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
83 static void readOptionFile(
String filename,
Options& output_options, list<Constraint*>& output_constraints,
const AtomContainer* ref_ligand = 0);
85 static void writeOptionFile(
String filename,
Options& input_options, list<Constraint*>& input_constraints);
96 void processMultiMoleculeFile(
string input_filename,
string output_filename,
double score_cutoff, vector<double>* min_atoms_in_ref_areas = 0,
String toolinfo=
"",
String timestamp=
"");
109 virtual void start();
113 virtual void pause();
117 virtual void proceed();
121 virtual void abort();
123 virtual void finish();
126 virtual void reset();
130 virtual bool hasFinished()
const;
142 virtual float getProgress()
const;
158 void setVisualizationPose(
const double& score);
160 double getVisualizationPoseScore();
169 void setMaxFps(
int no);
173 static void writeSubcategories_(
Options& category, std::ostream& out);
191 void mapLigandOntoReferenceLigand();
213 #endif // BALL_DOCKING_COMMON_DOCKINGALGORITHM_H