BALL 1.5.0
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BALL::DockingAlgorithm Class Reference

#include <BALL/DOCKING/COMMON/dockingAlgorithm.h>

Inheritance diagram for BALL::DockingAlgorithm:
BALL::EvolutionaryDocking BALL::GeometricFit BALL::IMGDock

Public Types

enum  DISPLAYMODE { NO_DISPLAY = 0 , BEST_INTERMEDIATE_POSES = 1 , ALL_INTERMEDIATE_POSES = 2 , NO_INTERMEDIATE_POSES = 3 }
 

Public Member Functions

 DockingAlgorithm ()
 
 DockingAlgorithm (System &receptor, System &ligand, Options &new_options)
 
 DockingAlgorithm (System &receptor, System &ligand)
 
virtual ~DockingAlgorithm ()
 
virtual void setup (System &receptor, System &ligand, Options &new_options)
 
virtual void setup (System &receptor, System &ligand)
 
virtual double dockLigand (AtomContainer &ligand, bool verbose=0)
 
ScoringFunctiongetScoringFunction ()
 
void setScoringFunction (ScoringFunction *scoring)
 
void processMultiMoleculeFile (string input_filename, string output_filename, double score_cutoff, vector< double > *min_atoms_in_ref_areas=0, String toolinfo="", String timestamp="")
 
void setLigand (AtomContainer *ligand)
 
const AtomContainergetLigand ()
 
const AtomContainergetReferenceLigand ()
 
const StringgetName ()
 
virtual void start ()
 
virtual void pause ()
 
virtual void proceed ()
 
virtual void abort ()
 
virtual void finish ()
 
virtual void reset ()
 
virtual bool hasFinished () const
 
virtual bool wasAborted () const
 
virtual bool wasPaused () const
 
virtual float getProgress () const
 
virtual ConformationSet getConformationSet (Index total_conformations=0)
 
double calculateRMSD (const AtomContainer &S1, const AtomContainer &S2, int *no_matched_atoms=NULL)
 
const AtomContainergetVisualizationPose ()
 
void setVisualizationPose (const double &score)
 
double getVisualizationPoseScore ()
 
DISPLAYMODE getDisplayMode ()
 
void setDisplayMode (DISPLAYMODE display_mode)
 
void setMaxFps (int no)
 

Static Public Member Functions

static void readOptionFile (String filename, Options &output_options, list< Constraint * > &output_constraints, const AtomContainer *ref_ligand=0)
 
static void writeOptionFile (String filename, Options &input_options, list< Constraint * > &input_constraints)
 
static Matrix4x4 mapCompounds (const AtomContainer &S1, const AtomContainer &S2, Size &no_matched_heavy_atoms, double &rmsd, double upper_bound, double lower_bound, double tolerance)
 

Public Attributes

Options options
 
bool new_pose_to_be_visualized
 

Static Public Attributes

static const String OPTION_FILE_PARAMETER_NAME
 

Protected Member Functions

void mapLigandOntoReferenceLigand ()
 

Static Protected Member Functions

static void writeSubcategories_ (Options &category, std::ostream &out)
 

Protected Attributes

Systemsystem1_
 
Systemsystem2_
 
bool pause_
 
bool abort_
 
bool finished_
 
AtomContainerreference_ligand_
 
String name_
 
AtomContainerreceptor_
 
AtomContainerligand_
 
ScoringFunctionscoring_function_
 
String parameter_filename_
 
String scoring_type_
 
DISPLAYMODE display_mode_
 
AtomContainer visualization_pose_
 
double visualization_pose_score_
 
double min_sec_between_visualizations_
 
Timer visualization_timer_
 

Detailed Description

Interface class for docking algorithms.

Definition at line 45 of file dockingAlgorithm.h.

Member Enumeration Documentation

◆ DISPLAYMODE

Enumerator
NO_DISPLAY 
BEST_INTERMEDIATE_POSES 
ALL_INTERMEDIATE_POSES 
NO_INTERMEDIATE_POSES 

Definition at line 49 of file dockingAlgorithm.h.

