "Descriptors/MoleculeDescriptor_impl.hpp"
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| 34 |
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| 35 | /****************************************** forward declarations *****************************/
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| 36 |
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| 37 | class atom;
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| 38 | class bond;
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| 39 | class BondedParticle;
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| 40 | class BondGraph;
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| 41 | class element;
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| 42 | class ForceMatrix;
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| 43 | class LinkedCell;
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| 44 | class molecule;
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| 45 | class MoleculeLeafClass;
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| 46 | class MoleculeListClass;
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| 47 | class periodentafel;
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| 48 | class Vector;
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| 49 | class Shape;
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| 50 | template <class> class StackClass;
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| 51 |
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| 52 | /******************************** Some definitions for easier reading **********************************/
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| 53 |
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| 54 | #define MoleculeList list <molecule *>
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| 55 | #define MoleculeListTest pair <MoleculeList::iterator, bool>
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| 56 |
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| 57 | #define DistancePair pair < double, atom* >
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| 58 | #define DistanceMap multimap < double, atom* >
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| 59 | #define DistanceTestPair pair < DistanceMap::iterator, bool>
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| 60 |
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| 61 |
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| 62 | /************************************* Class definitions ****************************************/
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| 63 |
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| 64 | /** Structure to contain parameters needed for evaluation of constraint potential.
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| 65 | */
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| 66 | struct EvaluatePotential
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| 67 | {
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| 68 | int startstep; //!< start configuration (MDStep in atom::trajectory)
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| 69 | int endstep; //!< end configuration (MDStep in atom::trajectory)
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| 70 | atom **PermutationMap; //!< gives target ptr for each atom, array of size molecule::AtomCount (this is "x" in \f$ V^{con}(x) \f$ )
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| 71 | DistanceMap **DistanceList; //!< distance list of each atom to each atom
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| 72 | DistanceMap::iterator *StepList; //!< iterator to ascend through NearestNeighbours \a **DistanceList
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| 73 | int *DoubleList; //!< count of which sources want to move to this target, basically the injective measure (>1 -> not injective)
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| 74 | DistanceMap::iterator *DistanceIterators; //!< marks which was the last picked target as injective candidate with smallest distance
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| 75 | bool IsAngstroem; //!< whether coordinates are in angstroem (true) or bohrradius (false)
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| 76 | double *PenaltyConstants; //!< penalty constant in front of each term
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| 77 | };
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| 78 |
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| 79 | /** The complete molecule.
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| 80 | * Class incorporates number of types
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| 81 | */
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| 82 | class molecule : public PointCloud , public Observable {
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| 83 | friend molecule *NewMolecule();
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| 84 | friend void DeleteMolecule(molecule *);
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| 85 |
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| 86 | public:
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| 87 | typedef ATOMSET(std::list) atomSet;
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| 88 | typedef std::set<atomId_t> atomIdSet;
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| 89 | typedef ObservedIterator<atomSet> iterator;
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| 90 | typedef atomSet::const_iterator const_iterator;
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| 91 |
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| 92 | const periodentafel * const elemente; //!< periodic table with each element
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| 93 | // old deprecated atom handling
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| 94 | //atom *start; //!< start of atom list
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| 95 | //atom *end; //!< end of atom list
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| 96 | //bond *first; //!< start of bond list
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| 97 | //bond *last; //!< end of bond list
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| 98 | int MDSteps; //!< The number of MD steps in Trajectories
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| 99 | //int AtomCount; //!< number of atoms, brought up-to-date by CountAtoms()
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| 100 | int BondCount; //!< number of atoms, brought up-to-date by CountBonds()
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| 101 | mutable int NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
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| 102 | mutable int NoNonBonds; //!< number of non-hydrogen bonds in molecule
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| 103 | mutable int NoCyclicBonds; //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
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| 104 | double BondDistance; //!< typical bond distance used in CreateAdjacencyList() and furtheron
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| 105 | bool ActiveFlag; //!< in a MoleculeListClass used to discern active from inactive molecules
