BALL  1.4.79
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BALL::GridedMM Member List

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

all_ligand_nonbonded_BALL::ScoringFunctionprotected
all_residues_hashgrid_BALL::ScoringFunctionprotected
allowed_intermolecular_overlap_BALL::ScoringFunctionprotected
allowed_intramolecular_overlap_BALL::ScoringFunctionprotected
assignRotamer(Residue *residue, ResidueRotamerSet *rotamer_set, const Rotamer *rotamer)BALL::ScoringFunction
atom_types_map_BALL::GridBasedScoringprotected
atoms_to_fragments_BALL::ScoringFunctionprotected
base_function_BALL::ScoringFunctionprotected
burial_depth_scale_BALL::ScoringFunctionprotected
calculateConstraintsScore()BALL::ScoringFunctionprotected
calculateGeometricalCenter(AtomContainer *s, int *no_ligand_atoms=NULL)BALL::ScoringFunctionprotected
calculateGridScore()BALL::GridBasedScoringprotected
calculateMoleculeRadius(AtomContainer *sys, Vector3 &center)BALL::ScoringFunctionprotected
calculateScore()BALL::ScoringFunction
calculateStaticLigandFragmentEnergy()BALL::ScoringFunctionprotectedvirtual
checkForAtomOverlaps(const AtomPairVector *pair_vector)BALL::ScoringFunctionprotected
clear()BALL::ScoringFunctionvirtual
clearStoredInteractions_()BALL::ScoringFunctionprotected
combine_operation_BALL::GridBasedScoringprotected
conformation_scale_BALL::ScoringFunctionprotected
constraintsBALL::ScoringFunction
convertTime(double seconds)BALL::ScoringFunction
countCovalentBonds(const Atom *atom, int threshold=-1)BALL::ScoringFunctionprotected
countNeighboringReceptorAtoms(const Atom *atom, double distance_threshold, bool onePerCell=0, int *number_of_overlaps=0) const BALL::ScoringFunction
createAllLigandNonBondedPairs()BALL::ScoringFunctionprotectedvirtual
createLigandNonbondedPairVector(bool intra_fragment, int &overlaps)BALL::ScoringFunctionprotected
createNonbondedPairVector(HashGrid3< Atom * > *hashgrid, int &overlaps, bool rec_lig, bool check_fragments=0, bool intra_fragment=0)BALL::ScoringFunctionprotected
createStaticLigandFragments()BALL::ScoringFunction
defineFlexibleResiduesGridSet()BALL::GridBasedScoring
defineGridSet(AtomContainer *sys, Vector3 &angstroem, double out_of_grid_penalty, bool enforce_grid_boundaries, double resolution, double interaction_no_scale=1)BALL::GridBasedScoring
defineGridSet(AtomContainer *sys, double out_of_grid_penalty, bool enforce_grid_boundaries, double resolution, double interaction_no_scale=1)BALL::GridBasedScoring
defineReceptorGridSet(Vector3 &origin, Vector3 &size, double out_of_grid_penalty, bool enforce_grid_boundaries, double resolution=0.5, double interaction_no_scale=1)BALL::GridBasedScoringprotected
DiffGridBasedScoring(AtomContainer &receptor, AtomContainer &ligand, Options &options)BALL::DiffGridBasedScoring
DiffGridBasedScoring(AtomContainer &receptor, Vector3 &hashgrid_origin, Options &options)BALL::DiffGridBasedScoring
enableAllComponents_()BALL::ScoringFunctionprotected
enableInteractionComponents_(const list< String > &type_names)BALL::ScoringFunctionprotected
enableStoreInteractions(bool b=true)BALL::ScoringFunction
enableStoreInteractionsOnlyForPhContraints()BALL::ScoringFunction
exp_energy_mean_BALL::ScoringFunctionprotected
exp_energy_stddev_BALL::ScoringFunctionprotected
fetchStaticLigandFragment(Atom *a1, int index)BALL::ScoringFunctionprotected
flex_gridset_id_BALL::GridBasedScoringprotected
flex_gridsets_BALL::GridBasedScoringprotected
flexible_residues_BALL::ScoringFunctionprotected
flexible_residues_hashgrid_BALL::ScoringFunctionprotected
flexres_org_positions_BALL::ScoringFunctionprotected
forcefield_parameters_BALL::GridedMMprotected
getAtomFragmentMap()BALL::ScoringFunction
getAtomTypes()BALL::GridedMMprotectedvirtual
getAtomTypesMap()BALL::GridBasedScoringprotected
getBaseFunction() const BALL::ScoringFunction
getBurialDepthScale()BALL::ScoringFunction
