source: src/bond.cpp@ ba9f5b

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Last change on this file since ba9f5b was 112b09, checked in by Tillmann Crueger <crueger@…>, 15 years ago

Added #include "Helpers/MemDebug.hpp" to all .cpp files

  • Property mode set to 100644
File size: 3.7 KB
Line 
1/** \file bond.cpp
2 *
3 * Function implementations for the classes BondLeaf, BondTree and bond.
4 *
5 */
6
7#include "Helpers/MemDebug.hpp"
8
9#include "atom.hpp"
10#include "bond.hpp"
11#include "element.hpp"
12#include "lists.hpp"
13
14
15/***************************************** Functions for class bond ********************************/
16
17/** Empty Constructor for class bond.
18 */
19bond::bond()
20 : leftatom(NULL), rightatom(NULL), previous(NULL), next(NULL), HydrogenBond(0),
21 BondDegree(0), nr(-1), Cyclic(false), Type(Undetermined), Used(white)
22{
23};
24
25/** Constructor for class bond, taking right and left bond partner
26 * \param *left left atom
27 * \param *right right atom
28 * \param degree bond degree
29 * \param number increasing index
30 */
31bond::bond(atom *left, atom *right, const int degree, const int number)
32 : leftatom(left), rightatom(right), previous(NULL), next(NULL), HydrogenBond(0),
33 BondDegree(degree), nr(number), Cyclic(false), Type(Undetermined), Used(white)
34{
35 if ((left != NULL) && (right != NULL)) {
36 if ((left->type != NULL) && (left->type->Z == 1))
37 HydrogenBond++;
38 if ((right->type != NULL) && (right->type->Z == 1))
39 HydrogenBond++;
40 }
41};
42
43/** Empty Destructor for class bond.
44 */
45bond::~bond()
46{
47 // remove this node from the list structure
48 if (leftatom != NULL)
49 leftatom->UnregisterBond(this);
50 if (rightatom != NULL)
51 rightatom->UnregisterBond(this);
52 unlink(this);
53};
54
55ostream & operator << (ostream &ost, const bond &b)
56{
57 ost << "[" << b.leftatom->getName() << " <" << b.BondDegree << "(H" << b.HydrogenBond << ")>" << b.rightatom->getName() << "]";
58 return ost;
59};
60
61/** Get the other atom in a bond if one is specified.
62 * \param *Atom the pointer to the one atom
63 * \return pointer to the other atom in the bond, NULL if no match (indicates something's wrong with the bond)
64 */
65atom * bond::GetOtherAtom(const ParticleInfo * const Atom) const
66{
67 if(leftatom == Atom)
68 return rightatom;
69 if(rightatom == Atom)
70 return leftatom;
71 DoeLog(1) && (eLog()<< Verbose(1) << "Bond " << *this << " does not contain atom " << *Atom << "!" << endl);
72 return NULL;
73};
74
75
76/** Returns whether vertex was used in DFS.
77 * \return bond::Used
78 */
79enum Shading bond::IsUsed()
80{
81 return Used;
82};
83
84/** Checks if an atom exists in a bond.
85 * \param *ptr pointer to atom
86 * \return true if it is either bond::leftatom or bond::rightatom, false otherwise
87 */
88bool bond::Contains(const ParticleInfo * const ptr)
89{
90 return ((leftatom == ptr) || (rightatom == ptr));
91};
92
93/** Checks if an atom exists in a bond.
94 * \param nr index of atom
95 * \return true if it is either bond::leftatom or bond::rightatom, false otherwise
96 */
97bool bond::Contains(const int number)
98{
99 return ((leftatom->nr == number) || (rightatom->nr == number));
100};
101
102/** Masks vertex as used in DFS.
103 * \return bond::Used, false if bond was already marked used
104 */
105bool bond::MarkUsed(const enum Shading color) {
106 if (Used == black) {
107 DoeLog(1) && (eLog()<< Verbose(1) << "Bond " << this << " was already marked black!." << endl);
108 return false;
109 } else {
110 Used = color;
111 return true;
112 }
113};
114
115/** Resets used flag in DFS.
116 * \return bond::Used
117 */
118void bond::ResetUsed() {
119 Used = white;
120};
121
122/** Calculates the bond length.
123 * \return |a - b| with a = bond::leftatom and b = bond::rightatom.
124 */
125double bond::GetDistance() const
126{
127 return (leftatom->node->distance(*rightatom->node));
128};
129
130/** Calculates the bond length.
131 * \return |a - b|^2 with a = bond::leftatom and b = bond::rightatom.
132 */
133double bond::GetDistanceSquared() const
134{
135 return (leftatom->node->DistanceSquared(*rightatom->node));
136};
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