[cee0b57] | 1 | /** \file molecule.hpp
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[14de469] | 2 | *
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[69eb71] | 3 | * Class definitions of atom and molecule, element and periodentafel
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[14de469] | 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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[f66195] | 9 | /*********************************************** includes ***********************************/
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| 10 |
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[962d8d] | 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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[edb93c] | 15 | //// STL headers
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[14de469] | 16 | #include <map>
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| 17 | #include <set>
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[a564be] | 18 | #include <stack>
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[14de469] | 19 | #include <deque>
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[d7e30c] | 20 | #include <list>
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[5e0d1f] | 21 | #include <vector>
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[14de469] | 22 |
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[520c8b] | 23 | #include <string>
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| 24 |
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[8e1f901] | 25 | #include "AtomIdSet.hpp"
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[6f0841] | 26 | #include "Atom/AtomSet.hpp"
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[ad011c] | 27 | #include "CodePatterns/Cacheable.hpp"
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[02ce36] | 28 | #include "CodePatterns/Observer/Observable.hpp"
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[30c753] | 29 | #include "Descriptors/AtomIdDescriptor.hpp"
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[07a47e] | 30 | #include "Fragmentation/HydrogenSaturation_enum.hpp"
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[389cc8] | 31 | #include "Formula.hpp"
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[30c753] | 32 | #include "Helpers/defs.hpp"
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[560bbe] | 33 | #include "IdPool_policy.hpp"
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| 34 | #include "IdPool.hpp"
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[c67ff9] | 35 | #include "Shapes/Shape.hpp"
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[30c753] | 36 | #include "types.hpp"
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[14de469] | 37 |
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[f66195] | 38 | /****************************************** forward declarations *****************************/
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| 39 |
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| 40 | class atom;
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| 41 | class bond;
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[b70721] | 42 | class BondedParticle;
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| 43 | class BondGraph;
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[49c059] | 44 | class DepthFirstSearchAnalysis;
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[f66195] | 45 | class element;
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| 46 | class ForceMatrix;
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[dadc74] | 47 | class Graph;
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[6bd7e0] | 48 | class LinkedCell_deprecated;
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[14de469] | 49 | class molecule;
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[2319ed] | 50 | class MoleculeLeafClass;
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[14de469] | 51 | class MoleculeListClass;
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[c67ff9] | 52 | class MoleculeUnittest;
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[1f91f4] | 53 | class RealSpaceMatrix;
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[f66195] | 54 | class Vector;
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[14de469] | 55 |
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| 56 | /************************************* Class definitions ****************************************/
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| 57 |
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| 58 | /** The complete molecule.
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| 59 | * Class incorporates number of types
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| 60 | */
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[34c43a] | 61 | class molecule : public Observable
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[e4afb4] | 62 | {
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[c67ff9] | 63 | //!> grant unit test access
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| 64 | friend class MoleculeUnittest;
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| 65 | //!> function may access cstor
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[cbc5fb] | 66 | friend molecule *NewMolecule();
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[c67ff9] | 67 | //!> function may access dstor
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[cbc5fb] | 68 | friend void DeleteMolecule(molecule *);
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[bd58fb] | 69 |
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[e4afb4] | 70 | public:
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[8e1f901] | 71 | typedef AtomIdSet::atomIdSet atomIdSet;
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| 72 | typedef AtomIdSet::iterator iterator;
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| 73 | typedef AtomIdSet::const_iterator const_iterator;
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[e4afb4] | 74 |
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| 75 | int MDSteps; //!< The number of MD steps in Trajectories
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| 76 | mutable int NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
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| 77 | mutable int NoNonBonds; //!< number of non-hydrogen bonds in molecule
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| 78 | mutable int NoCyclicBonds; //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
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| 79 | bool ActiveFlag; //!< in a MoleculeListClass used to discern active from inactive molecules
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| 80 | int IndexNr; //!< index of molecule in a MoleculeListClass
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| 81 | char name[MAXSTRINGSIZE]; //!< arbitrary name
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| 82 |
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| 83 | private:
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| 84 | Formula formula;
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[458c31] | 85 | Cacheable<int> AtomCount; //!< number of atoms, brought up-to-date by doCountAtoms()
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| 86 | Cacheable<int> BondCount; //!< number of atoms, brought up-to-date by doCountBonds()
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[e4afb4] | 87 | moleculeId_t id;
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[8e1f901] | 88 | AtomIdSet atomIds; //<!set of atomic ids to check uniqueness of atoms
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[560bbe] | 89 | IdPool<atomId_t, uniqueId> atomIdPool; //!< pool of internal ids such that way may guarantee uniqueness
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| 90 |
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[e4afb4] | 91 | protected:
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[ac9b56] | 92 |
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[4d2b33] | 93 | molecule();
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[e4afb4] | 94 | virtual ~molecule();
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[042f82] | 95 |
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[cbc5fb] | 96 | public:
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[520c8b] | 97 | //getter and setter
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[73a857] | 98 | const std::string getName() const;
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[ea7176] | 99 | int getAtomCount() const;
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| 100 | int doCountAtoms();
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[458c31] | 101 | int getBondCount() const;
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| 102 | int doCountBonds() const;
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[73a857] | 103 | moleculeId_t getId() const;
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[cbc5fb] | 104 | void setId(moleculeId_t);
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[520c8b] | 105 | void setName(const std::string);
