source: src/Parser/unittests/ParserTremoloUnitTest.cpp@ 3fb9ab

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Last change on this file since 3fb9ab was ed8a68, checked in by Frederik Heber <heber@…>, 9 years ago

Removed TremoloParser's ElementKeys, superceded by ParticleRegistry.

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[4fbca9c]1/*
2 * Project: MoleCuilder
3 * Description: creates and alters molecular systems
[0aa122]4 * Copyright (C) 2010-2012 University of Bonn. All rights reserved.
[5aaa43]5 * Copyright (C) 2013 Frederik Heber. All rights reserved.
[94d5ac6]6 *
7 *
8 * This file is part of MoleCuilder.
9 *
10 * MoleCuilder is free software: you can redistribute it and/or modify
11 * it under the terms of the GNU General Public License as published by
12 * the Free Software Foundation, either version 2 of the License, or
13 * (at your option) any later version.
14 *
15 * MoleCuilder is distributed in the hope that it will be useful,
16 * but WITHOUT ANY WARRANTY; without even the implied warranty of
17 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18 * GNU General Public License for more details.
19 *
20 * You should have received a copy of the GNU General Public License
21 * along with MoleCuilder. If not, see <http://www.gnu.org/licenses/>.
[4fbca9c]22 */
23
24/*
25 * ParserTremoloUnitTest.cpp
26 *
27 * Created on: Mar 3, 2010
28 * Author: metzler
29 */
30
31// include config.h
32#ifdef HAVE_CONFIG_H
33#include <config.h>
34#endif
35
36#include "ParserTremoloUnitTest.hpp"
37
38#include <cppunit/CompilerOutputter.h>
39#include <cppunit/extensions/TestFactoryRegistry.h>
40#include <cppunit/ui/text/TestRunner.h>
41
[5a667d]42#include "CodePatterns/Log.hpp"
43
[6f0841]44#include "Atom/atom.hpp"
[006e1e]45#include "Atom/AtomObserver.hpp"
[073a9e4]46#include "Descriptors/AtomTypeDescriptor.hpp"
[3bdb6d]47#include "Element/element.hpp"
48#include "Element/periodentafel.hpp"
[ed8a68]49#include "Parser/Exceptions.hpp"
[4fbca9c]50#include "Parser/TremoloParser.hpp"
[765f16]51#include "Parser/ChangeTracker.hpp"
[073a9e4]52#include "World.hpp"
53#include "WorldTime.hpp"
[4fbca9c]54
55#ifdef HAVE_TESTRUNNER
56#include "UnitTestMain.hpp"
57#endif /*HAVE_TESTRUNNER*/
58
59using namespace std;
60
61// Registers the fixture into the 'registry'
62CPPUNIT_TEST_SUITE_REGISTRATION( ParserTremoloUnitTest );
63
[4d4d33]64static string Tremolo_Atomdata1 = "\
[ccb487]65# ATOMDATA\tId\tname\ttype\tx=3\n\
66# Box\t20\t0\t0\t0\t20\t0\t0\t0\t20\n";
[4d4d33]67static string Tremolo_Atomdata2 = "\
68#\n\
[305e7e]69#ATOMDATA Id name type x=3\n\
[ccb487]70# Box\t20\t0\t0\t0\t20\t0\t0\t0\t20\n\
[4d4d33]711 hydrogen H 3.0 4.5 0.1\n\
72\n";
73static string Tremolo_invalidkey = "\
74#\n\
[305e7e]75#ATOMDATA Id name foo type x=3\n\
[ccb487]76# Box\t20\t0\t0\t0\t20\t0\t0\t0\t20\n\
[4d4d33]77\n\n";
78static string Tremolo_velocity = "\
79#\n\
[305e7e]80#ATOMDATA Id name type u=3\n\
[ccb487]81# Box\t20\t0\t0\t0\t20\t0\t0\t0\t20\n\
[4d4d33]821 hydrogen H 3.0 4.5 0.1\n\
83\n";
84static string Tremolo_neighbours = "#\n\
[305e7e]85#ATOMDATA Id type neighbors=2\n\
[ccb487]86# Box\t20\t0\t0\t0\t20\t0\t0\t0\t20\n\
[4d4d33]871 H 3 0\n\
882 H 3 0\n\
893 O 1 2\n";
90static string Tremolo_improper = "\
91#\n\
[305e7e]92#ATOMDATA Id type imprData\n\
[ccb487]93# Box\t20\t0\t0\t0\t20\t0\t0\t0\t20\n\
[4d4d33]948 H 9-10\n\
959 H 10-8,8-10\n\
9610 O -\n";
97static string Tremolo_torsion = "\
98#\n\
