Changeset e462b3 for molecuilder/src


Ignore:
Timestamp:
Nov 7, 2009, 12:25:32 PM (16 years ago)
Author:
Frederik Heber <heber@…>
Children:
e960b1
Parents:
1fcedd
git-author:
Frederik Heber <heber@…> (11/07/09 12:18:56)
git-committer:
Frederik Heber <heber@…> (11/07/09 12:25:32)
Message:

Two new bond analysis functions.

Location:
molecuilder/src
Files:
4 edited

Legend:

Unmodified
Added
Removed

  • molecuilder/src/analysis_bonds.cpp

    r1fcedd re462b3  
    66 */
    77
     8#include "analysis_bonds.hpp"
     9#include "atom.hpp"
     10#include "bond.hpp"
     11#include "log.hpp"
     12#include "molecule.hpp"
     13
     14/** Calculates the min, mean and maximum bond counts for the given molecule.
     15 * \param *mol molecule with atoms and atom::ListOfBonds
     16 * \param &Min minimum count on return
     17 * \param &Mean mean count on return
     18 * \param &Max maximum count on return
     19 */
     20void GetMaxMinMeanBondCount(const molecule * const mol, double &Min, double &Mean, double &Max)
     21{
     22  Min = 2e+6;
     23  Max = -2e+5;
     24  Mean = 0.;
     25
     26  atom *Walker = mol->start;
     27  int AtomCount = 0;
     28  while (Walker->next != mol->end) {
     29    Walker = Walker->next;
     30    const int count = Walker->ListOfBonds.size();
     31    if (Max < count)
     32      Max = count;
     33    if (Min > count)
     34      Min = count;
     35    Mean += count;
     36    AtomCount++;
     37  }
     38  if (((int)Mean % 2) != 0)
     39    eLog() << Verbose(1) << "Something is wrong with the bond structure, the number of bonds is not even!" << endl;
     40  Mean /= (double)AtomCount;
     41};
     42
     43/** Calculates the min and max bond distance of all atoms of two given elements.
     44 * \param *mol molecule with atoms
     45 * \param *type1 one element
     46 * \param *type2 other element
     47 * \param &Min minimum distance on return, 0 if no bond between the two elements
     48 * \param &Mean mean distance (i.e. sum of distance for matching element pairs, divided by number) on return, 0 if no bond between the two elements
     49 * \param &Max maximum distance on return, 0 if no bond between the two elements
     50 */
     51void MinMeanMaxBondDistanceBetweenElements(const molecule *mol, element *type1, element *type2, double &Min, double &Mean, double &Max)
     52{
     53  Min = 2e+6;
     54  Mean = 0.;
     55  Max = -2e+6;
     56
     57  int AtomNo = 0;
     58  atom *Walker = mol->start;
     59  while (Walker->next != mol->end) {
     60    Walker = Walker->next;
     61    if (Walker->type == type1)
     62      for (BondList::const_iterator BondRunner = Walker->ListOfBonds.begin(); BondRunner != Walker->ListOfBonds.end(); BondRunner++)
     63        if ((*BondRunner)->GetOtherAtom(Walker)->type == type2) {
     64          const double distance = (*BondRunner)->GetDistanceSquared();
     65          if (Min > distance)
     66            Min = distance;
     67          if (Max < distance)
     68            Max = distance;
     69          Mean += sqrt(distance);
     70          AtomNo++;
     71        }
     72  }
     73  if (Max < 0) {
     74    Max = Min = 0.;
     75  } else {
     76    Max = sqrt(Max);
     77    Min = sqrt(Min);
     78    Mean = Mean/(double)AtomNo;
     79  }
     80};

  • molecuilder/src/analysis_bonds.hpp

    r1fcedd re462b3  
    2121/****************************************** forward declarations *****************************/
    2222
     23class element;
     24class molecule;
    2325
    2426/********************************************** declarations *******************************/
    2527
     28void GetMaxMinMeanBondCount(const molecule * const mol, double &Min, double &Mean, double &Max);
     29void MinMeanMaxBondDistanceBetweenElements(const molecule *mol, element *type1, element *type2, double &Min, double &Mean, double &Max);
     30
    2631#endif /* ANALYSIS_BONDS_HPP_ */

