source: src/unittests/CountBondsUnitTest.cpp@ 9eb7580

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Last change on this file since 9eb7580 was bcf653, checked in by Frederik Heber <heber@…>, 15 years ago

Added copyright note to each .cpp file and an extensive one to builder.cpp.

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[bcf653]1/*
2 * Project: MoleCuilder
3 * Description: creates and alters molecular systems
4 * Copyright (C) 2010 University of Bonn. All rights reserved.
5 * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
6 */
7
[dfe8ef]8/*
9 * CountBondsUnitTest.cpp
10 *
11 * Created on: Mar 30, 2010
12 * Author: heber
13 */
14
[bf3817]15// include config.h
16#ifdef HAVE_CONFIG_H
17#include <config.h>
18#endif
[dfe8ef]19
20using namespace std;
21
22#include <cppunit/CompilerOutputter.h>
23#include <cppunit/extensions/TestFactoryRegistry.h>
24#include <cppunit/ui/text/TestRunner.h>
25
26#include <iostream>
27#include <stdio.h>
28#include <cstring>
29
[4eb4fe]30#include "Helpers/Assert.hpp"
31
[388049]32#include "analysis_bonds.hpp"
[dfe8ef]33#include "atom.hpp"
34#include "bond.hpp"
35#include "bondgraph.hpp"
36#include "element.hpp"
37#include "molecule.hpp"
38#include "periodentafel.hpp"
[5f612ee]39#include "World.hpp"
[dfe8ef]40#include "CountBondsUnitTest.hpp"
41
[5f612ee]42#ifdef HAVE_TESTRUNNER
43#include "UnitTestMain.hpp"
44#endif /*HAVE_TESTRUNNER*/
45
[dfe8ef]46/********************************************** Test classes **************************************/
47
48// Registers the fixture into the 'registry'
49CPPUNIT_TEST_SUITE_REGISTRATION( CountBondsTest );
50
51
52void CountBondsTest::setUp()
53{
54 atom *Walker = NULL;
55
56 // construct element
[4eb4fe]57 hydrogen = World::getInstance().getPeriode()->FindElement(1);
58 oxygen = World::getInstance().getPeriode()->FindElement(8);
59 CPPUNIT_ASSERT(hydrogen != NULL && "could not find element hydrogen");
60 CPPUNIT_ASSERT(oxygen != NULL && "could not find element oxygen");
[dfe8ef]61
62 // construct molecule (water molecule)
[5f612ee]63 TestMolecule1 = World::getInstance().createMolecule();
[4eb4fe]64 CPPUNIT_ASSERT(TestMolecule1 != NULL && "could not create first molecule");
[5f612ee]65 Walker = World::getInstance().createAtom();
[4eb4fe]66 CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
[d74077]67 Walker->setType(hydrogen);
68 Walker->setPosition(Vector(-0.2418, 0.9350, 0. ));
[dfe8ef]69 TestMolecule1->AddAtom(Walker);
[5f612ee]70 Walker = World::getInstance().createAtom();
[4eb4fe]71 CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
[d74077]72 Walker->setType(hydrogen);
73 Walker->setPosition(Vector(0.9658, 0., 0. ));
[dfe8ef]74 TestMolecule1->AddAtom(Walker);
[5f612ee]75 Walker = World::getInstance().createAtom();
[4eb4fe]76 CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
[d74077]77 Walker->setType(oxygen);
78 Walker->setPosition(Vector(0., 0., 0. ));
[dfe8ef]79 TestMolecule1->AddAtom(Walker);
80
[5f612ee]81 TestMolecule2 = World::getInstance().createMolecule();
[4eb4fe]82 CPPUNIT_ASSERT(TestMolecule2 != NULL && "could not create second molecule");
[5f612ee]83 Walker = World::getInstance().createAtom();
[4eb4fe]84 CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
[d74077]85 Walker->setType(hydrogen);
86 Walker->setPosition(Vector(-0.2418, 0.9350, 0. ));
[dfe8ef]87 TestMolecule2->AddAtom(Walker);
[5f612ee]88 Walker = World::getInstance().createAtom();
[4eb4fe]89 CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