[305e7e]99#ATOMDATA Id type torsion\n\
[ccb487]100# Box\t20\t0\t0\t0\t20\t0\t0\t0\t20\n\
[4d4d33]1018 H 9-10\n\
1029 H 10-8,8-10\n\
10310 O -\n";
104static string Tremolo_full = "\
[e6e4a0]105# ATOMDATA\tx=3\tu=3\tF=3\tstress\tId\tneighbors=5\timprData\tGroupMeasureTypeNo\ttype\textType\tname\tresName\tchainID\tresSeq\toccupancy\ttempFactor\tsegID\tCharge\tcharge\tGrpTypeNo\ttorsion\n\
[ccb487]106# Box\t20\t0\t0\t0\t20\t0\t0\t0\t20\n\
[e6e4a0]1070\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t-\t0\tH\t-\t-\t-\t0\t0\t0\t0\t0\t0\t0\t0\t-\t\n";
[4fbca9c]108
109void ParserTremoloUnitTest::setUp() {
110 World::getInstance();
111
[05e2ed]112 setVerbosity(2);
[5a667d]113
[765f16]114 parser = new FormatParser<tremolo>();
115
[4fbca9c]116 // we need hydrogens and oxygens in the following tests
117 CPPUNIT_ASSERT(World::getInstance().getPeriode()->FindElement(1) != NULL);
118 CPPUNIT_ASSERT(World::getInstance().getPeriode()->FindElement(8) != NULL);
119}
120
[765f16]121void ParserTremoloUnitTest::tearDown()
122{
123 delete parser;
[4fbca9c]124 ChangeTracker::purgeInstance();
125 World::purgeInstance();
[708277]126 AtomObserver::purgeInstance();
[4fbca9c]127}
128
129/************************************ tests ***********************************/
130
131void ParserTremoloUnitTest::readTremoloPreliminaryCommentsTest() {
[05e2ed]132// cout << "Testing the tremolo parser." << endl;
[4fbca9c]133 stringstream input, output;
134
135 // Atomdata beginning with "# ATOMDATA"
[73916f]136 {
137 input << Tremolo_Atomdata1;
[765f16]138 parser->load(&input);
[fac58f]139 std::vector<const atom *> atoms = const_cast<const World &>(World::getInstance()).
140 getAllAtoms();
[765f16]141 parser->save(&output, atoms);
[4d4d33]142// std::cout << output.str() << std::endl;
143// std::cout << Tremolo_Atomdata1 << std::endl;
[73916f]144 CPPUNIT_ASSERT(Tremolo_Atomdata1 == output.str());
145 input.clear();
146 output.clear();
147 }
[4fbca9c]148
149 // Atomdata beginning with "#ATOMDATA"
[73916f]150 {
151 input << Tremolo_Atomdata2;
[765f16]152 parser->load(&input);
[fac58f]153 std::vector<const atom *> atoms = const_cast<const World &>(World::getInstance()).
154 getAllAtoms();
[765f16]155 parser->save(&output, atoms);
[05e2ed]156// std::cout << output.str() << std::endl;
[73916f]157 CPPUNIT_ASSERT(output.str().find("hydrogen") != string::npos);
158 input.clear();
159 output.clear();
160 }
[4fbca9c]161
162 // Invalid key in Atomdata line
163 input << Tremolo_invalidkey;
[5a667d]164 CPPUNIT_ASSERT_THROW( parser->load(&input), IllegalParserKeyException);
[73916f]165 //TODO: prove invalidity
[4fbca9c]166 input.clear();
167}
168
[ca331c]169void ParserTremoloUnitTest::getsetAtomDataTest() {
170 stringstream input;
171 input << Tremolo_Atomdata1;
172 parser->load(&input);
173
174 CPPUNIT_ASSERT_EQUAL( std::string("Id name type x=3"), parser->getAtomData() );
175
176 // overwrite keys
177 const std::string fewkeys("Id type x=3 neighbors=2");
178 parser->resetAtomData(fewkeys);
179 CPPUNIT_ASSERT_EQUAL( fewkeys, parser->getAtomData() );
180
181 // add some keys
182 const std::string morekeys("charge");
183 parser->setAtomData(morekeys);
184 CPPUNIT_ASSERT_EQUAL( fewkeys+std::string(" ")+morekeys, parser->getAtomData() );
185
186 // add similar key
187 const std::string otherkey("neighbors=4");
188 parser->setAtomData(otherkey);
189 CPPUNIT_ASSERT( fewkeys+std::string(" ")+morekeys != parser->getAtomData() );
190}
191
