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BALL::GeometricFit Member List

This is the complete list of members for BALL::GeometricFit, including all inherited members.

abort() | BALL::DockingAlgorithm | virtual
abort_ | BALL::DockingAlgorithm | protected
ALL_INTERMEDIATE_POSES enum value | BALL::DockingAlgorithm |
BEST_INTERMEDIATE_POSES enum value | BALL::DockingAlgorithm |
calcConjugate_(ProteinIndex pro_idx) | BALL::GeometricFit | protected
calculateRMSD(const AtomContainer &S1, const AtomContainer &S2, int *no_matched_atoms=NULL) | BALL::DockingAlgorithm |
changeProteinOrientation_(System &system, Vector3 euler_ang) | BALL::GeometricFit | protected
CONNOLLY enum value | BALL::GeometricFit |
current_round_ | BALL::GeometricFit | protected
destroy_() | BALL::GeometricFit | protected
display_mode_ | BALL::DockingAlgorithm | protected
DISPLAYMODE enum name | BALL::DockingAlgorithm |
DockingAlgorithm() | BALL::DockingAlgorithm |
DockingAlgorithm(System &receptor, System &ligand, Options &new_options) | BALL::DockingAlgorithm |
DockingAlgorithm(System &receptor, System &ligand) | BALL::DockingAlgorithm |
dockLigand(AtomContainer &ligand, bool verbose=0) | BALL::DockingAlgorithm | virtual
doPreTranslation_(ProteinIndex pro_idx) | BALL::GeometricFit | protected
FFT_grid_a_ | BALL::GeometricFit | protected
FFT_grid_b_ | BALL::GeometricFit | protected
FFT_grid_lower_coord_ | BALL::GeometricFit | protected
FFT_grid_lower_index_ | BALL::GeometricFit | protected
FFT_grid_origin_ | BALL::GeometricFit | protected
FFT_grid_size_index_ | BALL::GeometricFit | protected
FFT_grid_upper_coord_ | BALL::GeometricFit | protected
FFT_grid_upper_index_ | BALL::GeometricFit | protected
FFTGridMulti_() | BALL::GeometricFit | protected
findConnollySurfacePoints_(System &system, ProteinIndex pro_idx) | BALL::GeometricFit | protected
findFTDockInsidePoints_(System &system, ProteinIndex pro_idx) | BALL::GeometricFit | protected
findFTDockSurfacePoints_(System &system, ProteinIndex pro_idx) | BALL::GeometricFit | protected
findInsidePoints_(System &system, ProteinIndex pro_idx) | BALL::GeometricFit | protected
findVanDerWaalsSurfacePoints_(System &system, ProteinIndex pro_idx) | BALL::GeometricFit | protected
finish() | BALL::DockingAlgorithm | virtual
finished_ | BALL::DockingAlgorithm | protected
FTDOCK enum value | BALL::GeometricFit |
GeometricFit() | BALL::GeometricFit |
GeometricFit(System &system1, System &system2) | BALL::GeometricFit |
GeometricFit(Options &new_options) | BALL::GeometricFit |
GeometricFit(System &system1, System &system2, Options &new_options) | BALL::GeometricFit |
GeometricFit(const GeometricFit &geo_fit) | BALL::GeometricFit |
getConformationSet(Index total_number=0) | BALL::GeometricFit | virtual
getDisplayMode() | BALL::DockingAlgorithm |
getGlobalPeak_(Peak_ *peak_list) | BALL::GeometricFit | protected
getLigand() | BALL::DockingAlgorithm |
getMassCenter_(System &system) | BALL::GeometricFit | protected
getName() | BALL::DockingAlgorithm |
getOrientation(Index con_num) const | BALL::GeometricFit |
getProgress() const | BALL::GeometricFit | virtual
getRadius_(System &system) | BALL::GeometricFit | protected
getReferenceLigand() | BALL::DockingAlgorithm |
getScoringFunction() | BALL::DockingAlgorithm |
getSeparation_(const Vector3 &mat_pos) | BALL::GeometricFit | protected
getTranslation(Index con_num) const | BALL::GeometricFit |
getTranslation_(const Vector3 &mat_pos) | BALL::GeometricFit | protected
getVisualizationPose() | BALL::DockingAlgorithm |
getVisualizationPoseScore() | BALL::DockingAlgorithm |
hasFinished() const | BALL::GeometricFit | virtual