Constructor & Destructor Documentation

◆ DockingAlgorithm() [1/3]

BALL::DockingAlgorithm::DockingAlgorithm ( )

◆ DockingAlgorithm() [2/3]

BALL::DockingAlgorithm::DockingAlgorithm ( System & receptor,
System & ligand,
Options & new_options )

◆ DockingAlgorithm() [3/3]

BALL::DockingAlgorithm::DockingAlgorithm ( System & receptor,
System & ligand )

◆ ~DockingAlgorithm()

virtual BALL::DockingAlgorithm::~DockingAlgorithm ( )
virtual

Member Function Documentation

◆ abort()

virtual void BALL::DockingAlgorithm::abort ( )
virtual

◆ calculateRMSD()

double BALL::DockingAlgorithm::calculateRMSD ( const AtomContainer & S1,
const AtomContainer & S2,
int * no_matched_atoms = NULL )

◆ dockLigand()

virtual double BALL::DockingAlgorithm::dockLigand ( AtomContainer & ligand,
bool verbose = 0 )
virtual

dock the given ligand and return its score

Reimplemented in BALL::EvolutionaryDocking, and BALL::IMGDock.

◆ finish()

virtual void BALL::DockingAlgorithm::finish ( )
virtual

◆ getConformationSet()

virtual ConformationSet BALL::DockingAlgorithm::getConformationSet ( Index total_conformations = 0)
virtual

Return total_conformations putative complexes, ordered according to their rank. If total_conformations == 0, the option TOP_N is used

Reimplemented in BALL::GeometricFit.

◆ getDisplayMode()

DISPLAYMODE BALL::DockingAlgorithm::getDisplayMode ( )

◆ getLigand()

const AtomContainer * BALL::DockingAlgorithm::getLigand ( )

◆ getName()

const String & BALL::DockingAlgorithm::getName ( )

get the name of this docking algorithm

◆ getProgress()

virtual float BALL::DockingAlgorithm::getProgress ( ) const
virtual

◆ getReferenceLigand()

const AtomContainer * BALL::DockingAlgorithm::getReferenceLigand ( )

◆ getScoringFunction()

ScoringFunction * BALL::DockingAlgorithm::getScoringFunction ( )

return the ScoringFunction that is used by this DockingAlgorithm

◆ getVisualizationPose()

const AtomContainer * BALL::DockingAlgorithm::getVisualizationPose ( )

◆ getVisualizationPoseScore()

double BALL::DockingAlgorithm::getVisualizationPoseScore ( )

◆ hasFinished()

virtual bool BALL::DockingAlgorithm::hasFinished ( ) const
virtual

Reimplemented in BALL::GeometricFit.

◆ mapCompounds()

static Matrix4x4 BALL::DockingAlgorithm::mapCompounds ( const AtomContainer & S1,
const AtomContainer & S2,
Size & no_matched_heavy_atoms,
double & rmsd,
double upper_bound,
double lower_bound,
double tolerance )
static

◆ mapLigandOntoReferenceLigand()

void BALL::DockingAlgorithm::mapLigandOntoReferenceLigand ( )
protected

◆ pause()

virtual void BALL::DockingAlgorithm::pause ( )
virtual

◆ proceed()

virtual void BALL::DockingAlgorithm::proceed ( )
virtual

◆ processMultiMoleculeFile()

void BALL::DockingAlgorithm::processMultiMoleculeFile ( string input_filename,
string output_filename,
double score_cutoff,
vector< double > * min_atoms_in_ref_areas = 0,
String toolinfo = "",
String timestamp = "" )

◆ readOptionFile()

static void BALL::DockingAlgorithm::readOptionFile ( String filename,
Options & output_options,
list< Constraint * > & output_constraints,
const AtomContainer * ref_ligand = 0 )
static

◆ reset()

virtual void BALL::DockingAlgorithm::reset ( )
virtual

resets Algorithm before new dock-run, e.g. sets finished_ to false

◆ setDisplayMode()

void BALL::DockingAlgorithm::setDisplayMode ( DISPLAYMODE display_mode)

◆ setLigand()

void BALL::DockingAlgorithm::setLigand ( AtomContainer * ligand)

◆ setMaxFps()

void BALL::DockingAlgorithm::setMaxFps ( int no)

Set the maximal number of frames per second for the visualization output. This affects only the number of poses that are written for visualization NOT the actual speed of the docking algorithm itself.

◆ setScoringFunction()

void BALL::DockingAlgorithm::setScoringFunction ( ScoringFunction * scoring)
inline

Definition at line 94 of file dockingAlgorithm.h.

◆ setup() [1/2]

virtual void BALL::DockingAlgorithm::setup ( System & receptor,
System & ligand )
virtual

Alternative setup. Assigns systems 1 and two without changing the options for this DockingAlgorithm.

Reimplemented in BALL::GeometricFit, and BALL::IMGDock.

