/usr/include/BALL/DOCKING/GENETICDOCK/dockProblem.h is in libball1.4-dev 1.4.3~beta1-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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// $Maintainer: Marcel Schumann $
// $Authors: Jan Fuhrmann, Marcel Schumann $
// ----------------------------------------------------
#ifndef BALL_DOCKING_GENETICDOCK_DOCKPROBLEM_H
#define BALL_DOCKING_GENETICDOCK_DOCKPROBLEM_H
#include <vector>
#include <string>
#include <BALL/MATHS/vector3.h>
#include <BALL/KERNEL/system.h>
#include <BALL/KERNEL/molecule.h>
#include <BALL/KERNEL/protein.h>
#include <BALL/MATHS/vector3.h>
#include <BALL/DOCKING/GENETICDOCK/rotateBonds.h>
#include <BALL/DOCKING/GENETICDOCK/geneticAlgorithm.h>
#include <BALL/DOCKING/GENETICDOCK/evolutionaryDocking.h>
#include <BALL/DOCKING/GENETICDOCK/parameter.h>
#include <BALL/SCORING/COMMON/scoringFunction.h>
#include <BALL/MATHS/matrix44.h>
#include <BALL/MATHS/quaternion.h>
#ifndef BALL_DOCKING_COMMON_CONFORMATIONSET_H
# include <BALL/DOCKING/COMMON/conformationSet.h>
#endif // BALL_DOCKING_COMMON_CONFORMATIONSET_H
namespace BALL
{
class BALL_EXPORT DockProblem
{
public:
/** constructor
*/
DockProblem();
/** constructor
*/
DockProblem(AtomContainer& sys_lig, BALL::ScoringFunction* sf,
EvolutionaryDocking* docker, bool post_dock_optimization);
/** destructor
*/
virtual ~DockProblem();
virtual void setup(AtomContainer& sys_lig);
/** calculate fitness score for one individual
*/
virtual double calculate();
/** move molecule according to vectors double_parameter_ and quaternion_parameter_, which are set by GeneticAlgorithm::calculate() */
void move();
/** true if best solution has changed
*/
bool redraw();
AtomContainer* getLigand();
void connectTo(GeneticAlgorithm* opt);
protected:
EvolutionaryDocking* docker_;
DoubleParameter double_parameter_;
QuaternionParameter quaternion_parameter_;
/** pointer to ligand molecule
*/
AtomContainer* ligand_, *draw_ligand_;
/** variables to store position and extentions of ligand and receptor
*/
Vector3 t_origin_, t_extension_;
Vector3 binding_pocket_center_;
/** calculate conformation score
*/
BALL::ScoringFunction* scoring_function_;
/** Vector to restore the position values of the ligand
*/
std::vector<Vector3 > ligand_positions_;
/** rotate bonds class
*/
RotateBonds* rb_;
/** set all rotable molecules to original positions
*/
void restore();
/** amber options
*/
Options opt_;
bool redraw_;
bool post_dock_optimization_;
};
}
#endif /* BALL_DOCKING_GENETICDOCK_DOCKPROBLEM_H */
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