getCoefficient(const ScoringComponent *component, float &coefficient) const BALL::ScoringFunction
getCoefficient(const String &name, float &coefficient) const BALL::ScoringFunction
getComponent(const String &name) const BALL::ScoringFunction
getComponent(const Size index) const BALL::ScoringFunction
getDefaultOptions(Options &options)BALL::ScoringFunctionstatic
getEquation()BALL::ScoringFunction
getES()BALL::GridedMMprotectedvirtual
getExpEnergyStddev()BALL::ScoringFunction
getFirstMolecule() const BALL::ScoringFunction
getGridAtomTypeName(int grid_id)BALL::GridBasedScoringprotected
getHashGrid()BALL::ScoringFunction
getIntercept() const BALL::ScoringFunction
getLigand() const BALL::ScoringFunction
getLigandCenter() const BALL::ScoringFunction
getLigandRadius() const BALL::ScoringFunction
getMaximumNumberOfErrors() const BALL::ScoringFunction
getName()BALL::ScoringFunction
getNoLigandAtoms()BALL::ScoringFunction
getNoNeighboringReceptorAtoms()BALL::GridBasedScoringvirtual
getOptions()BALL::ScoringFunction
getOptionsToModify()BALL::ScoringFunction
getReceptor() const BALL::ScoringFunction
getRotatableLigandBonds() const BALL::ScoringFunction
getScore()BALL::ScoringFunction
getScoreContributions(vector< double > &score_contributions, vector< String > &names)BALL::ScoringFunction
getScoreGridSets()BALL::GridBasedScoring
getSecondMolecule() const BALL::ScoringFunction
getStaticLigandFragments() const BALL::ScoringFunction
getUnassignedAtoms() const BALL::ScoringFunction
getUnassignedAtoms()BALL::ScoringFunction
grid_sets_BALL::GridBasedScoringprotected
GridBasedScoring(AtomContainer &receptor, AtomContainer &ligand, Options &options)BALL::GridBasedScoring
GridBasedScoring(AtomContainer &receptor, Vector3 &hashgrid_origin, Options &options)BALL::GridBasedScoring
GridedMM(AtomContainer &receptor, AtomContainer &ligand, Options &options)BALL::GridedMM
GridedMM(AtomContainer &receptor, Vector3 &hashgrid_origin, Options &options)BALL::GridedMM
gridsets_result_BALL::GridBasedScoringprotected
hasFlexibleResidues()BALL::ScoringFunction
hashgrid_BALL::ScoringFunctionprotected
hashgrid_search_radius_BALL::ScoringFunctionprotected
hasPharmacophoreConstraints_()BALL::ScoringFunctionprotected
ignore_h_clashes_BALL::ScoringFunctionprotected
initializeHashGrid(AtomContainer *sys, Vector3 &center, double &resolution, int hashgrid_size)BALL::ScoringFunctionstatic
insertComponent(ScoringComponent *component)BALL::ScoringFunction
insertComponent(ScoringComponent *component, float coefficient)BALL::ScoringFunction
intercept_BALL::ScoringFunctionprotected
isPeptideBond(const Bond *bond) const BALL::ScoringFunctionprotected
ligand_BALL::ScoringFunctionprotected
ligand_atoms_BALL::ScoringFunctionprotected
ligand_center_BALL::ScoringFunctionprotected
ligand_intramol_overlaps_BALL::ScoringFunctionprotected
ligand_radius_BALL::ScoringFunctionprotected
loadFlexibleResidueScoreGrids(std::list< std::pair< const Residue *, const Rotamer * > > residue_list)BALL::GridBasedScoring
max_number_of_errors_BALL::ScoringFunctionprotected
misplaced_ligand_atoms_BALL::ScoringFunctionprotected
name_BALL::ScoringFunctionprotected
neighbor_cutoff_2_BALL::ScoringFunctionprotected
neighboring_target_atoms_BALL::ScoringFunctionprotected
nonbonded_cutoff_BALL::ScoringFunctionprotected
nonbonded_cutoff_2_BALL::ScoringFunctionprotected
number_of_errors_BALL::ScoringFunctionprotected
operator=(const ScoringFunction &sf)BALL::ScoringFunction
options_BALL::ScoringFunctionprotected
overlaps_BALL::ScoringFunctionprotected
precalculateGrids(bool ony_flexRes_grids=false)BALL::GridBasedScoring
printResult()BALL::GridBasedScoring
BALL::ScoringFunction::printResult(bool detail=0)BALL::ScoringFunctionvirtual
readAdditionalGridSetFromFile(String file)BALL::GridBasedScoring
receptor_BALL::ScoringFunctionprotected