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| 106 | Vector Center; //!< Center of molecule in a global box
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| 107 | int IndexNr; //!< index of molecule in a MoleculeListClass
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| 108 | char name[MAXSTRINGSIZE]; //!< arbitrary name
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| 109 |
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| 110 | private:
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| 111 | Formula formula;
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| 112 | Cacheable<int> AtomCount;
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| 113 | moleculeId_t id;
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| 114 | atomSet atoms; //<!list of atoms
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| 115 | atomIdSet atomIds; //<!set of atomic ids to check uniqueness of atoms
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| 116 | protected:
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| 117 | //void CountAtoms();
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| 118 | /**
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| 119 | * this iterator type should be used for internal variables, \
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| 120 | * since it will not lock
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| 121 | */
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| 122 | typedef atomSet::iterator internal_iterator;
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| 123 |
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| 124 |
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| 125 | molecule(const periodentafel * const teil);
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| 126 | virtual ~molecule();
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| 127 |
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| 128 |
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| 129 | public:
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| 130 | //getter and setter
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| 131 | const std::string getName();
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| 132 | int getAtomCount() const;
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| 133 | int doCountAtoms();
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| 134 | moleculeId_t getId();
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| 135 | void setId(moleculeId_t);
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| 136 | void setName(const std::string);
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| 137 | const Formula &getFormula();
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| 138 | unsigned int getElementCount();
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| 139 | bool hasElement(const element*) const;
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| 140 | bool hasElement(atomicNumber_t) const;
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| 141 | bool hasElement(const std::string&) const;
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| 142 |
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| 143 |
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| 144 | iterator begin();
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| 145 | const_iterator begin() const;
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| 146 | iterator end();
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| 147 | const_iterator end() const;
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| 148 | bool empty() const;
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| 149 | size_t size() const;
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| 150 | const_iterator erase( const_iterator loc );
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| 151 | const_iterator erase( atom * key );
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| 152 | const_iterator find ( atom * key ) const;
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| 153 | pair<iterator,bool> insert ( atom * const key );
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| 154 | bool containsAtom(atom* key);
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| 155 |
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| 156 |
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| 157 | // re-definition of virtual functions from PointCloud
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| 158 | const char * const GetName() const;
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| 159 | Vector *GetCenter() const ;
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| 160 | TesselPoint *GetPoint() const ;
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| 161 | int GetMaxId() const;
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| 162 | void GoToNext() const ;
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| 163 | void GoToFirst() const ;
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| 164 | bool IsEmpty() const ;
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| 165 | bool IsEnd() const ;
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| 166 |
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| 167 | // templates for allowing global manipulation of molecule with each atom as single argument
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| 168 | template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) ) const;
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| 169 | template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) const) const;
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| 170 |
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| 171 | // templates for allowing global copying of molecule with each atom as single argument
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| 172 | template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) , molecule *copy) const;
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| 173 | template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) const, molecule *copy) const;
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| 174 |
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| 175 | // templates for allowing global manipulation of all atoms
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| 176 | template <typename res, typename typ> void ActOnAllAtoms( res (typ::*f)() ) const;
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| 177 | template <typename res, typename typ> void ActOnAllAtoms( res (typ::*f)() const) const;
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| 178 | template <typename res, typename typ, typename T> void ActOnAllAtoms( res (typ::*f)(T), T t ) const;
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| 179 | template <typename res, typename typ, typename T> void ActOnAllAtoms( res (typ::*f)(T) const, T t ) const;
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| 180 | template <typename res, typename typ, typename T, typename U> void ActOnAllAtoms( res (typ::*f)(T, U), T t, U u ) const;
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| 181 | template <typename res, typename typ, typename T, typename U> void ActOnAllAtoms( res (typ::*f)(T, U) const, T t, U u ) const;
