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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
#include <BALL/CONCEPT/classTest.h>
#include <BALLTestConfig.h>
#include <BALL/SCORING/COMMON/gridBasedScoring.h>
#include <BALL/SCORING/FUNCTIONS/MMScoring.h>
#include <BALL/DOCKING/COMMON/structurePreparer.h>
#include <BALL/DOCKING/IMGDOCK/IMGDock.h>
#include <BALL/FORMAT/PDBFile.h>
#include <BALL/FORMAT/MOL2File.h>
using namespace std;
using namespace BALL;
///////////////////////////
START_TEST(ScoringFunction)
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
PRECISION(1E-3)
Log.remove(cout);
PDBFile pdb(BALL_TEST_DATA_PATH(1b5i_pocket.pdb));
MOL2File mol2(BALL_TEST_DATA_PATH(1b5i_ligand.mol2));
System pocket; pdb >> pocket;
System ligand; mol2 >> ligand;
StructurePreparer sp;
sp.prepare(&pocket,"Amber/amber96-docking.ini");
sp.prepare(&ligand,"Amber/amber96-docking.ini");
CHECK(MMScoring)
Options options;
MMScoring scoring_function(pocket,ligand,options);
scoring_function.setLigand(ligand);
scoring_function.update();
scoring_function.updateScore();
vector<double> score_contributions;
vector<String> names;
scoring_function.getScoreContributions(score_contributions, names);
TEST_EQUAL(names.size(),5)
TEST_EQUAL(score_contributions.size(),5)
TEST_REAL_EQUAL(scoring_function.getScore(),-68.7552);
TEST_REAL_EQUAL(score_contributions[0],-8.52705) // ES
TEST_REAL_EQUAL(score_contributions[1],-19.7856) // vdW
TEST_REAL_EQUAL(score_contributions[2],-20.5528) // frag. solvation
TEST_REAL_EQUAL(score_contributions[3],-24.8898) // hydroggen bonds
TEST_REAL_EQUAL(score_contributions[4],5) // nRot
RESULT
// Do a fast re-docking, just in order to check whether it works. Note, that the below settings are therefore _not_ useful for a normal docking.
Options options;
options.set("iterations",1);
options.set("no_solutions",20);
options.set("step_width",90);
options.set("scoring_type","GridedMM");
options.set("scoregrid_resolution",1.0);
set<String> types;
types.insert("C");types.insert("H");
types.insert("O");types.insert("N");
IMGDock docker(pocket,ligand,options);
GridBasedScoring* grid_scoring = dynamic_cast<GridBasedScoring*>(docker.getScoringFunction());
TEST_NOT_EQUAL(grid_scoring,0);
grid_scoring->setAtomTypeNames(types);
CHECK(Grid Precalculation)
grid_scoring->precalculateGrids();
grid_scoring->update();
grid_scoring->updateScore(); // evaluate binding of reference ligand
// grid_scoring->printResult();
TEST_REAL_EQUAL(grid_scoring->getScore(),-57.424)
RESULT
CHECK(Scoregrid storing and loading)
grid_scoring->saveGridSetsToFile("test.grd","1b5i_pocket");
grid_scoring->replaceGridSetFromFile("test.grd");
grid_scoring->update();
grid_scoring->updateScore();
TEST_REAL_EQUAL(grid_scoring->getScore(),-57.424)
RESULT
CHECK(Compressed scoregrid storing and loading)
grid_scoring->saveGridSetsToFile("test.grd.gz","1b5i_pocket");
grid_scoring->replaceGridSetFromFile("test.grd.gz");
grid_scoring->update();
grid_scoring->updateScore();
TEST_REAL_EQUAL(grid_scoring->getScore(),-57.424)
RESULT
CHECK(Binary scoregrid storing and loading)
grid_scoring->saveGridSetsToFile("test.bngrd","1b5i_pocket");
grid_scoring->replaceGridSetFromFile("test.bngrd");
grid_scoring->update();
grid_scoring->updateScore();
TEST_REAL_EQUAL(grid_scoring->getScore(),-57.424)
RESULT
CHECK(IMeedyDock)
System ligand2 = ligand; // copy reference ligand for this simple test
// move ligand2 out of pocket
for(AtomIterator it=ligand2.beginAtom(); +it; it++)
{
it->setPosition(it->getPosition()+Vector3(20,20,20));
}
docker.dockLigand(ligand2);
TEST_REAL_EQUAL(docker.getScoringFunction()->getScore(),-59.7147);
MOL2File mol2res(BALL_TEST_DATA_PATH(1b5i_ligand-dockOut.mol2));
System expected_dockres;
mol2res >> expected_dockres;
AtomConstIterator it1 = ligand2.beginAtom();
AtomConstIterator it2 = expected_dockres.beginAtom();
for(; +it1 && +it2; it1++,it2++)
{
Vector3 position1 = it1->getPosition();
Vector3 position2 = it2->getPosition();
TEST_REAL_EQUAL(position1[0],position2[0])
TEST_REAL_EQUAL(position1[1],position2[1])
TEST_REAL_EQUAL(position1[2],position2[2])
}
RESULT
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
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