6 #ifndef BALL_DOCKING_COMMON_DOCKINGALGORITHM_H
7 #define BALL_DOCKING_COMMON_DOCKINGALGORITHM_H
9 #ifndef BALL_DATATYPE_OPTIONS_H
13 #ifndef BALL_KERNEL_SYSTEM_H
17 #ifndef BALL_DOCKING_COMMON_CONFORMATIONSET_H
21 #ifndef BALL_MATHS_MATRIX44_H
25 #ifndef BALL_SYSTEM_TIMER_H
29 #ifndef BALL_DOCKING_COMMON_CONSTRAINTS_H
39 class ScoringFunction;
52 BEST_INTERMEDIATE_POSES = 1,
53 ALL_INTERMEDIATE_POSES = 2,
54 NO_INTERMEDIATE_POSES = 3
static void readOptionFile(String filename, Options &output_options, list< Constraint * > &output_constraints, const AtomContainer *ref_ligand=0)
virtual ~DockingAlgorithm()
DISPLAYMODE getDisplayMode()
void setScoringFunction(ScoringFunction *scoring)
ScoringFunction * getScoringFunction()
AtomContainer visualization_pose_
double getVisualizationPoseScore()
double visualization_pose_score_
const AtomContainer * getLigand()
virtual bool wasPaused() const
AtomContainer * receptor_
static void writeOptionFile(String filename, Options &input_options, list< Constraint * > &input_constraints)
Timer visualization_timer_
void processMultiMoleculeFile(string input_filename, string output_filename, double score_cutoff, vector< double > *min_atoms_in_ref_areas=0, String toolinfo="", String timestamp="")
void setDisplayMode(DISPLAYMODE display_mode)
static const String OPTION_FILE_PARAMETER_NAME
virtual ConformationSet getConformationSet(Index total_conformations=0)
virtual void setup(System &receptor, System &ligand, Options &new_options)
double calculateRMSD(const AtomContainer &S1, const AtomContainer &S2, int *no_matched_atoms=NULL)
DockingAlgorithm(System &receptor, System &ligand, Options &new_options)
DockingAlgorithm(System &receptor, System &ligand)
String parameter_filename_
const AtomContainer * getReferenceLigand()
virtual void setup(System &receptor, System &ligand)
void setVisualizationPose(const double &score)
void mapLigandOntoReferenceLigand()
virtual double dockLigand(AtomContainer &ligand, bool verbose=0)
static Matrix4x4 mapCompounds(const AtomContainer &S1, const AtomContainer &S2, Size &no_matched_heavy_atoms, double &rmsd, double upper_bound, double lower_bound, double tolerance)
virtual float getProgress() const
const AtomContainer * getVisualizationPose()
AtomContainer * reference_ligand_
bool new_pose_to_be_visualized
void setLigand(AtomContainer *ligand)
static void writeSubcategories_(Options &category, std::ostream &out)
double min_sec_between_visualizations_
DISPLAYMODE display_mode_
virtual bool wasAborted() const
ScoringFunction * scoring_function_
virtual bool hasFinished() const