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BALL::DifferentiableScoringFunction Member List

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

all_ligand_nonbonded_ | BALL::ScoringFunction | protected
all_residues_hashgrid_ | BALL::ScoringFunction | protected
allowed_intermolecular_overlap_ | BALL::ScoringFunction | protected
allowed_intramolecular_overlap_ | BALL::ScoringFunction | protected
assignRotamer(Residue *residue, ResidueRotamerSet *rotamer_set, const Rotamer *rotamer) | BALL::ScoringFunction |
atoms_to_fragments_ | BALL::ScoringFunction | protected
base_function_ | BALL::ScoringFunction | protected
burial_depth_scale_ | BALL::ScoringFunction | protected
calculateConstraintsScore() | BALL::ScoringFunction | protected
calculateGeometricalCenter(AtomContainer *s, int *no_ligand_atoms=NULL) | BALL::ScoringFunction | protected
calculateMoleculeRadius(AtomContainer *sys, Vector3 &center) | BALL::ScoringFunction | protected
calculateScore() | BALL::ScoringFunction |
calculateStaticLigandFragmentEnergy() | BALL::ScoringFunction | protected virtual
checkForAtomOverlaps(const AtomPairVector *pair_vector) | BALL::ScoringFunction | protected
clear() | BALL::ScoringFunction | virtual
clearStoredInteractions_() | BALL::ScoringFunction | protected
conformation_scale_ | BALL::ScoringFunction | protected
constraints | BALL::ScoringFunction |
convertTime(double seconds) | BALL::ScoringFunction |
countCovalentBonds(const Atom *atom, int threshold=-1) | BALL::ScoringFunction | protected
countNeighboringReceptorAtoms(const Atom *atom, double distance_threshold, bool onePerCell=0, int *number_of_overlaps=0) const | BALL::ScoringFunction |
createAllLigandNonBondedPairs() | BALL::ScoringFunction | protected virtual
createLigandNonbondedPairVector(bool intra_fragment, int &overlaps) | BALL::ScoringFunction | protected
createNonbondedPairVector(HashGrid3< Atom * > *hashgrid, int &overlaps, bool rec_lig, bool check_fragments=0, bool intra_fragment=0) | BALL::ScoringFunction | protected
createStaticLigandFragments() | BALL::ScoringFunction |
DifferentiableScoringFunction(AtomContainer &receptor, AtomContainer &ligand, Options &options) | BALL::DifferentiableScoringFunction |
DifferentiableScoringFunction(AtomContainer &receptor, Vector3 &hashgrid_origin, Options &options) | BALL::DifferentiableScoringFunction |
enableAllComponents_() | BALL::ScoringFunction | protected
enableInteractionComponents_(const list< String > &type_names) | BALL::ScoringFunction | protected
enableStoreInteractions(bool b=true) | BALL::ScoringFunction |
enableStoreInteractionsOnlyForPhContraints() | BALL::ScoringFunction |
exp_energy_mean_ | BALL::ScoringFunction | protected
exp_energy_stddev_ | BALL::ScoringFunction | protected
fetchStaticLigandFragment(Atom *a1, int index) | BALL::ScoringFunction | protected
flexible_residues_ | BALL::ScoringFunction | protected
flexible_residues_hashgrid_ | BALL::ScoringFunction | protected
flexres_org_positions_ | BALL::ScoringFunction | protected
getAtomFragmentMap() | BALL::ScoringFunction |
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::ScoringFunction | static
getEquation() | BALL::ScoringFunction |
getES() | BALL::ScoringFunction | protected virtual
getExpEnergyStddev() | BALL::ScoringFunction |
getFirstMolecule() const | BALL::ScoringFunction |
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::ScoringFunction | virtual
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 |
getSecondMolecule() const | BALL::ScoringFunction |
getStaticLigandFragments() const | BALL::ScoringFunction |
getUnassignedAtoms() const | BALL::ScoringFunction |
