source: src/Analysis/unittests/CountBondsUnitTest.cpp@ 9317be

/*
 * Project: MoleCuilder
 * Description: creates and alters molecular systems
 * Copyright (C)  2010 University of Bonn. All rights reserved.
 * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
 */

/*
 * CountBondsUnitTest.cpp
 *
 *  Created on: Mar 30, 2010
 *      Author: heber
 */

// include config.h
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

using namespace std;

#include <cppunit/CompilerOutputter.h>
#include <cppunit/extensions/TestFactoryRegistry.h>
#include <cppunit/ui/text/TestRunner.h>

#include <iostream>
#include <stdio.h>
#include <cstring>

#include "CodePatterns/Assert.hpp"

#include "Analysis/analysis_bonds.hpp"
#include "atom.hpp"
#include "Bond/bond.hpp"
#include "Element/element.hpp"
#include "Graph/BondGraph.hpp"
#include "molecule.hpp"
#include "Element/periodentafel.hpp"
#include "World.hpp"

#include "CountBondsUnitTest.hpp"

#ifdef HAVE_TESTRUNNER
#include "UnitTestMain.hpp"
#endif /*HAVE_TESTRUNNER*/

/********************************************** Test classes **************************************/

// Registers the fixture into the 'registry'
CPPUNIT_TEST_SUITE_REGISTRATION( CountBondsTest );


void CountBondsTest::setUp()
{
  atom *Walker = NULL;

  // construct element
  hydrogen = World::getInstance().getPeriode()->FindElement(1);
  oxygen = World::getInstance().getPeriode()->FindElement(8);
  CPPUNIT_ASSERT(hydrogen != NULL && "could not find element hydrogen");
  CPPUNIT_ASSERT(oxygen != NULL && "could not find element oxygen");

  // construct molecule (water molecule)
  TestMolecule1 = World::getInstance().createMolecule();
  CPPUNIT_ASSERT(TestMolecule1 != NULL && "could not create first molecule");
  Walker = World::getInstance().createAtom();
  CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
  Walker->setType(hydrogen);
  Walker->setPosition(Vector(-0.2418, 0.9350, 0. ));
  TestMolecule1->AddAtom(Walker);
  Walker = World::getInstance().createAtom();
  CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
  Walker->setType(hydrogen);
  Walker->setPosition(Vector(0.9658, 0., 0. ));
  TestMolecule1->AddAtom(Walker);
  Walker = World::getInstance().createAtom();
  CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
  Walker->setType(oxygen);
  Walker->setPosition(Vector(0., 0., 0. ));
  TestMolecule1->AddAtom(Walker);

  TestMolecule2 = World::getInstance().createMolecule();
  CPPUNIT_ASSERT(TestMolecule2 != NULL && "could not create second molecule");
  Walker = World::getInstance().createAtom();
  CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
  Walker->setType(hydrogen);
  Walker->setPosition(Vector(-0.2418, 0.9350, 0. ));
  TestMolecule2->AddAtom(Walker);
  Walker = World::getInstance().createAtom();
  CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
  Walker->setType(hydrogen);
  Walker->setPosition(Vector(0.9658, 0., 0. ));
  TestMolecule2->AddAtom(Walker);
  Walker = World::getInstance().createAtom();
  CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
  Walker->setType(oxygen);
  Walker->setPosition(Vector(0., 0., 0. ));
  TestMolecule2->AddAtom(Walker);

  molecules = World::getInstance().getMolecules();
  CPPUNIT_ASSERT(molecules != NULL && "could not obtain list of molecules");
  molecules->insert(TestMolecule1);
  molecules->insert(TestMolecule2);

  // check that TestMolecule was correctly constructed
  CPPUNIT_ASSERT_EQUAL( TestMolecule1->getAtomCount(), 3 );
  CPPUNIT_ASSERT_EQUAL( TestMolecule2->getAtomCount(), 3 );

  // create a small file with table
  BG = new BondGraph(true);
  CPPUNIT_ASSERT(BG != NULL && "could not create BondGraph");

  // construct bond graphs
  World::AtomComposite Set1 = TestMolecule1->getAtomSet();
  BG->CreateAdjacency(Set1);
  CPPUNIT_ASSERT( TestMolecule1->getBondCount() != 0);
  World::AtomComposite Set2 = TestMolecule2->getAtomSet();
  BG->CreateAdjacency(Set2);
  CPPUNIT_ASSERT( TestMolecule2->getBondCount() != 0);
//  TestMolecule1->Output((ofstream *)&cout);
//  TestMolecule1->OutputBondsList(std::cout);
};


void CountBondsTest::tearDown()
{
  // remove the file
  delete(BG);

  World::purgeInstance();
};

/** UnitTest for CountBondsTest::BondsOfTwoTest().
 */
void CountBondsTest::BondsOfTwoTest()
{
  CPPUNIT_ASSERT_EQUAL( 4 , CountBondsOfTwo(molecules, hydrogen, oxygen) );
  CPPUNIT_ASSERT_EQUAL( 0 , CountBondsOfTwo(molecules, hydrogen, hydrogen) );
  CPPUNIT_ASSERT_EQUAL( 0 , CountBondsOfTwo(molecules, oxygen, oxygen) );
};

