Index

_

__call__() (molpher.algorithms.antidecoys.pathfinder.AntidecoysPathFinder method) (molpher.algorithms.bidirectional.pathfinder.BidirectionalPathFinder method) (molpher.swig_wrappers.core.CleanMorphsOper method) (molpher.swig_wrappers.core.ExtendTreeOper method) (molpher.swig_wrappers.core.FindLeavesOper method) (molpher.swig_wrappers.core.GenerateMorphsOper method) (molpher.swig_wrappers.core.PruneTreeOper method) (molpher.swig_wrappers.core.SortMorphsCallback method) (molpher.swig_wrappers.core.SortMorphsOper method) (molpher.swig_wrappers.core.TraverseCallback method) (molpher.swig_wrappers.core.TraverseOper method) (molpher.swig_wrappers.core.TreeOperation method)

__dict__ (molpher.algorithms.antidecoys.pathfinder.AntidecoysPathFinder attribute) (molpher.algorithms.bidirectional.pathfinder.BidirectionalPathFinder attribute) __init__() (molpher.algorithms.antidecoys.pathfinder.AntidecoysPathFinder method) (molpher.algorithms.bidirectional.pathfinder.BidirectionalPathFinder method) (molpher.algorithms.classic.pathfinder.ClassicPathFinder method) __module__ (molpher.algorithms.antidecoys.pathfinder.AntidecoysPathFinder attribute) (molpher.algorithms.bidirectional.pathfinder.BidirectionalPathFinder attribute) (molpher.algorithms.classic.pathfinder.ClassicPathFinder attribute) __weakref__ (molpher.algorithms.antidecoys.pathfinder.AntidecoysPathFinder attribute) (molpher.algorithms.bidirectional.pathfinder.BidirectionalPathFinder attribute)

A

accept_max (molpher.core.ExplorationData.ExplorationData property) accept_min (molpher.core.ExplorationData.ExplorationData property) AddAtom (class in molpher.core.morphing.operators.AddAtom) AddBond (class in molpher.core.morphing.operators.AddBond) ALL (molpher.swig_wrappers.core.FilterMorphsOper attribute) antidecoys_max_iters (molpher.algorithms.antidecoys.settings.AntidecoysSettings attribute) antidecoys_min_iters (molpher.algorithms.antidecoys.settings.AntidecoysSettings attribute) AntidecoysFilter (class in molpher.algorithms.antidecoys.custom_opers) AntidecoysPathFinder (class in molpher.algorithms.antidecoys.pathfinder) AntidecoysSettings (class in molpher.algorithms.antidecoys.settings) antifingerprint (molpher.algorithms.antidecoys.pathfinder.AntidecoysPathFinder attribute) antifp_scores (molpher.algorithms.antidecoys.custom_opers.AntiFpSortCallback attribute)

AntiFpSortCallback (class in molpher.algorithms.antidecoys.custom_opers) antitfp (molpher.algorithms.antidecoys.custom_opers.GatherAntiFPScores attribute) asData() (molpher.core.ExplorationTree.ExplorationTree method) (molpher.swig_wrappers.core.ExplorationTree method) asRDMol() (molpher.core.MolpherMol.MolpherMol method) assertOperatorValid() (molpher.core.tests.test_api.TestAPI method) atom_probabilities (molpher.core.morphing.AtomLibrary.AtomLibrary property) atomic_number (molpher.core.MolpherAtom.MolpherAtom property) AtomLibrary (class in molpher.core.morphing.AtomLibrary) (class in molpher.swig_wrappers.core) atoms (molpher.core.MolpherMol.MolpherMol property) (molpher.core.morphing.AtomLibrary.AtomLibrary property)

B

BidirectionalPathFinder (class in molpher.algorithms.bidirectional.pathfinder)