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| 182 | template <typename res, typename typ, typename T, typename U, typename V> void ActOnAllAtoms( res (typ::*f)(T, U, V), T t, U u, V v) const;
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| 183 | template <typename res, typename typ, typename T, typename U, typename V> void ActOnAllAtoms( res (typ::*f)(T, U, V) const, T t, U u, V v) const;
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| 184 | template <typename res, typename typ, typename T, typename U, typename V, typename W> void ActOnAllAtoms( res (typ::*f)(T, U, V, W), T t, U u, V v, W w) const;
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| 185 | template <typename res, typename typ, typename T, typename U, typename V, typename W> void ActOnAllAtoms( res (typ::*f)(T, U, V, W) const, T t, U u, V v, W w) const;
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| 186 |
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| 187 | // templates for allowing conditional global copying of molecule with each atom as single argument
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| 188 | template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) () ) const;
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| 189 | template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) () const ) const;
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| 190 | template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) () ) const;
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| 191 | template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) () const ) const;
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| 192 | template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T), T t ) const;
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| 193 | template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T) const, T t ) const;
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| 194 | template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T), T t ) const;
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| 195 | template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T) const, T t ) const;
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| 196 | template <typename res, typename T, typename U> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T, U), T t, U u ) const;
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| 197 | template <typename res, typename T, typename U> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T, U) const, T t, U u ) const;
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| 198 | template <typename res, typename T, typename U> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T, U), T t, U u ) const;
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| 199 | template <typename res, typename T, typename U> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T, U) const, T t, U u ) const;
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| 200 | template <typename res, typename T, typename U, typename V> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T, U, V), T t, U u, V v ) const;
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| 201 | template <typename res, typename T, typename U, typename V> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T, U, V) const, T t, U u, V v ) const;
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| 202 | template <typename res, typename T, typename U, typename V> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T, U, V), T t, U u, V v ) const;
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| 203 | template <typename res, typename T, typename U, typename V> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T, U, V) const, T t, U u, V v ) const;
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| 204 |
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| 205 | // templates for allowing global manipulation of an array with one entry per atom
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| 206 | void SetIndexedArrayForEachAtomTo ( atom **array, int ParticleInfo::* index) const;
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| 207 | template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *)) const;
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| 208 | template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *), T t) const;
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| 209 | template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *), T *t) const;
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| 210 | template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *)) const;
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| 211 | template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *), T t) const;
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| 212 | template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *), T *t) const;
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| 213 | template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &), typ atom::*value) const;
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| 214 | template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &) const, typ atom::*value) const;
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| 215 | template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &), typ &vect ) const;
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| 216 | template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &) const, typ &vect ) const;
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| 217 |
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| 218 | // templates for allowing global manipulation of each atom by entries in an array
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| 219 | template <typename T, typename typ, typename typ2> void SetAtomValueToIndexedArray ( T *array, int typ::*index, T typ2::*value ) const;
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| 220 | template <typename T, typename typ> void SetAtomValueToValue ( T value, T typ::*ptr ) const;
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| 221 |
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| 222 | template <typename res, typename typ> res SumPerAtom(res (typ::*f)() ) const;
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| 223 | template <typename res, typename typ> res SumPerAtom(res (typ::*f)() const ) const;
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| 224 | template <typename res, typename typ, typename T> res SumPerAtom(res (typ::*f)(T) , T t ) const;
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| 225 | template <typename res, typename typ, typename T> res SumPerAtom(res (typ::*f)(T) const, T t ) const;
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| 226 |
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| 227 | /// remove atoms from molecule.
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| 228 | bool AddAtom(atom *pointer);
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| 229 | bool RemoveAtom(atom *pointer);
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| 230 | bool UnlinkAtom(atom *pointer);
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| 231 | bool CleanupMolecule();
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| 232 |
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| 233 | /// Add/remove atoms to/from molecule.