initFFTGrid_(ProteinIndex pro_idx) | BALL::GeometricFit | protected
initGridSizes_() | BALL::GeometricFit | protected
ligand_ | BALL::DockingAlgorithm | protected
makeFFTGrid_(ProteinIndex pro_idx) | BALL::GeometricFit | protected
mapCompounds(const AtomContainer &S1, const AtomContainer &S2, Size &no_matched_heavy_atoms, double &rmsd, double upper_bound, double lower_bound, double tolerance) | BALL::DockingAlgorithm | static
mapLigandOntoReferenceLigand() | BALL::DockingAlgorithm | protected
min_sec_between_visualizations_ | BALL::DockingAlgorithm | protected
name_ | BALL::DockingAlgorithm | protected
new_pose_to_be_visualized | BALL::DockingAlgorithm |
NO_DISPLAY enum value | BALL::DockingAlgorithm |
NO_INTERMEDIATE_POSES enum value | BALL::DockingAlgorithm |
optimizeGridSize_(int raw_size) | BALL::GeometricFit | protected
OPTION_FILE_PARAMETER_NAME | BALL::DockingAlgorithm | static
options | BALL::GeometricFit |
orientations_ | BALL::GeometricFit | protected
parameter_filename_ | BALL::DockingAlgorithm | protected
pause() | BALL::DockingAlgorithm | virtual
pause_ | BALL::DockingAlgorithm | protected
peak_set_ | BALL::GeometricFit | protected
pre_translation_a_ | BALL::GeometricFit | protected
pre_translation_b_ | BALL::GeometricFit | protected
proceed() | BALL::DockingAlgorithm | virtual
processMultiMoleculeFile(string input_filename, string output_filename, double score_cutoff, vector< double > *min_atoms_in_ref_areas=0, String toolinfo="", String timestamp="") | BALL::DockingAlgorithm |
PROTEIN_A enum value | BALL::GeometricFit |
PROTEIN_B enum value | BALL::GeometricFit |
ProteinIndex enum name | BALL::GeometricFit |
radius_a_ | BALL::GeometricFit | protected
radius_b_ | BALL::GeometricFit | protected
readOptionFile(String filename, Options &output_options, list< Constraint * > &output_constraints, const AtomContainer *ref_ligand=0) | BALL::DockingAlgorithm | static
receptor_ | BALL::DockingAlgorithm | protected
reference_ligand_ | BALL::DockingAlgorithm | protected
reset() | BALL::DockingAlgorithm | virtual
scoring_function_ | BALL::DockingAlgorithm | protected
scoring_type_ | BALL::DockingAlgorithm | protected
setDisplayMode(DISPLAYMODE display_mode) | BALL::DockingAlgorithm |
setLigand(AtomContainer *ligand) | BALL::DockingAlgorithm |
setMaxFps(int no) | BALL::DockingAlgorithm |
setScoringFunction(ScoringFunction *scoring) | BALL::DockingAlgorithm | inline
setup(System &system1, System &system2, Options &new_options) | BALL::GeometricFit | virtual
setup(System &system1, System &system2) | BALL::GeometricFit | virtual
setVisualizationPose(const double &score) | BALL::DockingAlgorithm |
start() | BALL::GeometricFit | virtual
SurfaceType enum name | BALL::GeometricFit |
system1_ | BALL::DockingAlgorithm | protected
system2_ | BALL::DockingAlgorithm | protected
system_backup_a_ | BALL::GeometricFit | protected
system_backup_b_ | BALL::GeometricFit | protected
total_round_ | BALL::GeometricFit | protected
translations_ | BALL::GeometricFit | protected
VAN_DER_WAALS enum value | BALL::GeometricFit |
visualization_pose_ | BALL::DockingAlgorithm | protected
visualization_pose_score_ | BALL::DockingAlgorithm | protected
visualization_timer_ | BALL::DockingAlgorithm | protected
wasAborted() const | BALL::DockingAlgorithm | inline virtual
wasPaused() const | BALL::DockingAlgorithm | inline virtual
writeOptionFile(String filename, Options &input_options, list< Constraint * > &input_constraints) | BALL::DockingAlgorithm | static
writeSubcategories_(Options &category, std::ostream &out) | BALL::DockingAlgorithm | protected static
~DockingAlgorithm() | BALL::DockingAlgorithm | virtual
~GeometricFit() | BALL::GeometricFit |