C

Callback (class in molpher.core.operations.TraverseOper) candidate morphs candidates (molpher.core.ExplorationTree.ExplorationTree property) candidates_mask (molpher.core.ExplorationTree.ExplorationTree property) chemical operators chemical space chemical space path ClassicPathFinder (class in molpher.algorithms.classic.pathfinder) CleanMorphsOper (class in molpher.core.operations.CleanMorphsOper) (class in molpher.swig_wrappers.core) close_produce (molpher.core.ExplorationData.ExplorationData property) closest (molpher.algorithms.operations.FindClosest attribute)

CMAKE_INSTALL_PREFIX common_bits_max_thrs (molpher.algorithms.antidecoys.settings.AntidecoysSettings attribute) common_bits_mean_thrs (molpher.algorithms.antidecoys.settings.AntidecoysSettings attribute) common_bits_thrs (molpher.algorithms.antidecoys.custom_opers.AntidecoysFilter attribute) compute_anti_fp() (in module molpher.algorithms.antidecoys.utils) compute_antifp_scores() (in module molpher.algorithms.antidecoys.utils) connecting_molecule (molpher.algorithms.antidecoys.pathfinder.AntidecoysPathFinder attribute) ContractBond (class in molpher.core.morphing.operators.ContractBond) copy() (molpher.core.MolpherMol.MolpherMol method) (molpher.swig_wrappers.core.MolpherMol method) create() (molpher.core.ExplorationTree.ExplorationTree static method) (molpher.swig_wrappers.core.ExplorationTree static method)

D

deleteSubtree() (molpher.swig_wrappers.core.ExplorationTree method) descendents (molpher.core.MolpherMol.MolpherMol property)

dist_to_target (molpher.core.MolpherMol.MolpherMol property) distance_thrs (molpher.algorithms.antidecoys.settings.AntidecoysSettings attribute) DUPLICATES (molpher.swig_wrappers.core.FilterMorphsOper attribute)

E

environment variable CMAKE_INSTALL_PREFIX LD_LIBRARY_PATH PYTHONPATH exploration parameters exploration tree ExplorationData (class in molpher.core.ExplorationData) (class in molpher.swig_wrappers.core)

ExplorationData.UnknownParameterException ExplorationTree (class in molpher.core.ExplorationTree) (class in molpher.swig_wrappers.core) extend() (molpher.swig_wrappers.core.ExplorationTree method) ExtendTreeOper (class in molpher.core.operations.ExtendTreeOper) (class in molpher.swig_wrappers.core)

F

far_close_threshold (molpher.core.ExplorationData.ExplorationData property) far_produce (molpher.core.ExplorationData.ExplorationData property) fetchLeaves() (molpher.swig_wrappers.core.ExplorationTree method) (molpher.swig_wrappers.core.FindLeavesOper method) fetchMol() (molpher.core.ExplorationTree.ExplorationTree method) (molpher.swig_wrappers.core.ExplorationTree method) fetchPathTo() (molpher.core.ExplorationTree.ExplorationTree method) fg_bins (molpher.algorithms.antidecoys.settings.AntidecoysSettings attribute) fg_max_points (molpher.algorithms.antidecoys.settings.AntidecoysSettings attribute) fg_min_points (molpher.algorithms.antidecoys.settings.AntidecoysSettings attribute) filterMorphs() (molpher.swig_wrappers.core.ExplorationTree method) FilterMorphsOper (class in molpher.core.operations.FilterMorphsOper) (class in molpher.swig_wrappers.core) find_path() (in module molpher.algorithms.functions) FindClosest (class in molpher.algorithms.operations) FindLeavesOper (class in molpher.core.operations.FindLeavesOper) (class in molpher.swig_wrappers.core)