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| 234 | atom * AddCopyAtom(atom *pointer);
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| 235 | bool AddXYZFile(string filename);
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| 236 | bool AddHydrogenReplacementAtom(bond *Bond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bool IsAngstroem);
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| 237 | bond * AddBond(atom *first, atom *second, int degree = 1);
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| 238 | bool RemoveBond(bond *pointer);
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| 239 | bool RemoveBonds(atom *BondPartner);
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| 240 | bool hasBondStructure();
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| 241 | unsigned int CountBonds() const;
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| 242 |
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| 243 | /// Find atoms.
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| 244 | atom * FindAtom(int Nr) const;
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| 245 | atom * AskAtom(string text);
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| 246 |
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| 247 | /// Count and change present atoms' coordination.
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| 248 | bool CenterInBox();
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| 249 | bool BoundInBox();
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| 250 | void CenterEdge(Vector *max);
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| 251 | void CenterOrigin();
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| 252 | void CenterPeriodic();
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| 253 | void CenterAtVector(Vector *newcenter);
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| 254 | void Translate(const Vector *x);
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| 255 | void TranslatePeriodically(const Vector *trans);
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| 256 | void Mirror(const Vector *x);
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| 257 | void Align(Vector *n);
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| 258 | void Scale(const double ** const factor);
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| 259 | void DeterminePeriodicCenter(Vector ¢er);
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| 260 | Vector * DetermineCenterOfGravity() const;
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| 261 | Vector * DetermineCenterOfAll() const;
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| 262 | Vector * DetermineCenterOfBox() const;
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| 263 | void SetNameFromFilename(const char *filename);
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| 264 | void SetBoxDimension(Vector *dim);
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| 265 | void ScanForPeriodicCorrection();
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| 266 | bool VerletForceIntegration(char *file, config &configuration, const size_t offset);
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| 267 | void Thermostats(config &configuration, double ActualTemp, int Thermostat);
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| 268 | double VolumeOfConvexEnvelope(bool IsAngstroem);
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| 269 |
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| 270 | double ConstrainedPotential(struct EvaluatePotential &Params);
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| 271 | double MinimiseConstrainedPotential(atom **&permutation, int startstep, int endstep, bool IsAngstroem);
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| 272 | void EvaluateConstrainedForces(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force);
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| 273 | bool LinearInterpolationBetweenConfiguration(int startstep, int endstep, std::string &prefix, config &configuration, bool MapByIdentity);
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| 274 |
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| 275 | bool CheckBounds(const Vector *x) const;
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| 276 | void GetAlignvector(struct lsq_params * par) const;
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| 277 |
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| 278 | /// Initialising routines in fragmentation
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| 279 | void CreateAdjacencyListFromDbondFile(ifstream *output);
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| 280 | void CreateAdjacencyList(double bonddistance, bool IsAngstroem, void (BondGraph::*f)(BondedParticle * const , BondedParticle * const , double &, double &, bool), BondGraph *BG = NULL);
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| 281 | int CorrectBondDegree() const;
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| 282 | void OutputBondsList() const;
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| 283 | void CyclicBondAnalysis() const;
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| 284 | void OutputGraphInfoPerAtom() const;
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| 285 | void OutputGraphInfoPerBond() const;
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| 286 |
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| 287 |
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| 288 | // Graph analysis
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| 289 | MoleculeLeafClass * DepthFirstSearchAnalysis(class StackClass<bond *> *&BackEdgeStack) const;
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| 290 | void CyclicStructureAnalysis(class StackClass<bond *> *BackEdgeStack, int *&MinimumRingSize) const;
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| 291 | bool PickLocalBackEdges(atom **ListOfLocalAtoms, class StackClass<bond *> *&ReferenceStack, class StackClass<bond *> *&LocalStack) const;
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| 292 | bond * FindNextUnused(atom *vertex) const;
