| 1 | /*
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| 2 | * Project: MoleCuilder
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| 3 | * Description: creates and alters molecular systems
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| 4 | * Copyright (C) 2010 University of Bonn. All rights reserved.
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| 5 | * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
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| 6 | */
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| 7 |
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| 8 | /** \file Bond.cpp
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| 9 | *
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| 10 | * Function implementations for the classes BondLeaf, BondTree and bond.
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| 11 | *
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| 12 | */
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| 13 |
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| 14 | // include config.h
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| 15 | #ifdef HAVE_CONFIG_H
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| 16 | #include <config.h>
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| 17 | #endif
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| 18 |
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| 19 | #include "CodePatterns/MemDebug.hpp"
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| 20 |
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| 21 | #include "CodePatterns/Log.hpp"
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| 22 | #include "CodePatterns/Verbose.hpp"
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| 23 | #include "atom.hpp"
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| 24 | #include "Bond/bond.hpp"
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| 25 | #include "Element/element.hpp"
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| 26 |
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| 27 |
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| 28 | /***************************************** Functions for class bond ********************************/
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| 29 |
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| 30 | /** Empty Constructor for class bond.
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| 31 | */
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| 32 | bond::bond() :
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| 33 | leftatom(NULL),
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| 34 | rightatom(NULL),
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| 35 | HydrogenBond(0),
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| 36 | BondDegree(0)
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| 37 | {};
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| 38 |
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| 39 | /** Constructor for class bond, taking right and left bond partner
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| 40 | * \param *left left atom
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| 41 | * \param *right right atom
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| 42 | * \param degree bond degree
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| 43 | * \param number increasing index
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| 44 | */
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| 45 | bond::bond(atom *left, atom *right, const int degree) :
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| 46 | leftatom(left),
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| 47 | rightatom(right),
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| 48 | HydrogenBond(0),
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| 49 | BondDegree(degree)
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| 50 | {
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| 51 | if ((left != NULL) && (right != NULL)) {
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| 52 | if ((left->getType() != NULL) && (left->getType()->getAtomicNumber() == 1))
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| 53 | HydrogenBond++;
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| 54 | if ((right->getType() != NULL) && (right->getType()->getAtomicNumber() == 1))
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| 55 | HydrogenBond++;
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| 56 | }
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| 57 | };
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| 58 |
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| 59 | /** Empty Destructor for class bond.
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| 60 | */
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| 61 | bond::~bond()
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| 62 | {
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| 63 | // remove this node from the list structure
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| 64 | if (leftatom != NULL)
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| 65 | leftatom->removeBond(this);
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| 66 | // there might be self-bonds
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| 67 | if ((leftatom != rightatom) && (rightatom != NULL))
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| 68 | rightatom->removeBond(this);
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| 69 | };
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| 70 |
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| 71 | ostream & operator << (ostream &ost, const bond &b)
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| 72 | {
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| 73 | ost << "[" << b.leftatom->getName() << " <" << b.BondDegree << "(H" << b.HydrogenBond << ")>" << b.rightatom->getName() << "]";
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| 74 | return ost;
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| 75 | };
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| 76 |
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| 77 | /** Get the other atom in a bond if one is specified.
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| 78 | * \param *Atom the pointer to the one atom
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| 79 | * \return pointer to the other atom in the bond, NULL if no match (indicates something's wrong with the bond)
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| 80 | */
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| 81 | atom * bond::GetOtherAtom(const ParticleInfo * const Atom) const
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| 82 | {
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| 83 | if(leftatom == Atom)
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| 84 | return rightatom;
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| 85 | if(rightatom == Atom)
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| 86 | return leftatom;
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| 87 | DoeLog(1) && (eLog()<< Verbose(1) << "Bond " << *this << " does not contain atom " << *Atom << "!" << endl);
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| 88 | return NULL;
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| 89 | };
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| 90 |
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| 91 |
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| 92 | /** Checks if an atom exists in a bond.
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| 93 | * \param *ptr pointer to atom
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| 94 | * \return true if it is either bond::leftatom or bond::rightatom, false otherwise
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| 95 | */
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| 96 | bool bond::Contains(const ParticleInfo * const ptr) const
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| 97 | {
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| 98 | return ((leftatom == ptr) || (rightatom == ptr));
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| 99 | };
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| 100 |
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| 101 | /** Checks if an atom exists in a bond.
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| 102 | * \param Nr index of atom
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| 103 | * \return true if it is either bond::leftatom or bond::rightatom, false otherwise
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| 104 | */
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| 105 | bool bond::Contains(const int number) const
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| 106 | {
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| 107 | return ((leftatom->getNr() == number) || (rightatom->getNr() == number));
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| 108 | };
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| 109 |
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| 110 | /** Calculates the bond length.
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| 111 | * \return |a - b| with a = bond::leftatom and b = bond::rightatom.
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| 112 | */
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| 113 | double bond::GetDistance() const
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| 114 | {
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| 115 | return (leftatom->distance(*rightatom));
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| 116 | };
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| 117 |
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| 118 | /** Calculates the bond length.
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| 119 | * \return |a - b|^2 with a = bond::leftatom and b = bond::rightatom.
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| 120 | */
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| 121 | double bond::GetDistanceSquared() const
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| 122 | {
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| 123 | return (leftatom->DistanceSquared(*rightatom));
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| 124 | };
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