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[73a857] | 106 | const Formula &getFormula() const;
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| 107 | unsigned int getElementCount() const;
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[389cc8] | 108 | bool hasElement(const element*) const;
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| 109 | bool hasElement(atomicNumber_t) const;
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| 110 | bool hasElement(const std::string&) const;
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| 111 |
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[a7a087] | 112 | virtual bool changeId(atomId_t newId);
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[520c8b] | 113 |
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[9317be] | 114 | World::AtomComposite getAtomSet() const;
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[3738f0] | 115 |
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[8e1f901] | 116 | // simply pass on all functions to AtomIdSet
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| 117 | iterator begin() {
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| 118 | return atomIds.begin();
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| 119 | }
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| 120 | const_iterator begin() const
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| 121 | {
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| 122 | return atomIds.begin();
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| 123 | }
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| 124 | iterator end()
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| 125 | {
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| 126 | return atomIds.end();
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| 127 | }
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| 128 | const_iterator end() const
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| 129 | {
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| 130 | return atomIds.end();
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| 131 | }
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| 132 | bool empty() const
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| 133 | {
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| 134 | return atomIds.empty();
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| 135 | }
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| 136 | size_t size() const
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| 137 | {
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| 138 | return atomIds.size();
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| 139 | }
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| 140 | const_iterator find(atom * key) const
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| 141 | {
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| 142 | return atomIds.find(key);
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| 143 | }
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[c67ff9] | 144 |
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| 145 | /** Returns the set of atomic ids contained in this molecule.
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| 146 | *
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| 147 | * @return set of atomic ids
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| 148 | */
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[8e1f901] | 149 | const atomIdSet & getAtomIds() const {
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| 150 | return atomIds.getAtomIds();
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| 151 | }
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| 152 |
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| 153 | std::pair<iterator, bool> insert(atom * const key);
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| 154 |
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[6cfa36] | 155 | bool containsAtom(atom* key);
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[bd58fb] | 156 |
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[2e4105] | 157 | private:
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| 158 | friend void atom::removeFromMolecule();
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| 159 | /** Erase an atom from the list.
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| 160 | * \note This should only be called by atom::removeFromMolecule(),
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| 161 | * otherwise it is not assured that the atom knows about it.
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| 162 | *
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| 163 | * @param loc locator to atom in list
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| 164 | * @return iterator to just after removed item (compliant with standard)
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| 165 | */
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| 166 | const_iterator erase(const_iterator loc);
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[8e1f901] | 167 |
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[2e4105] | 168 | /** Erase an atom from the list.
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| 169 | * \note This should only be called by atom::removeFromMolecule(),
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| 170 | * otherwise it is not assured that the atom knows about it.
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| 171 | *
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| 172 | * @param *key key to atom in list
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| 173 | * @return iterator to just after removed item (compliant with standard)
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| 174 | */
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| 175 | const_iterator erase(atom * key);
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| 176 |
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[560bbe] | 177 | private:
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| 178 | friend bool atom::changeNr(int newId);
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| 179 | /**
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| 180 | * used when changing an ParticleInfo::Nr.
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| 181 | * Note that this number is local with this molecule.
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| 182 | * Unless you are calling this method from inside an atom don't fiddle with the third parameter.
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| 183 | *
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| 184 | * @param oldNr old Nr
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| 185 | * @param newNr new Nr to set
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| 186 | * @param *target ref to atom
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| 187 | * @return indicates wether the change could be done or not.
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| 188 | */
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| 189 | bool changeAtomNr(int oldNr, int newNr, atom* target=0);
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| 190 |
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| 191 | /** Sets the name of the atom.
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| 192 | *
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| 193 | * The name is set via its element symbol and its internal ParticleInfo::Nr.
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| 194 | *
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| 195 | * @param _atom atom whose name to set
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| 196 | */
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| 197 | void setAtomName(atom *_atom) const;
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| 198 |
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[2e4105] | 199 | public:
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| 200 |
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[c67ff9] | 201 | /** Function to create a bounding spherical shape for the currently associated atoms.
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| 202 | *
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| 203 | */
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| 204 | Shape getBoundingShape() const;
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| 205 |
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[042f82] | 206 | /// remove atoms from molecule.
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| 207 | bool AddAtom(atom *pointer);
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| 208 | bool RemoveAtom(atom *pointer);
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| 209 | bool UnlinkAtom(atom *pointer);
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| 210 | bool CleanupMolecule();
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[9df680] | 211 | void removeAtomsinMolecule();
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[042f82] | 212 |
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| 213 | /// Add/remove atoms to/from molecule.