  • molecuilder/src/unittests/analysisbondsunittest.cpp

    r1fcedd re462b3  
    1515#include <stdio.h>
    1616
     17#include "analysis_bonds.hpp"
     18#include "analysisbondsunittest.hpp"
    1719#include "atom.hpp"
    1820#include "bond.hpp"
    … …  
    2123#include "molecule.hpp"
    2224#include "periodentafel.hpp"
    23 #include "analysisbondsunittest.hpp"
    2425
    2526/********************************************** Test classes **************************************/
    … …  
    4142  hydrogen = new element;
    4243  hydrogen->Z = 1;
     44  hydrogen->Valence = 1;
     45  hydrogen->NoValenceOrbitals = 1;
    4346  strcpy(hydrogen->name, "hydrogen");
    4447  strcpy(hydrogen->symbol, "H");
    4548  carbon = new element;
    4649  carbon->Z = 1;
     50  carbon->Valence = 4;
     51  carbon->NoValenceOrbitals = 4;
    4752  strcpy(carbon->name, "carbon");
    4853  strcpy(carbon->symbol, "C");
    … …  
    5863  Walker = new atom();
    5964  Walker->type = hydrogen;
    60   Walker->node->Init(1., 0., 1. );
     65  Walker->node->Init(1.5, 0., 1.5 );
    6166  TestMolecule->AddAtom(Walker);
    6267  Walker = new atom();
    6368  Walker->type = hydrogen;
    64   Walker->node->Init(0., 1., 1. );
     69  Walker->node->Init(0., 1.5, 1.5 );
    6570  TestMolecule->AddAtom(Walker);
    6671  Walker = new atom();
    6772  Walker->type = hydrogen;
    68   Walker->node->Init(1., 1., 0. );
     73  Walker->node->Init(1.5, 1.5, 0. );
    6974  TestMolecule->AddAtom(Walker);
    7075  Walker = new atom();
    … …  
    7277  Walker->node->Init(0., 0., 0. );
    7378  TestMolecule->AddAtom(Walker);
     79  Walker = new atom();
     80  Walker->type = carbon;
     81  Walker->node->Init(0.5, 0.5, 0.5 );
     82  TestMolecule->AddAtom(Walker);
    7483
    7584  // check that TestMolecule was correctly constructed
    76   CPPUNIT_ASSERT_EQUAL( TestMolecule->AtomCount, 4 );
     85  CPPUNIT_ASSERT_EQUAL( TestMolecule->AtomCount, 5 );
    7786
    7887  // create a small file with table
    … …  
    8291  test << "H\t1.\t1.2\n";
    8392  test << "C\t1.2\t1.5\n";
     93  test.close();
    8494  BG = new BondGraph(true);
     95
     96  CPPUNIT_ASSERT_EQUAL( true , BG->LoadBondLengthTable(*filename) );
     97  CPPUNIT_ASSERT_EQUAL( 1., BG->GetBondLength(0,0) );
     98  CPPUNIT_ASSERT_EQUAL( 1.2, BG->GetBondLength(0,1) );
     99  CPPUNIT_ASSERT_EQUAL( 1.5, BG->GetBondLength(1,1) );
     100
     101  BG->ConstructBondGraph(TestMolecule);
    85102};
    86103
    … …  
    100117};
    101118
    102 /** UnitTest for AnalysisBondsTest::LoadBondLengthTable().
     119/** UnitTest for GetMaxMinMeanBondCount().
    103120 */
    104 void AnalysisBondsTest::BondsTest()
     121void AnalysisBondsTest::GetMaxMinMeanBondCountTest()
    105122{
    106   CPPUNIT_ASSERT_EQUAL( true , BG->LoadBondLengthTable(*filename) );
    107   CPPUNIT_ASSERT_EQUAL( 1., BG->GetBondLength(0,0) );
    108   CPPUNIT_ASSERT_EQUAL( 1.2, BG->GetBondLength(0,1) );
