1 | /*
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2 | * bond.hpp
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3 | *
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4 | * Created on: Aug 3, 2009
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5 | * Author: heber
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6 | */
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7 |
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8 | #ifndef BOND_HPP_
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9 | #define BOND_HPP_
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10 |
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11 | using namespace std;
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12 |
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13 | /*********************************************** includes ***********************************/
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14 |
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15 | // include config.h
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16 | #ifdef HAVE_CONFIG_H
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17 | #include <config.h>
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18 | #endif
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19 |
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20 | /****************************************** forward declarations *****************************/
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21 |
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22 | class atom;
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23 | class ParticleInfo;
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24 |
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25 | /********************************************** declarations *******************************/
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26 |
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27 | /** Bonds between atoms.
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28 | * Class incorporates bonds between atoms in a molecule.
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29 | * Note that we regard bond always as something in a molecule,
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30 | * as it is the glue making up the connected subgrapgh and
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31 | * hence the molecule. Thus, bonds belong globally to the molecule
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32 | * (and are free'd there) and only locally to the atom classs.
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33 | */
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34 | class bond {
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35 | public:
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36 | enum EdgeType { Undetermined, TreeEdge, BackEdge }; //!< edge type in a graph after Depth-First-Search analysis.
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37 |
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38 | enum Shading { white, lightgray, darkgray, black }; //!< color in Breadth-First-Search analysis
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39 |
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40 | atom *leftatom; //!< first bond partner
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41 | atom *rightatom; //!< second bond partner
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42 | int HydrogenBond; //!< Number of hydrogen atoms in the bond
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43 | int BondDegree; //!< single, double, triple, ... bond
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44 | int nr; //!< unique number in a molecule, updated by BondGraph::CreateAdjacencyForList()
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45 | bool Cyclic; //!< flag whether bond is part of a cycle or not, given in DepthFirstSearchAnalysis()
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46 | enum EdgeType Type;//!< whether this is a tree or back edge
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47 |
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48 | atom * GetOtherAtom(const ParticleInfo * const Atom) const;
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49 |
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50 | bool MarkUsed(const enum Shading color);
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51 | enum Shading IsUsed();
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52 | void ResetUsed();
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53 | bool Contains(const ParticleInfo * const ptr);
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54 | bool Contains(const int nr);
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55 | double GetDistance() const;
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56 | double GetDistanceSquared() const;
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57 |
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58 | bond();
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59 | bond(atom *left, atom *right, const int degree=1, const int number=0);
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60 | ~bond();
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61 |
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62 | string GetColor(enum Shading color) const;
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63 |
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64 | private:
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65 | enum Shading Used; //!< marker in depth-first search, DepthFirstSearchAnalysis()
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66 | };
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67 |
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68 | ostream & operator << (ostream &ost, const bond &b);
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69 |
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70 | #endif /* BOND_HPP_ */
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