fingerprint (molpher.core.ExplorationData.ExplorationData property) formal_charge (molpher.core.MolpherAtom.MolpherAtom property) FP_ATOM_PAIRS (in module molpher.core.selectors) FP_EXT_ATOM_PAIRS (in module molpher.core.selectors) FP_EXT_MORGAN (in module molpher.core.selectors) FP_EXT_TOPOLOGICAL (in module molpher.core.selectors) FP_EXT_TOPOLOGICAL_LAYERED_1 (in module molpher.core.selectors) FP_EXT_TOPOLOGICAL_LAYERED_2 (in module molpher.core.selectors) FP_EXT_TOPOLOGICAL_TORSION (in module molpher.core.selectors) FP_MORGAN (in module molpher.core.selectors) FP_TOPOLOGICAL (in module molpher.core.selectors) FP_TOPOLOGICAL_LAYERED_1 (in module molpher.core.selectors) FP_TOPOLOGICAL_LAYERED_2 (in module molpher.core.selectors) FP_TOPOLOGICAL_TORSION (in module molpher.core.selectors) FP_VECTORFP (in module molpher.core.selectors) fromMolBlock() (molpher.core.MolpherMol.MolpherMol static method)

G

GatherAntiFPScores (class in molpher.algorithms.antidecoys.custom_opers) generateMorphs() (molpher.core.ExplorationTree.ExplorationTree method) (molpher.swig_wrappers.core.ExplorationTree method) GenerateMorphsOper (class in molpher.core.operations.GenerateMorphsOper) (class in molpher.swig_wrappers.core) generation_count (molpher.core.ExplorationTree.ExplorationTree property) gens_without_improvement (molpher.core.MolpherMol.MolpherMol property) getAtom() (molpher.core.MolpherMol.MolpherMol method) getAtoms() (molpher.core.morphing.AtomLibrary.AtomLibrary method) getCandidateMorphs() (molpher.swig_wrappers.core.ExplorationTree method) getCandidateMorphsMask() (molpher.swig_wrappers.core.ExplorationTree method) getChemicalOperators() (molpher.swig_wrappers.core.ExplorationData method) getCntCandidatesToKeep() (molpher.swig_wrappers.core.ExplorationData method) getCntCandidatesToKeepMax() (molpher.swig_wrappers.core.ExplorationData method) getCntMaxMorphs() (molpher.swig_wrappers.core.ExplorationData method) getCntMorphs() (molpher.swig_wrappers.core.ExplorationData method) getCntMorphsInDepth() (molpher.swig_wrappers.core.ExplorationData method) getDefaultLibrary() (molpher.core.morphing.AtomLibrary.AtomLibrary static method) getDescendants() (molpher.swig_wrappers.core.MolpherMol method) getDistToTarget() (molpher.swig_wrappers.core.MolpherMol method) getDistToTargetDepthSwitch() (molpher.swig_wrappers.core.ExplorationData method) getFingerprint() (molpher.swig_wrappers.core.ExplorationData method) getGenerationCount() (molpher.swig_wrappers.core.ExplorationTree method) getHistoricDescendants() (molpher.swig_wrappers.core.MolpherMol method) getItersWithoutDistImprovement() (molpher.swig_wrappers.core.MolpherMol method) getItThreshold() (molpher.swig_wrappers.core.ExplorationData method) getMarkedAtoms() (molpher.core.morphing.operators.RemoveAtom.RemoveAtom method)

