Changeset 4fbca9c for src/unittests/ParserCommonUnitTest.cpp

Timestamp:

Dec 5, 2010, 12:01:43 AM (14 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

cabb46

Parents:

e828c0

git-author:

Frederik Heber <heber@…> (12/04/10 18:05:33)

git-committer:

Frederik Heber <heber@…> (12/05/10 00:01:43)

Message:

PdbParser::save() fully working.

• added UnitTest for PdbParser.
• split ParserUnitTest into Common and Tremolo.
• split off classes PdbAtomInfoContainer and PdbKey into own modules.
• PdbParser can now load ATOM and CONECT entries.

File:

• src/unittests/ParserCommonUnitTest.cpp (moved) (moved from src/unittests/ParserUnitTest.cpp ) (11 diffs)

src/unittests/ParserCommonUnitTest.cpp

@@ -7 +7 @@
 
 /*
- * ParserUnitTest.cpp
+ * ParserCommonUnitTest.cpp
  *
  *  Created on: Mar 3, 2010
@@ -18 +18 @@
 #endif
 
-#include "ParserUnitTest.hpp"
+#include "ParserCommonUnitTest.hpp"
 
 #include <cppunit/CompilerOutputter.h>
@@ -25 +25 @@
 
 #include "Parser/MpqcParser.hpp"
+#include "Parser/PdbParser.hpp"
 #include "Parser/PcpParser.hpp"
 #include "Parser/TremoloParser.hpp"
@@ -41 +42 @@
 
 // Registers the fixture into the 'registry'
-CPPUNIT_TEST_SUITE_REGISTRATION( ParserUnitTest );
+CPPUNIT_TEST_SUITE_REGISTRATION( ParserCommonUnitTest );
 
 static string waterPcp = "# ParallelCarParinello - main configuration file - created with molecuilder\n\
@@ -117 +118 @@
 Ion_Type1_1\t0.758602\t0.000000000\t0.504284\t0 # molecule nr 1\n\
 Ion_Type1_2\t0.758602\t0.000000000\t-0.504284\t0 # molecule nr 2\n";
+//----|----*|---||--*||---|***|-------|-------|-------|-----|---------------|-|-
+//000000011111111112222222222333333333344444444445555555555666666666677777777778
+//345678901234567890123456789012345678901234567890123456789012345678901234567890
+static string waterPdb = "\
+REMARK  This is a test water molecule as written by TREMOLO.\n\
+ATOM      1  OT  GMT-    0       1.583   1.785   1.480  1.00178.02           O-2\n\
+ATOM      2  HT  GMT-    0       1.186   1.643   2.213  1.00103.58           H+1\n\
+ATOM      3  HT  GMT-    0       2.642   1.896   1.730  1.00126.00           H+1\n\
+ATOM      4  OT  GMT-    1       3.583   1.785   1.480  1.00178.02           O-2\n\
+ATOM      5  HT  GMT-    1       3.186   1.643   2.213  1.00103.58           H+1\n\
+ATOM      6  HT  GMT-    1       4.642   1.896   1.730  1.00126.00           H+1\n\
+CONECT    1    2    3\n\
+CONECT    2    1\n\
+CONECT    3    1\n\
+CONECT    4    5    6\n\
+CONECT    5    4\n\
+CONECT    6    4\n\
+END";
 static string waterMpqc ="% Created by MoleCuilder\n\
 mpqc: (\n\
@@ -144 +163 @@
 )\n";
 static string waterXyz = "3\n\tH2O: water molecule\nO\t0\t0\t0\nH\t0.758602\t0\t0.504284\nH\t0.758602\t0\t-0.504284\n";
-static string Tremolo_Atomdata1 = "# ATOMDATA\tId\tname\tType\tx=3\n";
-static string Tremolo_Atomdata2 = "#\n#ATOMDATA Id name Type x=3\n1 hydrogen H 3.0 4.5 0.1\n\n";
-static string Tremolo_invalidkey = "#\n#ATOMDATA Id name foo Type x=3\n\n\n";
-static string Tremolo_velocity = "#\n#ATOMDATA Id name Type u=3\n1 hydrogen H 3.0 4.5 0.1\n\n";
-static string Tremolo_neighbours = "#\n#ATOMDATA Id Type neighbors=2\n1 H 3 0\n2 H 3 0\n3 O 1 2\n";
-static string Tremolo_improper = "#\n#ATOMDATA Id Type imprData\n8 H 9-10\n9 H 10-8,8-10\n10 O -\n";
-static string Tremolo_torsion = "#\n#ATOMDATA Id Type torsion\n8 H 9-10\n9 H 10-8,8-10\n10 O -\n";
-static string Tremolo_full = "# ATOMDATA\tx=3\tu=3\tF\tstress\tId\tneighbors=5\timprData\tGroupMeasureTypeNo\tType\textType\tname\tresName\tchainID\tresSeq\toccupancy\ttempFactor\tsegID\tCharge\tcharge\tGrpTypeNo\ttorsion\n0\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";
-
-void ParserUnitTest::setUp() {
+
+void ParserCommonUnitTest::setUp() {
   World::getInstance();
+
+  setVerbosity(2);
 
   // we need hydrogens and oxygens in the following tests
@@ -161 +174 @@
 }
 
-void ParserUnitTest::tearDown() {
+void ParserCommonUnitTest::tearDown() {
   ChangeTracker::purgeInstance();
   World::purgeInstance();
@@ -168 +181 @@
 /************************************ tests ***********************************/
 
-void ParserUnitTest::rewriteAnXyzTest() {
+void ParserCommonUnitTest::rewriteAnXyzTest() {
   cout << "Testing the XYZ parser." << endl;
   XyzParser* testParser = new XyzParser();
@@ -185 +198 @@
 }
 