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| 214 | atom * AddCopyAtom(atom *pointer);
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[e138de] | 215 | bool AddHydrogenReplacementAtom(bond *Bond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bool IsAngstroem);
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[cee0b57] | 216 | bond * AddBond(atom *first, atom *second, int degree = 1);
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[042f82] | 217 | bool RemoveBond(bond *pointer);
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| 218 | bool RemoveBonds(atom *BondPartner);
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[e4afb4] | 219 | bool hasBondStructure() const;
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[042f82] | 220 |
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| 221 | /// Find atoms.
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| 222 | atom * FindAtom(int Nr) const;
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[955b91] | 223 | atom * AskAtom(std::string text);
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[59fff1] | 224 | bool isInMolecule(const atom * const _atom);
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[042f82] | 225 |
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| 226 | /// Count and change present atoms' coordination.
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[e138de] | 227 | bool CenterInBox();
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| 228 | bool BoundInBox();
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| 229 | void CenterEdge(Vector *max);
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| 230 | void CenterOrigin();
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| 231 | void CenterPeriodic();
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| 232 | void CenterAtVector(Vector *newcenter);
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[042f82] | 233 | void Translate(const Vector *x);
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| 234 | void TranslatePeriodically(const Vector *trans);
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| 235 | void Mirror(const Vector *x);
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| 236 | void Align(Vector *n);
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[776b64] | 237 | void Scale(const double ** const factor);
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[07a47e] | 238 | void DeterminePeriodicCenter(Vector ¢er, const enum HydrogenSaturation _saturation = DoSaturate);
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[4bb63c] | 239 | Vector * DetermineCenterOfGravity() const;
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[e138de] | 240 | Vector * DetermineCenterOfAll() const;
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[eddea2] | 241 | Vector * DetermineCenterOfBox() const;
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[437922] | 242 | void SetNameFromFilename(const char *filename);
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[042f82] | 243 | void SetBoxDimension(Vector *dim);
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[3c58f8] | 244 | bool ScanForPeriodicCorrection();
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[e138de] | 245 | double VolumeOfConvexEnvelope(bool IsAngstroem);
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[1f91f4] | 246 | RealSpaceMatrix getInertiaTensor() const;
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| 247 | void RotateToPrincipalAxisSystem(Vector &Axis);
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[042f82] | 248 |
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| 249 | bool CheckBounds(const Vector *x) const;
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| 250 | void GetAlignvector(struct lsq_params * par) const;
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| 251 |
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| 252 | /// Initialising routines in fragmentation
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[e138de] | 253 | void OutputBondsList() const;
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[49c059] | 254 |
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[266237] | 255 | bond * CopyBond(atom *left, atom *right, bond *CopyBond);
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| 256 |
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[c67ff9] | 257 | molecule *CopyMolecule(const Vector &offset = zeroVec) const;
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[c550dd] | 258 | molecule* CopyMoleculeFromSubRegion(const Shape&) const;
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[042f82] | 259 |
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| 260 | /// Fragment molecule by two different approaches:
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[e4afb4] | 261 | bool StoreBondsToFile(std::string filename, std::string path = "");
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| 262 | bool StoreAdjacencyToFile(std::string filename, std::string path = "");
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[9879f6] | 263 | bool CreateFatherLookupTable(atom **&LookupTable, int count = 0);
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[b9772a] | 264 |
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[042f82] | 265 | // Recognize doubly appearing molecules in a list of them
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[e138de] | 266 | int * GetFatherSonAtomicMap(molecule *OtherMolecule);
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[99752a] | 267 | bool FillBondStructureFromReference(const molecule * const reference, atom **&ListOfLocalAtoms, bool FreeList = false);
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[c6123b] | 268 | bool FillListOfLocalAtoms(atom **&ListOfLocalAtoms, const int GlobalAtomCount);
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[042f82] | 269 |
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| 270 | // Output routines.
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[e4afb4] | 271 | bool Output(std::ostream * const output) const;
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| 272 | bool OutputTrajectories(ofstream * const output) const;
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[e138de] | 273 | void OutputListOfBonds() const;
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| 274 | bool OutputXYZ(ofstream * const output) const;
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| 275 | bool OutputTrajectoriesXYZ(ofstream * const output);
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| 276 | bool Checkout(ofstream * const output) const;
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[042f82] | 277 |
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[c68025] | 278 | // Manipulation routines
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| 279 | void flipActiveFlag();
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| 280 |
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[e4afb4] | 281 | private:
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| 282 | int last_atom; //!< number given to last atom
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[14de469] | 283 | };
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| 284 |
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[cbc5fb] | 285 | molecule *NewMolecule();
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| 286 | void DeleteMolecule(molecule* mol);
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| 287 |
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[14de469] | 288 |
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| 289 |
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| 290 | #endif /*MOLECULES_HPP_*/
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| 291 |
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