getMaxAcceptableMolecularWeight() (molpher.swig_wrappers.core.ExplorationData method) getMinAcceptableMolecularWeight() (molpher.swig_wrappers.core.ExplorationData method) getMolecularWeight() (molpher.swig_wrappers.core.MolpherMol method) getMorphs() (molpher.core.morphing.Molpher.Molpher method) getOpenAtoms() (molpher.core.morphing.operators.AddAtom.AddAtom method) getOpenBonds() (molpher.core.morphing.operators.AddBond.AddBond method) (molpher.core.morphing.operators.RemoveBond.RemoveBond method) getOriginal() (molpher.core.morphing.operators.AddAtom.AddAtom method) (molpher.core.morphing.operators.AddBond.AddBond method) (molpher.core.morphing.operators.ContractBond.ContractBond method) (molpher.core.morphing.operators.InterlayAtom.InterlayAtom method) (molpher.core.morphing.operators.MorphingOperator.MorphingOperator method) (molpher.core.morphing.operators.MutateAtom.MutateAtom method) (molpher.core.morphing.operators.RemoveAtom.RemoveAtom method) (molpher.core.morphing.operators.RemoveBond.RemoveBond method) (molpher.core.morphing.operators.RerouteBond.RerouteBond method) getParentSMILES() (molpher.swig_wrappers.core.MolpherMol method) getPathToMol() (molpher.core.tests.test_api.TestAPI static method) getRandomAtom() (molpher.core.morphing.AtomLibrary.AtomLibrary method) getSAScore() (molpher.swig_wrappers.core.MolpherMol method) getSimilarityCoefficient() (molpher.swig_wrappers.core.ExplorationData method) getSMILES() (molpher.swig_wrappers.core.MolpherMol method) getSource() (molpher.swig_wrappers.core.ExplorationData method) getTarget() (molpher.swig_wrappers.core.ExplorationData method) getThreadCount() (molpher.swig_wrappers.core.ExplorationTree method) getTree() (molpher.core.operations.TreeOperation.TreeOperation method) (molpher.swig_wrappers.core.MolpherMol method) (molpher.swig_wrappers.core.TreeOperation method)

H

hasMol() (molpher.swig_wrappers.core.ExplorationTree method) high-throughput screening

historic_descendents (molpher.core.MolpherMol.MolpherMol property) HISTORIC_DESCENDENTS (molpher.swig_wrappers.core.FilterMorphsOper attribute)

I

InterlayAtom (class in molpher.core.morphing.operators.InterlayAtom)

is_locked (molpher.core.MolpherAtom.MolpherAtom property) is_valid (molpher.core.ExplorationData.ExplorationData property)

L

LD_LIBRARY_PATH leaves (molpher.core.ExplorationTree.ExplorationTree property) (molpher.core.operations.FindLeavesOper.FindLeavesOper property) load() (molpher.core.ExplorationData.ExplorationData static method) (molpher.swig_wrappers.core.ExplorationData static method)

load_data_from (C++ function) load_SAScore() (in module molpher) lock_info (molpher.core.MolpherAtom.MolpherAtom property) lockAtoms() (molpher.swig_wrappers.core.MolpherMol method) locking_mask (molpher.core.MolpherAtom.MolpherAtom property)