reference_neighbors_BALL::ScoringFunctionprotected
removeComponent(const ScoringComponent *component)BALL::ScoringFunction
removeComponent(const String &name)BALL::ScoringFunction
replaceGridSetFromFile(String file)BALL::GridBasedScoring
resetFlexibleResidues()BALL::ScoringFunction
resetResiduePositions(Residue *residue, list< Vector3 > &old_positions)BALL::ScoringFunction
resolution_BALL::ScoringFunctionprotected
result_BALL::ScoringFunctionprotected
rotatable_ligand_bonds_BALL::ScoringFunctionprotected
saveGridSetsToFile(String file, String receptor_name)BALL::GridBasedScoring
score_BALL::ScoringFunctionprotected
scoregrid_interpolation_BALL::GridBasedScoringprotected
scoregrid_resolution_BALL::GridBasedScoringprotected
scoring_components_BALL::ScoringFunctionprotected
ScoringFunction()BALL::ScoringFunction
ScoringFunction(const ScoringFunction &sf)BALL::ScoringFunction
ScoringFunction(AtomContainer &receptor, AtomContainer &ligand)BALL::ScoringFunction
ScoringFunction(AtomContainer &receptor, AtomContainer &ligand, const Options &options)BALL::ScoringFunction
ScoringFunction(AtomContainer &receptor, AtomContainer &ligand, Options &options)BALL::ScoringFunction
ScoringFunction(AtomContainer &receptor, Vector3 &hashgrid_origin, Options &options)BALL::ScoringFunction
setAtomType(Atom *atom, const String &type_name)BALL::GridBasedScoringprotectedvirtual
setAtomTypeNames(std::set< String > &types)BALL::GridBasedScoring
setBaseFunction(ScoringBaseFunction &base_function)BALL::ScoringFunction
setCoefficient(const ScoringComponent *component, float coefficient)BALL::ScoringFunction
setCoefficient(const String &name, float coefficient)BALL::ScoringFunction
setCombineOperation(int i)BALL::GridBasedScoring
setFirstMolecule(AtomContainer &molecule1)BALL::ScoringFunction
setFlexibleResidues(const std::set< Residue * > &flexible_residues)BALL::ScoringFunction
setIntercept(double intercept)BALL::ScoringFunction
setLigand(AtomContainer *sys)BALL::DiffGridBasedScoringvirtual
BALL::GridBasedScoring::setLigand(AtomContainer &ligand)BALL::ScoringFunction
setMaximumNumberOfErrors(Size nr)BALL::ScoringFunction
setName(String name)BALL::ScoringFunctionprotected
setNormalizationParameters(double stddev, double mean)BALL::ScoringFunction
setReceptor(AtomContainer &receptor)BALL::ScoringFunction
setSecondMolecule(AtomContainer &molecule2)BALL::ScoringFunction
setup()BALL::GridedMMprotected
BALL::ScoringFunction::setup(AtomContainer &receptor, AtomContainer &ligand)BALL::ScoringFunction
BALL::ScoringFunction::setup(AtomContainer &receptor, AtomContainer &ligand, const Options &options)BALL::ScoringFunction
setupFlexibleResidues_()BALL::ScoringFunctionprotected
setupReferenceLigand()BALL::GridBasedScoringvirtual
static_ligand_energy_BALL::ScoringFunctionprotected
static_ligand_fragments_BALL::ScoringFunctionprotected
static_residues_hashgrid_BALL::ScoringFunctionprotected
store_interactions_BALL::ScoringFunctionprotected
store_interactions_phC_only_BALL::ScoringFunctionprotected
storeInteractionsEnabled()BALL::ScoringFunction
testOverlaps(Vector3 &position, HashGrid3< Atom * > *hashg=NULL)BALL::DiffGridBasedScoring
unassigned_atoms_BALL::ScoringFunctionprotected
unsetTrainingParameters()BALL::ScoringFunction
update()BALL::DiffGridBasedScoringvirtual
updateComponent(int id, AtomPairList *)BALL::ScoringFunctionprotected
updatePrecalculatedScore(Size set)BALL::DiffGridBasedScoringprotectedvirtual
updateScore()BALL::DiffGridBasedScoringvirtual
use_all_lig_nonb_BALL::ScoringFunctionprotected
use_static_lig_fragments_BALL::ScoringFunctionprotected
validateGridSets()BALL::GridBasedScoring
valueToString(double value)BALL::ScoringFunction
~DiffGridBasedScoring()BALL::DiffGridBasedScoring
~GridBasedScoring()BALL::GridBasedScoringvirtual
~ScoringFunction()BALL::ScoringFunctionvirtual
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