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| 293 | void SetNextComponentNumber(atom *vertex, int nr) const;
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| 294 | void ResetAllBondsToUnused() const;
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| 295 | int CountCyclicBonds();
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| 296 | bool CheckForConnectedSubgraph(KeySet *Fragment);
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| 297 | string GetColor(enum Shading color) const;
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| 298 | bond * CopyBond(atom *left, atom *right, bond *CopyBond);
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| 299 |
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| 300 |
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| 301 | molecule *CopyMolecule();
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| 302 | molecule* CopyMoleculeFromSubRegion(const Shape&) const;
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| 303 |
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| 304 | /// Fragment molecule by two different approaches:
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| 305 | int FragmentMolecule(int Order, std::string &prefix);
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| 306 | bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, std::string path = "");
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| 307 | bool StoreBondsToFile(std::string &filename, std::string path = "");
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| 308 | bool StoreAdjacencyToFile(std::string &filename, std::string path = "");
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| 309 | bool CheckAdjacencyFileAgainstMolecule(std::string &path, atom **ListOfAtoms);
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| 310 | bool ParseOrderAtSiteFromFile(std::string &path);
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| 311 | bool StoreOrderAtSiteFile(std::string &path);
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| 312 | bool StoreForcesFile(MoleculeListClass *BondFragments, std::string &path, int *SortIndex);
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| 313 | bool CreateMappingLabelsToConfigSequence(int *&SortIndex);
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| 314 | bool CreateFatherLookupTable(atom **&LookupTable, int count = 0);
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| 315 | void BreadthFirstSearchAdd(molecule *Mol, atom **&AddedAtomList, bond **&AddedBondList, atom *Root, bond *Bond, int BondOrder, bool IsAngstroem);
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| 316 | /// -# BOSSANOVA
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| 317 | void FragmentBOSSANOVA(Graph *&FragmentList, KeyStack &RootStack, int *MinimumRingSize);
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| 318 | int PowerSetGenerator(int Order, struct UniqueFragments &FragmentSearch, KeySet RestrictedKeySet);
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| 319 | bool BuildInducedSubgraph(const molecule *Father);
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| 320 | molecule * StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem);
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| 321 | void SPFragmentGenerator(struct UniqueFragments *FragmentSearch, int RootDistance, bond **BondsSet, int SetDimension, int SubOrder);
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| 322 | int LookForRemovalCandidate(KeySet *&Leaf, int *&ShortestPathList);
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| 323 | int GuesstimateFragmentCount(int order);
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| 324 |
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| 325 | // Recognize doubly appearing molecules in a list of them
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| 326 | int * IsEqualToWithinThreshold(molecule *OtherMolecule, double threshold);
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| 327 | int * GetFatherSonAtomicMap(molecule *OtherMolecule);
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| 328 |
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| 329 | // Output routines.
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| 330 | bool Output(std::ostream * const output);
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| 331 | bool OutputTrajectories(ofstream * const output);
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| 332 | void OutputListOfBonds() const;
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| 333 | bool OutputXYZ(ofstream * const output) const;
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| 334 | bool OutputTrajectoriesXYZ(ofstream * const output);
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| 335 | bool Checkout(ofstream * const output) const;
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| 336 | bool OutputTemperatureFromTrajectories(ofstream * const output, int startstep, int endstep);
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| 337 |
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| 338 | // Manipulation routines
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| 339 | void flipActiveFlag();
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| 340 |
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| 341 | private:
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| 342 | int last_atom; //!< number given to last atom
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| 343 | mutable internal_iterator InternalPointer; //!< internal pointer for PointCloud
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| 344 | };
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| 345 |
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| 346 | molecule *NewMolecule();
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| 347 | void DeleteMolecule(molecule* mol);
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| 348 |
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| 349 | #include "molecule_template.hpp"
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| 350 |
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| 351 | /** A list of \a molecule classes.