M

main() (in module molpher.examples.algorithms_basics) (in module molpher.examples.bidirectional) (in module molpher.examples.classic) (in module molpher.examples.exploration_basics) mass (molpher.core.MolpherAtom.MolpherAtom property) MAX_DERIVATIONS (molpher.swig_wrappers.core.FilterMorphsOper attribute) max_iters (molpher.algorithms.settings.Settings attribute) max_morphs_total (molpher.core.ExplorationData.ExplorationData property) max_threads (molpher.algorithms.settings.Settings attribute) maximum_common_bits_perc (molpher.algorithms.antidecoys.custom_opers.AntiFpSortCallback attribute) min_accepted (molpher.algorithms.antidecoys.settings.AntidecoysSettings attribute) minimum_accept (molpher.algorithms.antidecoys.custom_opers.AntidecoysFilter attribute) minimum_common_bits_perc (molpher.algorithms.antidecoys.custom_opers.AntiFpSortCallback attribute) module molpher molpher.algorithms molpher.algorithms.antidecoys molpher.algorithms.antidecoys.custom_opers molpher.algorithms.antidecoys.pathfinder molpher.algorithms.antidecoys.run molpher.algorithms.antidecoys.settings molpher.algorithms.antidecoys.utils molpher.algorithms.bidirectional molpher.algorithms.bidirectional.pathfinder molpher.algorithms.bidirectional.run molpher.algorithms.classic molpher.algorithms.classic.pathfinder molpher.algorithms.classic.run molpher.algorithms.functions molpher.algorithms.operations molpher.algorithms.settings molpher.core molpher.core.ExplorationData molpher.core.ExplorationTree molpher.core.MolpherAtom molpher.core.MolpherMol molpher.core.morphing molpher.core.morphing.AtomLibrary molpher.core.morphing.Molpher molpher.core.morphing.MorphCollector molpher.core.morphing.operators molpher.core.morphing.operators.AddAtom molpher.core.morphing.operators.AddBond molpher.core.morphing.operators.ContractBond molpher.core.morphing.operators.InterlayAtom molpher.core.morphing.operators.MorphingOperator molpher.core.morphing.operators.MutateAtom molpher.core.morphing.operators.RemoveAtom molpher.core.morphing.operators.RemoveBond molpher.core.morphing.operators.RerouteBond molpher.core.operations molpher.core.operations.callbacks molpher.core.operations.CleanMorphsOper molpher.core.operations.ExtendTreeOper molpher.core.operations.FilterMorphsOper molpher.core.operations.FindLeavesOper molpher.core.operations.GenerateMorphsOper molpher.core.operations.PruneTreeOper molpher.core.operations.SortMorphsOper molpher.core.operations.TraverseOper molpher.core.operations.TreeOperation molpher.core.selectors molpher.core.tests molpher.core.tests.test_api molpher.examples.algorithms_basics molpher.examples.bidirectional molpher.examples.classic molpher.examples.exploration_basics molpher.swig_wrappers mol_count (molpher.core.ExplorationTree.ExplorationTree property) molecular fingerprint molecular morphing Molpher molpher (class in molpher.core.morphing.Molpher) (class in molpher.swig_wrappers.core) module molpher.algorithms module molpher.algorithms.antidecoys module molpher.algorithms.antidecoys.custom_opers module molpher.algorithms.antidecoys.pathfinder module molpher.algorithms.antidecoys.run module molpher.algorithms.antidecoys.settings module molpher.algorithms.antidecoys.utils module molpher.algorithms.bidirectional module molpher.algorithms.bidirectional.pathfinder module molpher.algorithms.bidirectional.run module molpher.algorithms.classic module molpher.algorithms.classic.pathfinder module molpher.algorithms.classic.run module molpher.algorithms.functions module

molpher.algorithms.operations module molpher.algorithms.settings module molpher.core module molpher.core.ExplorationData module molpher.core.ExplorationTree module molpher.core.MolpherAtom module molpher.core.MolpherMol module molpher.core.morphing module molpher.core.morphing.AtomLibrary module molpher.core.morphing.Molpher module molpher.core.morphing.MorphCollector module molpher.core.morphing.operators module molpher.core.morphing.operators.AddAtom module molpher.core.morphing.operators.AddBond module molpher.core.morphing.operators.ContractBond module molpher.core.morphing.operators.InterlayAtom module molpher.core.morphing.operators.MorphingOperator module molpher.core.morphing.operators.MutateAtom module molpher.core.morphing.operators.RemoveAtom module molpher.core.morphing.operators.RemoveBond module molpher.core.morphing.operators.RerouteBond module molpher.core.operations module molpher.core.operations.callbacks module molpher.core.operations.CleanMorphsOper module molpher.core.operations.ExtendTreeOper module molpher.core.operations.FilterMorphsOper module molpher.core.operations.FindLeavesOper module molpher.core.operations.GenerateMorphsOper module molpher.core.operations.PruneTreeOper module molpher.core.operations.SortMorphsOper module molpher.core.operations.TraverseOper module molpher.core.operations.TreeOperation module molpher.core.selectors module molpher.core.tests module molpher.core.tests.test_api module molpher.examples.algorithms_basics module molpher.examples.bidirectional module molpher.examples.classic module molpher.examples.exploration_basics module molpher.swig_wrappers module MolpherAtom (class in molpher.core.MolpherAtom) (class in molpher.swig_wrappers.core) MolpherMol (class in molpher.core.MolpherMol) (class in molpher.swig_wrappers.core) morph morph generation morph() (molpher.core.morphing.operators.AddAtom.AddAtom method) (molpher.core.morphing.operators.AddBond.AddBond method) (molpher.core.morphing.operators.ContractBond.ContractBond method) (molpher.core.morphing.operators.InterlayAtom.InterlayAtom method) (molpher.core.morphing.operators.MutateAtom.MutateAtom method) (molpher.core.morphing.operators.RemoveAtom.RemoveAtom method) (molpher.core.morphing.operators.RemoveBond.RemoveBond method) (molpher.core.morphing.operators.RerouteBond.RerouteBond method) MorphCollector (class in molpher.core.morphing.MorphCollector) morphing iteration morphing parameters morphing_operators (molpher.core.ExplorationTree.ExplorationTree property) MorphingOperator (class in molpher.core.morphing.operators.MorphingOperator) (class in molpher.swig_wrappers.core) morphs (molpher.core.morphing.Molpher.Molpher property) MutateAtom (class in molpher.core.morphing.operators.MutateAtom) MyFilterMorphs (class in molpher.examples.algorithms_basics)