[d74077]90 Walker->setType(hydrogen);
91 Walker->setPosition(Vector(0.9658, 0., 0. ));
[dfe8ef]92 TestMolecule2->AddAtom(Walker);
[5f612ee]93 Walker = World::getInstance().createAtom();
[4eb4fe]94 CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
[d74077]95 Walker->setType(oxygen);
96 Walker->setPosition(Vector(0., 0., 0. ));
[dfe8ef]97 TestMolecule2->AddAtom(Walker);
[5f612ee]98
99 molecules = World::getInstance().getMolecules();
[4eb4fe]100 CPPUNIT_ASSERT(molecules != NULL && "could not obtain list of molecules");
[5f612ee]101 molecules->insert(TestMolecule1);
[dfe8ef]102 molecules->insert(TestMolecule2);
103
104 // check that TestMolecule was correctly constructed
[a7b761b]105 CPPUNIT_ASSERT_EQUAL( TestMolecule1->getAtomCount(), 3 );
106 CPPUNIT_ASSERT_EQUAL( TestMolecule2->getAtomCount(), 3 );
[dfe8ef]107
108 // create a small file with table
109 BG = new BondGraph(true);
[4eb4fe]110 CPPUNIT_ASSERT(BG != NULL && "could not create BondGraph");
[dfe8ef]111
112 // construct bond graphs
113 CPPUNIT_ASSERT_EQUAL( true , BG->ConstructBondGraph(TestMolecule1) );
114 CPPUNIT_ASSERT_EQUAL( true , BG->ConstructBondGraph(TestMolecule2) );
115// TestMolecule1->Output((ofstream *)&cout);
116// TestMolecule1->OutputBondsList();
117};
118
119
120void CountBondsTest::tearDown()
121{
122 // remove the file
123 delete(BG);
124
[5f612ee]125 World::purgeInstance();
[dfe8ef]126};
127
128/** UnitTest for CountBondsTest::BondsOfTwoTest().
129 */
130void CountBondsTest::BondsOfTwoTest()
131{
132 CPPUNIT_ASSERT_EQUAL( 4 , CountBondsOfTwo(molecules, hydrogen, oxygen) );
133 CPPUNIT_ASSERT_EQUAL( 0 , CountBondsOfTwo(molecules, hydrogen, hydrogen) );
134 CPPUNIT_ASSERT_EQUAL( 0 , CountBondsOfTwo(molecules, oxygen, oxygen) );
135};
136
137/** UnitTest for CountBondsTest::BondsOfThreeTest().
138 */
139void CountBondsTest::BondsOfThreeTest()
140{
141 CPPUNIT_ASSERT_EQUAL( 2 , CountBondsOfThree(molecules, hydrogen, oxygen, hydrogen) );
142 CPPUNIT_ASSERT_EQUAL( 0 , CountBondsOfThree(molecules, oxygen, hydrogen, oxygen) );
143};
144
[62c9c0]145void OutputTestMolecule(molecule *mol, const char *name)
146{
147 ofstream output(name);
148 mol->OutputXYZ(&output);
149 output.close();
150}
151
[dfe8ef]152/** UnitTest for CountBondsTest::HydrogenBridgeBondsTest().
153 */
154void CountBondsTest::HydrogenBridgeBondsTest()
155{
156 double *mirror = new double[3];
[4eb4fe]157 CPPUNIT_ASSERT(mirror != NULL && "could not create array of doubles");
[dfe8ef]158 for (int i=0;i<3;i++)
159 mirror[i] = -1.;
160 Vector Translator;
[62c9c0]161
162 //OutputTestMolecule(TestMolecule1, "testmolecule1.xyz");
163
[fe238c]164 cout << "Case 1: offset of (3,0,0), hence angles are (104.5, 0, 75.5, 180) < 30." << endl;
[8cbb97]165 Translator = Vector(3,0,0);
[dfe8ef]166 TestMolecule2->Translate(&Translator);
[bfd839]167 CPPUNIT_ASSERT_EQUAL( 1 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
168 CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, oxygen, NULL) );
[62c9c0]169 //OutputTestMolecule(TestMolecule2, "testmolecule2-1.xyz");
[8cbb97]170 Translator = Vector(-3,0,0);
[dfe8ef]171 TestMolecule2->Translate(&Translator);
172
[fe238c]173 cout << "Case 2: offset of (0,3,0), hence angle are (14.5, 165.5, 90) < 30 (only three, because other 90 is missing due to first H01 only fulfilling H-bond criteria)." << endl;
[8cbb97]174 Translator = Vector(0,3,0);
[dfe8ef]175 TestMolecule2->Translate(&Translator);
