BALL  1.4.79
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BALL::SLICKEnergy Member List

This is the complete list of members for BALL::SLICKEnergy, 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
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
calculateMoleculeRadius(AtomContainer *sys, Vector3 &center)BALL::ScoringFunctionprotected
calculateScore()BALL::ScoringFunction
calculateStaticLigandFragmentEnergy()BALL::ScoringFunctionprotectedvirtual
checkForAtomOverlaps(const AtomPairVector *pair_vector)BALL::ScoringFunctionprotected
clear()BALL::SLICKEnergyvirtual
clearStoredInteractions_()BALL::ScoringFunctionprotected
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
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
flexible_residues_BALL::ScoringFunctionprotected
flexible_residues_hashgrid_BALL::ScoringFunctionprotected
flexres_org_positions_BALL::ScoringFunctionprotected
getAtomFragmentMap()BALL::ScoringFunction
getBaseFunction() const BALL::ScoringFunction
getBurialDepthScale()BALL::ScoringFunction
getCHPIScore() const BALL::SLICKEnergy
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::ScoringFunctionprotectedvirtual
getExpEnergyStddev()BALL::ScoringFunction
getFirstMolecule() const BALL::ScoringFunction
getHashGrid()BALL::ScoringFunction
getHydrogenBondScore() const BALL::SLICKEnergy
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::ScoringFunctionvirtual
getNonpolarSolvationScore() const BALL::SLICKEnergy
getOptions()BALL::ScoringFunction
getOptionsToModify()BALL::ScoringFunction
getPolarSolvationScore() const BALL::SLICKEnergy
getReceptor() const BALL::ScoringFunction
getRotatableLigandBonds() const BALL::ScoringFunction
getScore()BALL::ScoringFunction
getScoreContributions(vector< double > &score_contributions, vector< String > &names)BALL::ScoringFunction
getSecondMolecule() const BALL::ScoringFunction
getStaticLigandFragments() const BALL::ScoringFunction
getUnassignedAtoms() const BALL::ScoringFunction
getUnassignedAtoms()BALL::ScoringFunction
getVDWScore() const BALL::SLICKEnergy
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
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 SLICKEnergy &slick)BALL::SLICKEnergy
BALL::ScoringFunction::operator=(const ScoringFunction &sf)BALL::ScoringFunction
options_BALL::ScoringFunctionprotected
overlaps_BALL::ScoringFunctionprotected
printResult(bool detail=0)BALL::ScoringFunctionvirtual
receptor_BALL::ScoringFunctionprotected
reference_neighbors_BALL::ScoringFunctionprotected
removeComponent(const ScoringComponent *component)BALL::ScoringFunction
removeComponent(const String &name)BALL::ScoringFunction
resetFlexibleResidues()BALL::ScoringFunction
resetResiduePositions(Residue *residue, list< Vector3 > &old_positions)BALL::ScoringFunction
resolution_BALL::ScoringFunctionprotected
result_BALL::ScoringFunctionprotected
rotatable_ligand_bonds_BALL::ScoringFunctionprotected
score_BALL::ScoringFunctionprotected
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
setBaseFunction(ScoringBaseFunction &base_function)BALL::ScoringFunction
setCoefficient(const ScoringComponent *component, float coefficient)BALL::ScoringFunction
setCoefficient(const String &name, float coefficient)BALL::ScoringFunction
setFirstMolecule(AtomContainer &molecule1)BALL::ScoringFunction
setFlexibleResidues(const std::set< Residue * > &flexible_residues)BALL::ScoringFunction
setIntercept(double intercept)BALL::ScoringFunction
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::SLICKEnergy
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::ScoringFunctionprotectedvirtual
SLICKEnergy()BALL::SLICKEnergy
SLICKEnergy(Molecule &protein, Molecule &ligand)BALL::SLICKEnergy
SLICKEnergy(Molecule &protein, Molecule &ligand, Options &options)BALL::SLICKEnergy
SLICKEnergy(const SLICKEnergy &slick)BALL::SLICKEnergy
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
unassigned_atoms_BALL::ScoringFunctionprotected
unsetTrainingParameters()BALL::ScoringFunction
update()BALL::ScoringFunctionvirtual
updateComponent(int id, AtomPairList *)BALL::ScoringFunctionprotected
updateScore()BALL::ScoringFunctionvirtual
use_all_lig_nonb_BALL::ScoringFunctionprotected
use_static_lig_fragments_BALL::ScoringFunctionprotected
valueToString(double value)BALL::ScoringFunction
~ScoringFunction()BALL::ScoringFunctionvirtual
~SLICKEnergy()BALL::SLICKEnergyvirtual
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