N

name (molpher.core.morphing.operators.MorphingOperator.MorphingOperator property) next() (molpher.core.morphing.Molpher.Molpher method)

non-producing molecule non_producing_survive (molpher.core.ExplorationData.ExplorationData property)

O

OP_ADD_ATOM (in module molpher.core.selectors) OP_ADD_BOND (in module molpher.core.selectors) OP_BOND_CONTRACTION (in module molpher.core.selectors) OP_BOND_REROUTE (in module molpher.core.selectors) OP_INTERLAY_ATOM (in module molpher.core.selectors)

OP_MUTATE_ATOM (in module molpher.core.selectors) OP_REMOVE_ATOM (in module molpher.core.selectors) OP_REMOVE_BOND (in module molpher.core.selectors) operators (molpher.core.ExplorationData.ExplorationData property) original (molpher.core.morphing.operators.MorphingOperator.MorphingOperator property) out (molpher.algorithms.antidecoys.custom_opers.GatherAntiFPScores attribute)

P

param_dict (molpher.core.ExplorationData.ExplorationData property) params (molpher.core.ExplorationTree.ExplorationTree property) parent_operator (molpher.core.MolpherMol.MolpherMol property) parent_smiles (molpher.core.MolpherMol.MolpherMol property) path (molpher.algorithms.antidecoys.pathfinder.AntidecoysPathFinder attribute) (molpher.algorithms.bidirectional.pathfinder.BidirectionalPathFinder attribute)

path_found (molpher.core.ExplorationTree.ExplorationTree property) PROBABILITY (molpher.swig_wrappers.core.FilterMorphsOper attribute) prune() (molpher.swig_wrappers.core.ExplorationTree method) PruneTreeOper (class in molpher.core.operations.PruneTreeOper) (class in molpher.swig_wrappers.core) PYTHONPATH

R

RemoveAtom (class in molpher.core.morphing.operators.RemoveAtom) RemoveBond (class in molpher.core.morphing.operators.RemoveBond) RerouteBond (class in molpher.core.morphing.operators.RerouteBond)

run() (in module molpher.algorithms.antidecoys.run) (in module molpher.algorithms.bidirectional.run) (in module molpher.algorithms.classic.run) runOperation() (molpher.swig_wrappers.core.ExplorationTree method)