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| 352 | */
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| 353 | class MoleculeListClass : public Observable {
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| 354 | public:
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| 355 | MoleculeList ListOfMolecules; //!< List of the contained molecules
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| 356 | int MaxIndex;
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| 357 |
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| 358 | MoleculeListClass(World *world);
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| 359 | ~MoleculeListClass();
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| 360 |
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| 361 | bool AddHydrogenCorrection(std::string &path);
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| 362 | bool StoreForcesFile(std::string &path, int *SortIndex);
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| 363 | void insert(molecule *mol);
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| 364 | void erase(molecule *mol);
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| 365 | molecule * ReturnIndex(int index);
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| 366 | bool OutputConfigForListOfFragments(std::string &prefix, int *SortIndex);
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| 367 | int NumberOfActiveMolecules();
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| 368 | void Enumerate(ostream *out);
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| 369 | void Output(ofstream *out);
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| 370 | void DissectMoleculeIntoConnectedSubgraphs(const periodentafel * const periode, config * const configuration);
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| 371 | int CountAllAtoms() const;
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| 372 |
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| 373 | // Methods moved here from the menus
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| 374 | // TODO: more refactoring needed on these methods
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| 375 | void flipChosen();
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| 376 | void createNewMolecule(periodentafel *periode);
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| 377 | void loadFromXYZ(periodentafel *periode);
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| 378 | void setMoleculeFilename();
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|---|
| 379 | void parseXYZIntoMolecule();
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|---|
| 380 | void eraseMolecule();
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|---|
| 381 |
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| 382 |
|
|---|
| 383 | // merging of molecules
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|---|
| 384 | bool SimpleMerge(molecule *mol, molecule *srcmol);
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| 385 | bool SimpleAdd(molecule *mol, molecule *srcmol);
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|---|
| 386 | bool SimpleMultiMerge(molecule *mol, int *src, int N);
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|---|
| 387 | bool SimpleMultiAdd(molecule *mol, int *src, int N);
|
|---|
| 388 | bool ScatterMerge(molecule *mol, int *src, int N);
|
|---|
| 389 | bool EmbedMerge(molecule *mol, molecule *srcmol);
|
|---|
| 390 |
|
|---|
| 391 | private:
|
|---|
| 392 | World *world; //!< The world this List belongs to. Needed to avoid deadlocks in the destructor
|
|---|
| 393 | };
|
|---|
| 394 |
|
|---|
| 395 |
|
|---|
| 396 | /** A leaf for a tree of \a molecule class
|
|---|
| 397 | * Wraps molecules in a tree structure
|
|---|
| 398 | */
|
|---|
| 399 | class MoleculeLeafClass {
|
|---|
| 400 | public:
|
|---|
| 401 | molecule *Leaf; //!< molecule of this leaf
|
|---|
| 402 | //MoleculeLeafClass *UpLeaf; //!< Leaf one level up
|
|---|
| 403 | //MoleculeLeafClass *DownLeaf; //!< First leaf one level down
|
|---|
| 404 | MoleculeLeafClass *previous; //!< Previous leaf on this level
|
|---|
| 405 | MoleculeLeafClass *next; //!< Next leaf on this level
|
|---|
| 406 |
|
|---|
| 407 | //MoleculeLeafClass(MoleculeLeafClass *Up, MoleculeLeafClass *Previous);
|
|---|
| 408 | MoleculeLeafClass(MoleculeLeafClass *PreviousLeaf);
|
|---|
| 409 | ~MoleculeLeafClass();
|
|---|
| 410 |
|
|---|
| 411 | bool AddLeaf(molecule *ptr, MoleculeLeafClass *Previous);
|
|---|
| 412 | bool FillBondStructureFromReference(const molecule * const reference, atom **&ListOfLocalAtoms, bool FreeList = false);
|
|---|
| 413 | bool FillRootStackForSubgraphs(KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter);
|
|---|
| 414 | bool AssignKeySetsToFragment(molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList = false);
|
|---|
| 415 | bool FillListOfLocalAtoms(atom **&ListOfLocalAtoms, const int GlobalAtomCount, bool &FreeList);
|
|---|
| 416 | void TranslateIndicesToGlobalIDs(Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph);
|
|---|
| 417 | int Count() const;
|
|---|
| 418 | };
|
|---|
| 419 |
|
|---|
| 420 |
|
|---|
| 421 | #endif /*MOLECULES_HPP_*/
|
|---|
| 422 |
|
|---|