[4fbca9c]192void ParserTremoloUnitTest::readTremoloCoordinatesTest() {
193 stringstream input;
194
195 // One simple data line
196 input << Tremolo_Atomdata2;
[765f16]197 parser->load(&input);
[f01769]198 CPPUNIT_ASSERT(const_cast<const World &>(World::getInstance()).getAtom(AtomByType(1))->at(0) == 3.0);
[4fbca9c]199 input.clear();
200}
201
202void ParserTremoloUnitTest::readTremoloVelocityTest() {
203 stringstream input;
204
205 // One simple data line
206 input << Tremolo_velocity;
[765f16]207 parser->load(&input);
[f01769]208 CPPUNIT_ASSERT(const_cast<const World &>(World::getInstance()).getAtom(AtomByType(1))->getAtomicVelocity()[0] == 3.0);
[4fbca9c]209 input.clear();
210}
211
212void ParserTremoloUnitTest::readTremoloNeighborInformationTest() {
213 stringstream input;
214
215 // Neighbor data
216 input << Tremolo_neighbours;
[765f16]217 parser->load(&input);
[4fbca9c]218
219 CPPUNIT_ASSERT_EQUAL(3, World::getInstance().numAtoms());
[f01769]220 CPPUNIT_ASSERT(const_cast<const World &>(World::getInstance()).getAtom(AtomByType(8))->
221 IsBondedTo(WorldTime::getTime(), const_cast<const World &>(World::getInstance()).getAtom(AtomByType(1))));
[4fbca9c]222 input.clear();
223}
224
225void ParserTremoloUnitTest::readAndWriteTremoloImprDataInformationTest() {
226 stringstream input, output;
227
228 // Neighbor data
[73916f]229 {
230 input << Tremolo_improper;
[765f16]231 parser->load(&input);
[fac58f]232 std::vector<const atom *> atoms = const_cast<const World &>(World::getInstance()).
233 getAllAtoms();
[765f16]234 parser->save(&output, atoms);
[fac58f]235 CPPUNIT_ASSERT_EQUAL(3, const_cast<const World &>(World::getInstance()).numAtoms());
[05e2ed]236// std::cout << output.str() << std::endl;
237 CPPUNIT_ASSERT(output.str().find("3-1,1-3") != string::npos);
[73916f]238 input.clear();
239 output.clear();
240 }
[4fbca9c]241}
242
243void ParserTremoloUnitTest::readAndWriteTremoloTorsionInformationTest() {
244 stringstream input, output;
245
246 // Neighbor data
[73916f]247 {
248 input << Tremolo_torsion;
[765f16]249 parser->load(&input);
[fac58f]250 std::vector<const atom *> atoms = const_cast<const World &>(World::getInstance()).
251 getAllAtoms();
[765f16]252 parser->save(&output, atoms);
[fac58f]253 CPPUNIT_ASSERT_EQUAL(3, const_cast<const World &>(World::getInstance()).numAtoms());
[05e2ed]254// std::cout << output.str() << std::endl;
255 CPPUNIT_ASSERT(output.str().find("3-1,1-3") != string::npos);
[73916f]256 input.clear();
257 output.clear();
258 }
[4fbca9c]259}
260
261void ParserTremoloUnitTest::writeTremoloTest() {
262 stringstream output;
263
264 // with the maximum number of fields and minimal information, default values are printed
[73916f]265 {
266 atom* newAtom = World::getInstance().createAtom();
267 newAtom->setType(1);
[e6e4a0]268 parser->setAtomData("x=3 u=3 F=3 stress Id neighbors=5 imprData GroupMeasureTypeNo type extType name resName chainID resSeq occupancy tempFactor segID Charge charge GrpTypeNo torsion");
[fac58f]269 std::vector<const atom *> atoms = const_cast<const World &>(World::getInstance()).
270 getAllAtoms();
[765f16]271 parser->save(&output, atoms);
[ccb487]272// std::cout << output.str() << std::endl;
273// std::cout << Tremolo_full << std::endl;
[73916f]274 CPPUNIT_ASSERT(output.str() == Tremolo_full);
275 }
[4fbca9c]276
[05e2ed]277// cout << "testing the tremolo parser is done" << endl;
[4fbca9c]278}
[765f16]279
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