BALL  1.5.0
Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
BALL::DockProblem Class Reference

#include <BALL/DOCKING/GENETICDOCK/dockProblem.h>

Public Member Functions

 DockProblem ()
 
 DockProblem (AtomContainer &sys_lig, BALL::ScoringFunction *sf, EvolutionaryDocking *docker, bool post_dock_optimization)
 
virtual ~DockProblem ()
 
virtual void setup (AtomContainer &sys_lig)
 
virtual double calculate ()
 
void move ()
 
bool redraw ()
 
AtomContainergetLigand ()
 
void connectTo (GeneticAlgorithm *opt)
 

Protected Member Functions

void restore ()
 

Protected Attributes

EvolutionaryDockingdocker_
 
DoubleParameter double_parameter_
 
QuaternionParameter quaternion_parameter_
 
AtomContainerligand_
 
AtomContainerdraw_ligand_
 
Vector3 t_origin_
 
Vector3 t_extension_
 
Vector3 binding_pocket_center_
 
BALL::ScoringFunctionscoring_function_
 
std::vector< Vector3ligand_positions_
 
RotateBondsrb_
 
Options opt_
 
bool redraw_
 
bool post_dock_optimization_
 

Detailed Description

Definition at line 35 of file dockProblem.h.

Constructor & Destructor Documentation

◆ DockProblem() [1/2]

BALL::DockProblem::DockProblem ( )

constructor

◆ DockProblem() [2/2]

BALL::DockProblem::DockProblem ( AtomContainer sys_lig,
BALL::ScoringFunction sf,
EvolutionaryDocking docker,
bool  post_dock_optimization 
)

constructor

◆ ~DockProblem()

virtual BALL::DockProblem::~DockProblem ( )
virtual

destructor

Member Function Documentation

◆ calculate()

virtual double BALL::DockProblem::calculate ( )
virtual

calculate fitness score for one individual

◆ connectTo()

void BALL::DockProblem::connectTo ( GeneticAlgorithm opt)

◆ getLigand()

AtomContainer* BALL::DockProblem::getLigand ( )

◆ move()

void BALL::DockProblem::move ( )

move molecule according to vectors double_parameter_ and quaternion_parameter_, which are set by GeneticAlgorithm::calculate()

◆ redraw()

bool BALL::DockProblem::redraw ( )

true if best solution has changed

◆ restore()

void BALL::DockProblem::restore ( )
protected

set all rotable molecules to original positions

◆ setup()

virtual void BALL::DockProblem::setup ( AtomContainer sys_lig)
virtual

Member Data Documentation

◆ binding_pocket_center_

Vector3 BALL::DockProblem::binding_pocket_center_
protected

Definition at line 90 of file dockProblem.h.

◆ docker_

EvolutionaryDocking* BALL::DockProblem::docker_
protected

Definition at line 76 of file dockProblem.h.

◆ double_parameter_

DoubleParameter BALL::DockProblem::double_parameter_
protected

Definition at line 78 of file dockProblem.h.

◆ draw_ligand_

AtomContainer * BALL::DockProblem::draw_ligand_
protected

Definition at line 84 of file dockProblem.h.

◆ ligand_

AtomContainer* BALL::DockProblem::ligand_
protected

pointer to ligand molecule

Definition at line 84 of file dockProblem.h.

◆ ligand_positions_

std::vector<Vector3 > BALL::DockProblem::ligand_positions_
protected

Vector to restore the position values of the ligand

Definition at line 98 of file dockProblem.h.

◆ opt_

Options BALL::DockProblem::opt_
protected

amber options

Definition at line 112 of file dockProblem.h.

◆ post_dock_optimization_

bool BALL::DockProblem::post_dock_optimization_
protected

Definition at line 116 of file dockProblem.h.

◆ quaternion_parameter_

QuaternionParameter BALL::DockProblem::quaternion_parameter_
protected

Definition at line 80 of file dockProblem.h.

◆ rb_

RotateBonds* BALL::DockProblem::rb_
protected

rotate bonds class

Definition at line 102 of file dockProblem.h.

◆ redraw_

bool BALL::DockProblem::redraw_
protected

Definition at line 114 of file dockProblem.h.

◆ scoring_function_

BALL::ScoringFunction* BALL::DockProblem::scoring_function_
protected

calculate conformation score

Definition at line 94 of file dockProblem.h.

◆ t_extension_

Vector3 BALL::DockProblem::t_extension_
protected

Definition at line 88 of file dockProblem.h.

◆ t_origin_

Vector3 BALL::DockProblem::t_origin_
protected

variables to store position and extentions of ligand and receptor

Definition at line 88 of file dockProblem.h.