-void ParserUnitTest::readTremoloPreliminaryCommentsTest() {
-  cout << "Testing the tremolo parser." << endl;
-  TremoloParser* testParser = new TremoloParser();
-  stringstream input, output;
-
-  // Atomdata beginning with "# ATOMDATA"
-  input << Tremolo_Atomdata1;
-  testParser->load(&input);
-  testParser->save(&output);
-  CPPUNIT_ASSERT(Tremolo_Atomdata1 == output.str());
-  input.clear();
-  output.clear();
-
-  // Atomdata beginning with "#ATOMDATA"
-  input << Tremolo_Atomdata2;
-  testParser->load(&input);
-  testParser->save(&output);
-  CPPUNIT_ASSERT(output.str().find("hydrogen") != string::npos);
-  input.clear();
-  output.clear();
-
-  // Invalid key in Atomdata line
-  input << Tremolo_invalidkey;
-  testParser->load(&input);
-  //TODO: proove invalidity
-  input.clear();
-}
-
-void ParserUnitTest::readTremoloCoordinatesTest() {
-  TremoloParser* testParser = new TremoloParser();
-  stringstream input;
-
-  // One simple data line
-  input << Tremolo_Atomdata2;
-  testParser->load(&input);
-  CPPUNIT_ASSERT(World::getInstance().getAtom(AtomByType(1))->at(0) == 3.0);
-  input.clear();
-}
-
-void ParserUnitTest::readTremoloVelocityTest() {
-  TremoloParser* testParser = new TremoloParser();
-  stringstream input;
-
-  // One simple data line
-  input << Tremolo_velocity;
-  testParser->load(&input);
-  CPPUNIT_ASSERT(World::getInstance().getAtom(AtomByType(1))->AtomicVelocity[0] == 3.0);
-  input.clear();
-}
-
-void ParserUnitTest::readTremoloNeighborInformationTest() {
-  TremoloParser* testParser = new TremoloParser();
-  stringstream input;
-
-  // Neighbor data
-  input << Tremolo_neighbours;
-  testParser->load(&input);
-
-  CPPUNIT_ASSERT_EQUAL(3, World::getInstance().numAtoms());
-  CPPUNIT_ASSERT(World::getInstance().getAtom(AtomByType(8))->
-      IsBondedTo(World::getInstance().getAtom(AtomByType(1))));
-  input.clear();
-}
-
-void ParserUnitTest::readAndWriteTremoloImprDataInformationTest() {
-  TremoloParser* testParser = new TremoloParser();
-  stringstream input, output;
-
-  // Neighbor data
-  input << Tremolo_improper;
-  testParser->load(&input);
-  testParser->save(&output);
-  CPPUNIT_ASSERT_EQUAL(3, World::getInstance().numAtoms());
-  CPPUNIT_ASSERT(output.str().find("2-0,0-2") != string::npos);
-  input.clear();
-  output.clear();
-}
-
-void ParserUnitTest::readAndWriteTremoloTorsionInformationTest() {
-  TremoloParser* testParser = new TremoloParser();
-  stringstream input, output;
-
-  // Neighbor data
-  input << Tremolo_torsion;
-  testParser->load(&input);
-  testParser->save(&output);
-  CPPUNIT_ASSERT_EQUAL(3, World::getInstance().numAtoms());
-  CPPUNIT_ASSERT(output.str().find("2-0,0-2") != string::npos);
-  input.clear();
-  output.clear();
-}
-
-void ParserUnitTest::writeTremoloTest() {
-  TremoloParser* testParser = new TremoloParser();
-  stringstream output;
-
-  // with the maximum number of fields and minimal information, default values are printed
-  atom* newAtom = World::getInstance().createAtom();
-  newAtom->setType(1);
-  testParser->setFieldsForSave("x=3 u=3 F stress Id neighbors=5 imprData GroupMeasureTypeNo Type extType name resName chainID resSeq occupancy tempFactor segID Charge charge GrpTypeNo torsion");
-  testParser->save(&output);
-  CPPUNIT_ASSERT(output.str() == Tremolo_full);
-
-  cout << "testing the tremolo parser is done" << endl;
-}
-
-void ParserUnitTest::readwritePcpTest() {
+void ParserCommonUnitTest::readwritePcpTest() {
   stringstream input(waterPcp);
   PcpParser* testParser = new PcpParser();
@@ -299 +206 @@
   CPPUNIT_ASSERT_EQUAL(3, World::getInstance().numAtoms());
 
-  string newWaterPcp = "";
-  stringstream output;
-  testParser->save(&output);
-
-  input << output;
+  // check that equality function is ok
+  CPPUNIT_ASSERT(*testParser == *testParser);
+
+  stringstream output;
+  testParser->save(&output);
+
+  input << output.str();
   PcpParser* testParser2 = new PcpParser();
   testParser2->load(&input);
@@ -312 +221 @@
 }
 
-void ParserUnitTest::writeMpqcTest() {
+void ParserCommonUnitTest::readwritePdbTest() {
+  stringstream input;
+  input << waterPdb;
+  PdbParser* testParser = new PdbParser();
+  testParser->load(&input);
+  input.clear();
+
+  CPPUNIT_ASSERT_EQUAL(6, World::getInstance().numAtoms());
+
+  stringstream output;
+  testParser->save(&output);
+
+//  std::cout << "Save PDB is:" << std::endl;
+//  std::cout << output.str() << std::endl;
+
+  input << output.str();
+  PdbParser* testParser2 = new PdbParser();
+  testParser2->load(&input);
+
+  CPPUNIT_ASSERT_EQUAL(12, World::getInstance().numAtoms());
+}
+
+void ParserCommonUnitTest::writeMpqcTest() {
   // build up water molecule
   atom *Walker = NULL;