[bfd839]176 CPPUNIT_ASSERT_EQUAL( 1 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
[62c9c0]177 //OutputTestMolecule(TestMolecule2, "testmolecule2-2.xyz");
[8cbb97]178 Translator = Vector(0,-3,0);
[dfe8ef]179 TestMolecule2->Translate(&Translator);
180
[fe238c]181 cout << "Case 3: offset of (0,-3,0) and mirror, hence angle are (165.5, 90, 165.5, 90) > 30." << endl;
[8cbb97]182 Translator = Vector(0,-3,0);
[dfe8ef]183 TestMolecule2->Scale((const double ** const)&mirror);
184 TestMolecule2->Translate(&Translator);
[bfd839]185 CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
[62c9c0]186 //OutputTestMolecule(TestMolecule2, "testmolecule2-3.xyz");
[8cbb97]187 Translator = Vector(0,3,0);
[dfe8ef]188 TestMolecule2->Translate(&Translator);
189 TestMolecule2->Scale((const double ** const)&mirror);
190
[fe238c]191 cout << "Case 4: offset of (2,1,0), hence angle are (78, 26.6, 102, 153.4) < 30." << endl;
[8cbb97]192 Translator = Vector(2,1,0);
[dfe8ef]193 TestMolecule2->Translate(&Translator);
[bfd839]194 CPPUNIT_ASSERT_EQUAL( 1 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
[62c9c0]195 //OutputTestMolecule(TestMolecule2, "testmolecule2-4.xyz");
[8cbb97]196 Translator = Vector(-2,-1,0);
[dfe8ef]197 TestMolecule2->Translate(&Translator);
198
[fe238c]199 cout << "Case 5: offset of (0,0,3), hence angle are (90, 90, 90, 90) > 30." << endl;
[8cbb97]200 Translator = Vector(0,0,3);
[dfe8ef]201 TestMolecule2->Translate(&Translator);
[bfd839]202 CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
[62c9c0]203 //OutputTestMolecule(TestMolecule2, "testmolecule2-5.xyz");
[8cbb97]204 Translator = Vector(0,0,-3);
[dfe8ef]205 TestMolecule2->Translate(&Translator);
206
[fe238c]207 cout << "Case 6: offset of (-3,0,0) and mirror, hence angle are (75.5, 180, 104.5, 180) > 30." << endl;
[8cbb97]208 Translator = Vector(-3,0,0);
[dfe8ef]209 TestMolecule2->Scale((const double ** const)&mirror);
210 TestMolecule2->Translate(&Translator);
[bfd839]211 CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
[62c9c0]212 //OutputTestMolecule(TestMolecule2, "testmolecule2-6.xyz");
[8cbb97]213 Translator = Vector(3,0,0);
[dfe8ef]214 TestMolecule2->Translate(&Translator);
215 TestMolecule2->Scale((const double ** const)&mirror);
[fe238c]216
217 cout << "Case 7: offset of (3,0,0) and mirror, hence angles are (104.5, 0, 104.5, 0) < 30, but interfering hydrogens." << endl;
[8cbb97]218 Translator = Vector(3,0,0);
[fe238c]219 TestMolecule2->Scale((const double ** const)&mirror);
220 TestMolecule2->Translate(&Translator);
[bfd839]221 CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
[fe238c]222 //OutputTestMolecule(TestMolecule2, "testmolecule2-7.xyz");
[8cbb97]223 Translator = Vector(-3,0,0);
[fe238c]224 TestMolecule2->Translate(&Translator);
225 TestMolecule2->Scale((const double ** const)&mirror);
226
227 cout << "Case 8: offset of (0,3,0), hence angle are (14.5, 90, 14.5, 90) < 30, but interfering hydrogens." << endl;
[8cbb97]228 Translator = Vector(0,3,0);
[fe238c]229 TestMolecule2->Scale((const double ** const)&mirror);
230 TestMolecule2->Translate(&Translator);
231 //OutputTestMolecule(TestMolecule2, "testmolecule2-8.xyz");
[bfd839]232 CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
[8cbb97]233 Translator = Vector(0,-3,0);
[fe238c]234 TestMolecule2->Translate(&Translator);
235 TestMolecule2->Scale((const double ** const)&mirror);
236
[5f612ee]237 delete[](mirror);
[dfe8ef]238};
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