    109   CPPUNIT_ASSERT_EQUAL( 1.5, BG->GetBondLength(1,1) );
    110 
    111   CPPUNIT_ASSERT_EQUAL( true , true );
     123  double Min = 20.; // check that initialization resets these arbitrary values
     124  double Mean = 200.;
     125  double Max = 1e-6;
     126  GetMaxMinMeanBondCount(TestMolecule, Min, Mean, Max);
     127  CPPUNIT_ASSERT_EQUAL( 1., Min );
     128  CPPUNIT_ASSERT_EQUAL( 1.6, Mean );
     129  CPPUNIT_ASSERT_EQUAL( 4., Max );
    112130
    113131};
     132
     133/** UnitTest for MinMaxBondDistanceBetweenElements().
     134 */
     135void AnalysisBondsTest::MinMeanMaxBondDistanceBetweenElementsTest()
     136{
     137  double Min = 20.; // check that initialization resets these arbitrary values
     138  double Mean = 2e+6;
     139  double Max = 1e-6;
     140  double Min2 = 20.;
     141  double Mean2 = 2e+6;
     142  double Max2 = 1e-6;
     143  const double maxbondlength = sqrt(1.*1. + 1.*1. + .5*.5);
     144  const double minbondlength = sqrt(.5*.5 + .5*.5 + .5*.5);
     145  const double meanbondlength = (minbondlength+3.*maxbondlength)/4.;
     146  // check bond lengths C-H
     147  MinMeanMaxBondDistanceBetweenElements(TestMolecule, hydrogen, carbon, Min, Mean, Max);
     148  CPPUNIT_ASSERT_EQUAL( minbondlength , Min );
     149  CPPUNIT_ASSERT_EQUAL( meanbondlength , Mean );
     150  CPPUNIT_ASSERT_EQUAL( maxbondlength , Max );
     151
     152  // check that elements are symmetric, i.e. C-H == H-C
     153  MinMeanMaxBondDistanceBetweenElements(TestMolecule, carbon, hydrogen, Min2, Mean2, Max2);
     154  CPPUNIT_ASSERT_EQUAL( Min , Min2 );
     155  CPPUNIT_ASSERT_EQUAL( Mean , Mean2 );
     156  CPPUNIT_ASSERT_EQUAL( Max , Max2 );
     157
     158  // check no bond case (no bonds H-H in system!)
     159  MinMeanMaxBondDistanceBetweenElements(TestMolecule, hydrogen, hydrogen, Min, Mean, Max);
     160  CPPUNIT_ASSERT_EQUAL( 0. , Min );
     161  CPPUNIT_ASSERT_EQUAL( 0. , Mean );
     162  CPPUNIT_ASSERT_EQUAL( 0. , Max );
     163};
     164
    114165
    115166/********************************************** Main routine **************************************/

  • molecuilder/src/unittests/analysisbondsunittest.hpp

    r1fcedd re462b3  
    1111#include <cppunit/extensions/HelperMacros.h>
    1212
    13 #include "bondgraph.hpp"
    14 
     13class BondGraph;
    1514class element;
    1615class molecule;
    … …  
    2221{
    2322    CPPUNIT_TEST_SUITE( AnalysisBondsTest) ;
    24     CPPUNIT_TEST ( BondsTest );
     23    CPPUNIT_TEST ( GetMaxMinMeanBondCountTest );
     24    CPPUNIT_TEST ( MinMeanMaxBondDistanceBetweenElementsTest );
    2525    CPPUNIT_TEST_SUITE_END();
    2626
    … …  
    2828      void setUp();
    2929      void tearDown();
    30       void BondsTest();
     30      void GetMaxMinMeanBondCountTest();
     31      void MinMeanMaxBondDistanceBetweenElementsTest();
    3132
    3233private:
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