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bondgraph.hpp@ 8bc524

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Last change on this file since 8bc524 was 5f697c, checked in by Frederik Heber <heber@…>, 16 years ago

BondGraph parses a file containing bond lengths and basically has a member function which gives lower and upper bounds on when two atoms are bonded and when not.
- BondGraph::LoadBondLengthTable() - basically uses MatrixContainer::ParseMatrix()
- BondGraph::ConstructBondGraph() - uses molecule::CreateAdjacency() but with different bounds-function.
- BondGraph::GetBondLength() - returns entry from parsed bond length matrix
- BondGraph::CovalentMinMaxDistance() - bounds function using covalent radii of involved elements
- BondGraph::BondLengthMatrixMinMaxDistance() - bounds function which uses the parsed bond length matrix
Unit test written for BondGraph.
molecule::CreateAdjacencyList() - rewritten, takes now a bounds BondGraph member function, if NULL is given, creates its own BondGraph and uses standard covalent bounds function (which does not need any scanning).
new function BondedParticle::IsBondedTo() which checks whether given BondedPasrticle is contained in ListOfBonds.
builder.cpp: calls to molecule::CreateAdjacencyList() adapted to new syntax.

File size: 1.3 KB

Line
1	/*
2	* bondgraph.hpp
3	*
4	* Created on: Oct 29, 2009
5	* Author: heber
6	*/
7
8	#ifndef BONDGRAPH_HPP_
9	#define BONDGRAPH_HPP_
10
11	using namespace std;
12
13	/********************************************* includes *********************************/
14
15	// include config.h
16	#ifdef HAVE_CONFIG_H
17	#include <config.h>
18	#endif
19
20	#include <iostream>
21
22	/**************************************** forward declarations ***************************/
23
24	class molecule;
25	class MatrixContainer;
26
27	/******************************************** definitions *******************************/
28
29	/******************************************** declarations *****************************/
30
31
32	class BondGraph {
33	public:
34	BondGraph(bool IsA);
35	~BondGraph();
36	bool LoadBondLengthTable(ofstream * const out, const string &filename);
37	bool ConstructBondGraph(ofstream * const out, molecule * const mol);
38	double GetBondLength(int firstelement, int secondelement);
39
40	void BondLengthMatrixMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem);
41	void CovalentMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem);
42
43	private:
44	MatrixContainer *BondLengthMatrix;
45	double max_distance;
46	bool IsAngstroem;
47	};
48
49	#endif /* BONDGRAPH_HPP_ */

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