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