| [a0bcf1] | 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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| [70b7aa] | 7 | #include "atom.hpp"
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| [834ff3] | 8 | #include "bond.hpp"
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| [17b3a5c] | 9 | #include "element.hpp"
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| 10 | #include "lists.hpp"
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| 11 |
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| [a0bcf1] | 12 |
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| 13 | /***************************************** Functions for class bond ********************************/
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| 14 |
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| 15 | /** Empty Constructor for class bond.
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| 16 | */
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| 17 | bond::bond()
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| 18 | {
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| [560995] | 19 | leftatom = NULL;
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| 20 | rightatom = NULL;
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| [a0bcf1] | 21 | previous = NULL;
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| 22 | next = NULL;
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| [560995] | 23 | nr = -1;
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| 24 | HydrogenBond = 0;
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| 25 | BondDegree = 0;
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| [a0bcf1] | 26 | Used = white;
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| 27 | Cyclic = false;
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| 28 | Type = Undetermined;
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| 29 | };
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| 30 |
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| 31 | /** Constructor for class bond, taking right and left bond partner
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| 32 | * \param *left left atom
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| 33 | * \param *right right atom
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| 34 | * \param degree bond degree
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| 35 | * \param number increasing index
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| 36 | */
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| 37 | bond::bond(atom *left, atom *right, int degree=1, int number=0)
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| 38 | {
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| [560995] | 39 | leftatom = left;
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| 40 | rightatom = right;
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| [a0bcf1] | 41 | previous = NULL;
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| 42 | next = NULL;
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| [560995] | 43 | HydrogenBond = 0;
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| [a0bcf1] | 44 | if ((left != NULL) && (right != NULL)) {
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| [560995] | 45 | if ((left->type != NULL) && (left->type->Z == 1))
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| 46 | HydrogenBond++;
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| 47 | if ((right->type != NULL) && (right->type->Z == 1))
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| 48 | HydrogenBond++;
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| [a0bcf1] | 49 | }
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| 50 | BondDegree = degree;
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| 51 | nr = number;
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| 52 | Used = white;
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| 53 | Cyclic = false;
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| 54 | };
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| [872b51] | 55 |
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| [a0bcf1] | 56 | bond::bond(atom *left, atom *right)
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| 57 | {
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| 58 | leftatom = left;
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| 59 | rightatom = right;
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| 60 | previous = NULL;
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| 61 | next = NULL;
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| 62 | HydrogenBond = 0;
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| 63 | if ((left != NULL) && (right != NULL)) {
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| 64 | if ((left->type != NULL) && (left->type->Z == 1))
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| 65 | HydrogenBond++;
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| 66 | if ((right->type != NULL) && (right->type->Z == 1))
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| 67 | HydrogenBond++;
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| 68 | }
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| 69 | BondDegree = 1;
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| 70 | nr = 0;
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| 71 | Used = white;
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| 72 | Cyclic = false;
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| 73 | };
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| 74 |
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| 75 | /** Empty Destructor for class bond.
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| 76 | */
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| 77 | bond::~bond()
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| 78 | {
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| 79 | // remove this node from the list structure
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| [872b51] | 80 | if (leftatom != NULL)
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| 81 | leftatom->UnregisterBond(this);
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| 82 | if (rightatom != NULL)
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| 83 | rightatom->UnregisterBond(this);
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| 84 | unlink(this);
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| [a0bcf1] | 85 | };
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| 86 |
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| [a7b3b8] | 87 | ostream & operator << (ostream &ost, const bond &b)
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| [a0bcf1] | 88 | {
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| 89 | ost << "[" << b.leftatom->Name << " <" << b.BondDegree << "(H" << b.HydrogenBond << ")>" << b.rightatom->Name << "]";
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| 90 | return ost;
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| 91 | };
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| 92 |
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| 93 | /** Get the other atom in a bond if one is specified.
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| 94 | * \param *Atom the pointer to the one atom
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| 95 | * \return pointer to the other atom in the bond, NULL if no match (indicates something's wrong with the bond)
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| 96 | */
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| [6b937bd] | 97 | atom * bond::GetOtherAtom(const ParticleInfo *Atom) const
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| [a0bcf1] | 98 | {
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| 99 | if(leftatom == Atom)
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| 100 | return rightatom;
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| 101 | if(rightatom == Atom)
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| 102 | return leftatom;
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| [a7b3b8] | 103 | cerr << "Bond " << *this << " does not contain atom " << *Atom << "!" << endl;
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| [a0bcf1] | 104 | return NULL;
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| 105 | };
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| 106 |
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| 107 |
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| 108 | /** Returns whether vertex was used in DFS.
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| 109 | * \return bond::Used
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| 110 | */
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| 111 | enum Shading bond::IsUsed()
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| 112 | {
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| 113 | return Used;
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| 114 | };
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| 115 |
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| 116 | /** Checks if an atom exists in a bond.
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| 117 | * \param *ptr pointer to atom
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| 118 | * \return true if it is either bond::leftatom or bond::rightatom, false otherwise
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| 119 | */
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| [6b937bd] | 120 | bool bond::Contains(const ParticleInfo *ptr)
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| [a0bcf1] | 121 | {
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| 122 | return ((leftatom == ptr) || (rightatom == ptr));
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| 123 | };
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| 124 |
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| 125 | /** Checks if an atom exists in a bond.
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| 126 | * \param nr index of atom
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| 127 | * \return true if it is either bond::leftatom or bond::rightatom, false otherwise
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| 128 | */
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| [75793b2] | 129 | bool bond::Contains(const int number)
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| [a0bcf1] | 130 | {
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| [75793b2] | 131 | return ((leftatom->nr == number) || (rightatom->nr == number));
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| [a0bcf1] | 132 | };
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| 133 |
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| 134 | /** Masks vertex as used in DFS.
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| 135 | * \return bond::Used, false if bond was already marked used
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| 136 | */
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| 137 | bool bond::MarkUsed(enum Shading color) {
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| 138 | if (Used == black) {
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| 139 | cerr << "ERROR: Bond " << this << " was already marked black!." << endl;
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| 140 | return false;
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| 141 | } else {
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| 142 | Used = color;
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| 143 | return true;
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| 144 | }
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| 145 | };
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| 146 |
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| 147 | /** Resets used flag in DFS.
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| 148 | * \return bond::Used
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| 149 | */
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| 150 | void bond::ResetUsed() {
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| 151 | Used = white;
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| 152 | };
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