[14de469] | 1 | /** \file bond.cpp
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| 2 | *
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| 3 | * Function implementations for the classes BondLeaf, BondTree and bond.
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| 4 | *
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| 5 | */
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| 6 |
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[112b09] | 7 | #include "Helpers/MemDebug.hpp"
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| 8 |
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[36166d] | 9 | #include "verbose.hpp"
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[e41951] | 10 | #include "atom.hpp"
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[357fba] | 11 | #include "bond.hpp"
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[f66195] | 12 | #include "element.hpp"
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| 13 | #include "lists.hpp"
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| 14 |
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[14de469] | 15 |
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| 16 | /***************************************** Functions for class bond ********************************/
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| 17 |
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| 18 | /** Empty Constructor for class bond.
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| 19 | */
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[b8d4a3] | 20 | bond::bond()
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| 21 | : leftatom(NULL), rightatom(NULL), previous(NULL), next(NULL), HydrogenBond(0),
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| 22 | BondDegree(0), nr(-1), Cyclic(false), Type(Undetermined), Used(white)
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[14de469] | 23 | {
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| 24 | };
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| 25 |
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| 26 | /** Constructor for class bond, taking right and left bond partner
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| 27 | * \param *left left atom
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| 28 | * \param *right right atom
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| 29 | * \param degree bond degree
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| 30 | * \param number increasing index
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| 31 | */
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[b8d4a3] | 32 | bond::bond(atom *left, atom *right, const int degree, const int number)
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| 33 | : leftatom(left), rightatom(right), previous(NULL), next(NULL), HydrogenBond(0),
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| 34 | BondDegree(degree), nr(number), Cyclic(false), Type(Undetermined), Used(white)
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[14de469] | 35 | {
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| 36 | if ((left != NULL) && (right != NULL)) {
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[ce5ac3] | 37 | if ((left->type != NULL) && (left->type->Z == 1))
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| 38 | HydrogenBond++;
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| 39 | if ((right->type != NULL) && (right->type->Z == 1))
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| 40 | HydrogenBond++;
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[14de469] | 41 | }
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| 42 | };
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| 43 |
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| 44 | /** Empty Destructor for class bond.
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| 45 | */
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| 46 | bond::~bond()
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| 47 | {
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| 48 | // remove this node from the list structure
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[266237] | 49 | if (leftatom != NULL)
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| 50 | leftatom->UnregisterBond(this);
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| 51 | if (rightatom != NULL)
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| 52 | rightatom->UnregisterBond(this);
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| 53 | unlink(this);
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[14de469] | 54 | };
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| 55 |
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[fb73b8] | 56 | ostream & operator << (ostream &ost, const bond &b)
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[14de469] | 57 | {
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[68f03d] | 58 | ost << "[" << b.leftatom->getName() << " <" << b.BondDegree << "(H" << b.HydrogenBond << ")>" << b.rightatom->getName() << "]";
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[14de469] | 59 | return ost;
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| 60 | };
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| 61 |
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| 62 | /** Get the other atom in a bond if one is specified.
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| 63 | * \param *Atom the pointer to the one atom
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| 64 | * \return pointer to the other atom in the bond, NULL if no match (indicates something's wrong with the bond)
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| 65 | */
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[fb73b8] | 66 | atom * bond::GetOtherAtom(const ParticleInfo * const Atom) const
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[14de469] | 67 | {
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| 68 | if(leftatom == Atom)
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| 69 | return rightatom;
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| 70 | if(rightatom == Atom)
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| 71 | return leftatom;
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[58ed4a] | 72 | DoeLog(1) && (eLog()<< Verbose(1) << "Bond " << *this << " does not contain atom " << *Atom << "!" << endl);
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[14de469] | 73 | return NULL;
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| 74 | };
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| 75 |
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| 76 |
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| 77 | /** Returns whether vertex was used in DFS.
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| 78 | * \return bond::Used
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| 79 | */
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| 80 | enum Shading bond::IsUsed()
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| 81 | {
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| 82 | return Used;
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| 83 | };
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| 84 |
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| 85 | /** Checks if an atom exists in a bond.
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| 86 | * \param *ptr pointer to atom
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| 87 | * \return true if it is either bond::leftatom or bond::rightatom, false otherwise
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| 88 | */
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[fb73b8] | 89 | bool bond::Contains(const ParticleInfo * const ptr)
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[14de469] | 90 | {
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| 91 | return ((leftatom == ptr) || (rightatom == ptr));
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| 92 | };
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| 93 |
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| 94 | /** Checks if an atom exists in a bond.
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| 95 | * \param nr index of atom
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| 96 | * \return true if it is either bond::leftatom or bond::rightatom, false otherwise
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| 97 | */
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[fa40b5] | 98 | bool bond::Contains(const int number)
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[14de469] | 99 | {
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[fa40b5] | 100 | return ((leftatom->nr == number) || (rightatom->nr == number));
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[14de469] | 101 | };
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| 102 |
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| 103 | /** Masks vertex as used in DFS.
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| 104 | * \return bond::Used, false if bond was already marked used
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| 105 | */
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[fb73b8] | 106 | bool bond::MarkUsed(const enum Shading color) {
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[14de469] | 107 | if (Used == black) {
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[58ed4a] | 108 | DoeLog(1) && (eLog()<< Verbose(1) << "Bond " << this << " was already marked black!." << endl);
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[14de469] | 109 | return false;
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| 110 | } else {
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| 111 | Used = color;
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| 112 | return true;
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| 113 | }
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| 114 | };
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| 115 |
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| 116 | /** Resets used flag in DFS.
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| 117 | * \return bond::Used
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| 118 | */
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| 119 | void bond::ResetUsed() {
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| 120 | Used = white;
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| 121 | };
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[b9947d] | 122 |
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| 123 | /** Calculates the bond length.
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| 124 | * \return |a - b| with a = bond::leftatom and b = bond::rightatom.
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| 125 | */
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| 126 | double bond::GetDistance() const
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| 127 | {
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[1513a74] | 128 | return (leftatom->node->distance(*rightatom->node));
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[b9947d] | 129 | };
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| 130 |
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| 131 | /** Calculates the bond length.
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| 132 | * \return |a - b|^2 with a = bond::leftatom and b = bond::rightatom.
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| 133 | */
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| 134 | double bond::GetDistanceSquared() const
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| 135 | {
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[273382] | 136 | return (leftatom->node->DistanceSquared(*rightatom->node));
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[b9947d] | 137 | };
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