getUnassignedAtoms() | BALL::ScoringFunction |
hasFlexibleResidues() | BALL::ScoringFunction |
hashgrid_ | BALL::ScoringFunction | protected
hashgrid_search_radius_ | BALL::ScoringFunction | protected
hasPharmacophoreConstraints_() | BALL::ScoringFunction | protected
ignore_h_clashes_ | BALL::ScoringFunction | protected
initializeHashGrid(AtomContainer *sys, Vector3 &center, double &resolution, int hashgrid_size) | BALL::ScoringFunction | static
insertComponent(ScoringComponent *component) | BALL::ScoringFunction |
insertComponent(ScoringComponent *component, float coefficient) | BALL::ScoringFunction |
intercept_ | BALL::ScoringFunction | protected
isPeptideBond(const Bond *bond) const | BALL::ScoringFunction | protected
ligand_ | BALL::ScoringFunction | protected
ligand_atoms_ | BALL::ScoringFunction | protected
ligand_center_ | BALL::ScoringFunction | protected
ligand_intramol_overlaps_ | BALL::ScoringFunction | protected
ligand_radius_ | BALL::ScoringFunction | protected
max_number_of_errors_ | BALL::ScoringFunction | protected
misplaced_ligand_atoms_ | BALL::ScoringFunction | protected
name_ | BALL::ScoringFunction | protected
neighbor_cutoff_2_ | BALL::ScoringFunction | protected
neighboring_target_atoms_ | BALL::ScoringFunction | protected
nonbonded_cutoff_ | BALL::ScoringFunction | protected
nonbonded_cutoff_2_ | BALL::ScoringFunction | protected
number_of_errors_ | BALL::ScoringFunction | protected
operator=(const ScoringFunction &sf) | BALL::ScoringFunction |
options_ | BALL::ScoringFunction | protected
overlaps_ | BALL::ScoringFunction | protected
printResult(bool detail=0) | BALL::ScoringFunction | virtual
receptor_ | BALL::ScoringFunction | protected
reference_neighbors_ | BALL::ScoringFunction | protected
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::ScoringFunction | protected
result_ | BALL::ScoringFunction | protected
rotatable_ligand_bonds_ | BALL::ScoringFunction | protected
score_ | BALL::ScoringFunction | protected
scoring_components_ | BALL::ScoringFunction | protected
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::ScoringFunction | protected
setNormalizationParameters(double stddev, double mean) | BALL::ScoringFunction |
setReceptor(AtomContainer &receptor) | BALL::ScoringFunction |
setSecondMolecule(AtomContainer &molecule2) | BALL::ScoringFunction |
setup() | BALL::ScoringFunction |
setup(AtomContainer &receptor, AtomContainer &ligand) | BALL::ScoringFunction |
setup(AtomContainer &receptor, AtomContainer &ligand, const Options &options) | BALL::ScoringFunction |
setupFlexibleResidues_() | BALL::ScoringFunction | protected
setupReferenceLigand() | BALL::ScoringFunction | protected virtual
static_ligand_energy_ | BALL::ScoringFunction | protected
static_ligand_fragments_ | BALL::ScoringFunction | protected
static_residues_hashgrid_ | BALL::ScoringFunction | protected
store_interactions_ | BALL::ScoringFunction | protected
store_interactions_phC_only_ | BALL::ScoringFunction | protected
storeInteractionsEnabled() | BALL::ScoringFunction |
SUBCATEGORY_NAME | BALL::ScoringFunction | static
unassigned_atoms_ | BALL::ScoringFunction | protected
unsetTrainingParameters() | BALL::ScoringFunction |
update() | BALL::ScoringFunction | virtual
updateComponent(int id, AtomPairList *) | BALL::ScoringFunction | protected
updateScore() | BALL::ScoringFunction | virtual
use_all_lig_nonb_ | BALL::ScoringFunction | protected
use_static_lig_fragments_ | BALL::ScoringFunction | protected
valueToString(double value) | BALL::ScoringFunction |
~ScoringFunction() | BALL::ScoringFunction | virtual