◆ setup() [2/2]

virtual void BALL::DockingAlgorithm::setup ( System & receptor,
System & ligand,
Options & new_options )
virtual

Operations Full setup. Assigns systems 1 and two and the options for this DockingAlgorithm.

Reimplemented in BALL::EvolutionaryDocking, BALL::GeometricFit, and BALL::IMGDock.

◆ setVisualizationPose()

void BALL::DockingAlgorithm::setVisualizationPose ( const double & score)

◆ start()

virtual void BALL::DockingAlgorithm::start ( )
virtual

◆ wasAborted()

virtual bool BALL::DockingAlgorithm::wasAborted ( ) const
inlinevirtual

Definition at line 133 of file dockingAlgorithm.h.

◆ wasPaused()

virtual bool BALL::DockingAlgorithm::wasPaused ( ) const
inlinevirtual

Definition at line 137 of file dockingAlgorithm.h.

◆ writeOptionFile()

static void BALL::DockingAlgorithm::writeOptionFile ( String filename,
Options & input_options,
list< Constraint * > & input_constraints )
static

◆ writeSubcategories_()

static void BALL::DockingAlgorithm::writeSubcategories_ ( Options & category,
std::ostream & out )
staticprotected

Member Data Documentation

◆ abort_

bool BALL::DockingAlgorithm::abort_
protected

Definition at line 179 of file dockingAlgorithm.h.

◆ display_mode_

DISPLAYMODE BALL::DockingAlgorithm::display_mode_
protected

Definition at line 200 of file dockingAlgorithm.h.

◆ finished_

bool BALL::DockingAlgorithm::finished_
protected

Definition at line 180 of file dockingAlgorithm.h.

◆ ligand_

AtomContainer* BALL::DockingAlgorithm::ligand_
protected

Definition at line 189 of file dockingAlgorithm.h.

◆ min_sec_between_visualizations_

double BALL::DockingAlgorithm::min_sec_between_visualizations_
protected

Definition at line 207 of file dockingAlgorithm.h.

◆ name_

String BALL::DockingAlgorithm::name_
protected

the name of the docking algorithm

Definition at line 185 of file dockingAlgorithm.h.

◆ new_pose_to_be_visualized

bool BALL::DockingAlgorithm::new_pose_to_be_visualized

Definition at line 162 of file dockingAlgorithm.h.

◆ OPTION_FILE_PARAMETER_NAME

const String BALL::DockingAlgorithm::OPTION_FILE_PARAMETER_NAME
static

Definition at line 154 of file dockingAlgorithm.h.

◆ options

Options BALL::DockingAlgorithm::options

Attributes

Definition at line 67 of file dockingAlgorithm.h.

◆ parameter_filename_

String BALL::DockingAlgorithm::parameter_filename_
protected

Definition at line 195 of file dockingAlgorithm.h.

◆ pause_

bool BALL::DockingAlgorithm::pause_
protected

Definition at line 178 of file dockingAlgorithm.h.

◆ receptor_

AtomContainer* BALL::DockingAlgorithm::receptor_
protected

Definition at line 187 of file dockingAlgorithm.h.

◆ reference_ligand_

AtomContainer* BALL::DockingAlgorithm::reference_ligand_
protected

Definition at line 182 of file dockingAlgorithm.h.

◆ scoring_function_

ScoringFunction* BALL::DockingAlgorithm::scoring_function_
protected

Definition at line 193 of file dockingAlgorithm.h.

◆ scoring_type_

String BALL::DockingAlgorithm::scoring_type_
protected

name of the ScoringFunction to be used

Definition at line 198 of file dockingAlgorithm.h.

◆ system1_

System* BALL::DockingAlgorithm::system1_
protected

Definition at line 175 of file dockingAlgorithm.h.

◆ system2_

System* BALL::DockingAlgorithm::system2_
protected

Definition at line 176 of file dockingAlgorithm.h.

◆ visualization_pose_

AtomContainer BALL::DockingAlgorithm::visualization_pose_
protected

copy of a intermediate pose that is to be visualized.

Definition at line 203 of file dockingAlgorithm.h.

◆ visualization_pose_score_

double BALL::DockingAlgorithm::visualization_pose_score_
protected

Definition at line 205 of file dockingAlgorithm.h.

◆ visualization_timer_

Timer BALL::DockingAlgorithm::visualization_timer_
protected

Definition at line 208 of file dockingAlgorithm.h.