source: src/bond.cpp@ 88104f

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Last change on this file since 88104f was 8de375, checked in by Frederik Heber <heber@…>, 15 years ago

Merge branch 'StructureRefactoring' into CommandLineActionMapping

Conflicts:

molecuilder/src/atom_particleinfo.cpp
molecuilder/src/builder.cpp

The following conflicts were solved:

  • in atom_particleinfo constructor the bugfix could not be merged automatically
  • in builder.cpp at the end of main() cleanup and memory:getstate() were still present.
  • Property mode set to 100644
File size: 3.6 KB
Line 
1/** \file bond.cpp
2 *
3 * Function implementations for the classes BondLeaf, BondTree and bond.
4 *
5 */
6
7#include "atom.hpp"
8#include "bond.hpp"
9#include "element.hpp"
10#include "lists.hpp"
11
12
13/***************************************** Functions for class bond ********************************/
14
15/** Empty Constructor for class bond.
16 */
17bond::bond()
18 : leftatom(NULL), rightatom(NULL), previous(NULL), next(NULL), HydrogenBond(0),
19 BondDegree(0), nr(-1), Cyclic(false), Type(Undetermined), Used(white)
20{
21};
22
23/** Constructor for class bond, taking right and left bond partner
24 * \param *left left atom
25 * \param *right right atom
26 * \param degree bond degree
27 * \param number increasing index
28 */
29bond::bond(atom *left, atom *right, const int degree, const int number)
30 : leftatom(left), rightatom(right), previous(NULL), next(NULL), HydrogenBond(0),
31 BondDegree(degree), nr(number), Cyclic(false), Type(Undetermined), Used(white)
32{
33 if ((left != NULL) && (right != NULL)) {
34 if ((left->type != NULL) && (left->type->Z == 1))
35 HydrogenBond++;
36 if ((right->type != NULL) && (right->type->Z == 1))
37 HydrogenBond++;
38 }
39};
40
41/** Empty Destructor for class bond.
42 */
43bond::~bond()
44{
45 // remove this node from the list structure
46 if (leftatom != NULL)
47 leftatom->UnregisterBond(this);
48 if (rightatom != NULL)
49 rightatom->UnregisterBond(this);
50 unlink(this);
51};
52
53ostream & operator << (ostream &ost, const bond &b)
54{
55 ost << "[" << b.leftatom->getName() << " <" << b.BondDegree << "(H" << b.HydrogenBond << ")>" << b.rightatom->getName() << "]";
56 return ost;
57};
58
59/** Get the other atom in a bond if one is specified.
60 * \param *Atom the pointer to the one atom
61 * \return pointer to the other atom in the bond, NULL if no match (indicates something's wrong with the bond)
62 */
63atom * bond::GetOtherAtom(const ParticleInfo * const Atom) const
64{
65 if(leftatom == Atom)
66 return rightatom;
67 if(rightatom == Atom)
68 return leftatom;
69 DoeLog(1) && (eLog()<< Verbose(1) << "Bond " << *this << " does not contain atom " << *Atom << "!" << endl);
70 return NULL;
71};
72
73
74/** Returns whether vertex was used in DFS.
75 * \return bond::Used
76 */
77enum Shading bond::IsUsed()
78{
79 return Used;
80};
81
82/** Checks if an atom exists in a bond.
83 * \param *ptr pointer to atom
84 * \return true if it is either bond::leftatom or bond::rightatom, false otherwise
85 */
86bool bond::Contains(const ParticleInfo * const ptr)
87{
88 return ((leftatom == ptr) || (rightatom == ptr));
89};
90
91/** Checks if an atom exists in a bond.
92 * \param nr index of atom
93 * \return true if it is either bond::leftatom or bond::rightatom, false otherwise
94 */
95bool bond::Contains(const int number)
96{
97 return ((leftatom->nr == number) || (rightatom->nr == number));
98};
99
100/** Masks vertex as used in DFS.
101 * \return bond::Used, false if bond was already marked used
102 */
103bool bond::MarkUsed(const enum Shading color) {
104 if (Used == black) {
105 DoeLog(1) && (eLog()<< Verbose(1) << "Bond " << this << " was already marked black!." << endl);
106 return false;
107 } else {
108 Used = color;
109 return true;
110 }
111};
112
113/** Resets used flag in DFS.
114 * \return bond::Used
115 */
116void bond::ResetUsed() {
117 Used = white;
118};
119
120/** Calculates the bond length.
121 * \return |a - b| with a = bond::leftatom and b = bond::rightatom.
122 */
123double bond::GetDistance() const
124{
125 return (leftatom->node->distance(*rightatom->node));
126};
127
128/** Calculates the bond length.
129 * \return |a - b|^2 with a = bond::leftatom and b = bond::rightatom.
130 */
131double bond::GetDistanceSquared() const
132{
133 return (leftatom->node->DistanceSquared(*rightatom->node));
134};
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