/** UnitTest for CountBondsTest::BondsOfThreeTest().
 */
void CountBondsTest::BondsOfThreeTest()
{
  CPPUNIT_ASSERT_EQUAL( 2 , CountBondsOfThree(molecules, hydrogen, oxygen, hydrogen) );
  CPPUNIT_ASSERT_EQUAL( 0 , CountBondsOfThree(molecules, oxygen, hydrogen, oxygen) );
};

void OutputTestMolecule(molecule *mol, const char *name)
{
  ofstream output(name);
  mol->OutputXYZ(&output);
  output.close();
}

/** UnitTest for CountBondsTest::HydrogenBridgeBondsTest().
 */
void CountBondsTest::HydrogenBridgeBondsTest()
{
  double *mirror = new double[3];
  CPPUNIT_ASSERT(mirror != NULL && "could not create array of doubles");
  for (int i=0;i<3;i++)
    mirror[i] = -1.;
  Vector Translator;

  //OutputTestMolecule(TestMolecule1, "testmolecule1.xyz");

  cout << "Case 1: offset of (3,0,0), hence angles are (104.5, 0, 75.5, 180) < 30." << endl;
  Translator  = Vector(3,0,0);
  TestMolecule2->Translate(&Translator);
  CPPUNIT_ASSERT_EQUAL( 1 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, oxygen, NULL) );
  //OutputTestMolecule(TestMolecule2, "testmolecule2-1.xyz");
  Translator = Vector(-3,0,0);
  TestMolecule2->Translate(&Translator);

  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;
  Translator = Vector(0,3,0);
  TestMolecule2->Translate(&Translator);
  CPPUNIT_ASSERT_EQUAL( 1 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
  //OutputTestMolecule(TestMolecule2, "testmolecule2-2.xyz");
  Translator = Vector(0,-3,0);
  TestMolecule2->Translate(&Translator);

  cout << "Case 3: offset of (0,-3,0) and mirror, hence angle are (165.5, 90, 165.5, 90) > 30." << endl;
  Translator = Vector(0,-3,0);
  TestMolecule2->Scale((const double ** const)&mirror);
  TestMolecule2->Translate(&Translator);
  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
  //OutputTestMolecule(TestMolecule2, "testmolecule2-3.xyz");
  Translator = Vector(0,3,0);
  TestMolecule2->Translate(&Translator);
  TestMolecule2->Scale((const double ** const)&mirror);

  cout << "Case 4: offset of (2,1,0), hence angle are (78, 26.6, 102, 153.4) < 30." << endl;
  Translator = Vector(2,1,0);
  TestMolecule2->Translate(&Translator);
  CPPUNIT_ASSERT_EQUAL( 1 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
  //OutputTestMolecule(TestMolecule2, "testmolecule2-4.xyz");
  Translator = Vector(-2,-1,0);
  TestMolecule2->Translate(&Translator);

  cout << "Case 5: offset of (0,0,3), hence angle are (90, 90, 90, 90) > 30." << endl;
  Translator = Vector(0,0,3);
  TestMolecule2->Translate(&Translator);
  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
  //OutputTestMolecule(TestMolecule2, "testmolecule2-5.xyz");
  Translator = Vector(0,0,-3);
  TestMolecule2->Translate(&Translator);

  cout << "Case 6: offset of (-3,0,0) and mirror, hence angle are (75.5, 180, 104.5, 180) > 30." << endl;
  Translator = Vector(-3,0,0);
  TestMolecule2->Scale((const double ** const)&mirror);
  TestMolecule2->Translate(&Translator);
  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
  //OutputTestMolecule(TestMolecule2, "testmolecule2-6.xyz");
  Translator = Vector(3,0,0);
  TestMolecule2->Translate(&Translator);
  TestMolecule2->Scale((const double ** const)&mirror);

  cout << "Case 7: offset of (3,0,0) and mirror, hence angles are (104.5, 0, 104.5, 0) < 30, but interfering hydrogens." << endl;
  Translator = Vector(3,0,0);
  TestMolecule2->Scale((const double ** const)&mirror);
  TestMolecule2->Translate(&Translator);
  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
  //OutputTestMolecule(TestMolecule2, "testmolecule2-7.xyz");
  Translator = Vector(-3,0,0);
  TestMolecule2->Translate(&Translator);
  TestMolecule2->Scale((const double ** const)&mirror);

  cout << "Case 8: offset of (0,3,0), hence angle are (14.5, 90, 14.5, 90) < 30, but interfering hydrogens." << endl;
  Translator = Vector(0,3,0);
  TestMolecule2->Scale((const double ** const)&mirror);
  TestMolecule2->Translate(&Translator);
  //OutputTestMolecule(TestMolecule2, "testmolecule2-8.xyz");
  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
  Translator = Vector(0,-3,0);
  TestMolecule2->Translate(&Translator);
  TestMolecule2->Scale((const double ** const)&mirror);

  delete[](mirror);
};