S

SAScore sascore (molpher.core.MolpherMol.MolpherMol property) SAScore.dat save() (molpher.swig_wrappers.core.ExplorationData method) (molpher.swig_wrappers.core.ExplorationTree method) SC_ALL_BIT (in module molpher.core.selectors) SC_ASYMMETRIC (in module molpher.core.selectors) SC_BRAUN_BLANQUET (in module molpher.core.selectors) SC_COSINE (in module molpher.core.selectors) SC_DICE (in module molpher.core.selectors) SC_KULCZYNSKI (in module molpher.core.selectors) SC_MC_CONNAUGHEY (in module molpher.core.selectors) SC_ON_BIT (in module molpher.core.selectors) SC_RUSSEL (in module molpher.core.selectors) SC_SOKAL (in module molpher.core.selectors) SC_TANIMOTO (in module molpher.core.selectors) SC_TVERSKY_SUBSTRUCTURE (in module molpher.core.selectors) SC_TVERSKY_SUPERSTRUCTURE (in module molpher.core.selectors) scores (molpher.algorithms.antidecoys.custom_opers.AntidecoysFilter attribute) selectors setCandidateMorphsMask() (molpher.swig_wrappers.core.ExplorationTree method) setChemicalOperators() (molpher.swig_wrappers.core.ExplorationData method) setCntCandidatesToKeep() (molpher.swig_wrappers.core.ExplorationData method) setCntCandidatesToKeepMax() (molpher.swig_wrappers.core.ExplorationData method) setCntMaxMorphs() (molpher.swig_wrappers.core.ExplorationData method) setCntMorphs() (molpher.swig_wrappers.core.ExplorationData method) setCntMorphsInDepth() (molpher.swig_wrappers.core.ExplorationData method) setDistToTarget() (molpher.swig_wrappers.core.MolpherMol method) setDistToTargetDepthSwitch() (molpher.swig_wrappers.core.ExplorationData method) setFingerprint() (molpher.swig_wrappers.core.ExplorationData method) setItersWithoutDistImprovement() (molpher.swig_wrappers.core.MolpherMol method) setItThreshold() (molpher.swig_wrappers.core.ExplorationData method)

setMaxAcceptableMolecularWeight() (molpher.swig_wrappers.core.ExplorationData method) setMinAcceptableMolecularWeight() (molpher.swig_wrappers.core.ExplorationData method) setOriginal() (molpher.core.morphing.operators.MorphingOperator.MorphingOperator method) setSAScore() (molpher.swig_wrappers.core.MolpherMol method) setSimilarityCoefficient() (molpher.swig_wrappers.core.ExplorationData method) setSource() (molpher.swig_wrappers.core.ExplorationData method) setTarget() (molpher.swig_wrappers.core.ExplorationData method) setThreadCount() (molpher.swig_wrappers.core.ExplorationTree method) Settings (class in molpher.algorithms.settings) settings (molpher.algorithms.antidecoys.custom_opers.GatherAntiFPScores attribute) (molpher.algorithms.antidecoys.pathfinder.AntidecoysPathFinder attribute) setTree() (molpher.swig_wrappers.core.TreeOperation method) setUp() (molpher.core.tests.test_api.TestAPI method) similarity (molpher.core.ExplorationData.ExplorationData property) similarity measure smiles (molpher.core.MolpherMol.MolpherMol property) sortMorphs() (molpher.swig_wrappers.core.ExplorationTree method) SortMorphsCallback (class in molpher.swig_wrappers.core) SortMorphsOper (class in molpher.core.operations.SortMorphsOper) (class in molpher.swig_wrappers.core) SortMorphsOper.SortCallback (class in molpher.core.operations.SortMorphsOper) source (molpher.algorithms.antidecoys.pathfinder.AntidecoysPathFinder attribute) (molpher.algorithms.settings.Settings attribute) (molpher.core.ExplorationData.ExplorationData property) (molpher.core.ExplorationTree.ExplorationTree property) source molecule source_target (molpher.algorithms.antidecoys.pathfinder.AntidecoysPathFinder attribute) (molpher.algorithms.bidirectional.pathfinder.BidirectionalPathFinder attribute) source_target_min (molpher.algorithms.antidecoys.pathfinder.AntidecoysPathFinder attribute) (molpher.algorithms.bidirectional.pathfinder.BidirectionalPathFinder attribute) storage_dir (molpher.algorithms.settings.Settings attribute) symbol (molpher.core.MolpherAtom.MolpherAtom property) SYNTHESIS (molpher.swig_wrappers.core.FilterMorphsOper attribute)

T

target (molpher.algorithms.antidecoys.pathfinder.AntidecoysPathFinder attribute) (molpher.algorithms.settings.Settings attribute) (molpher.core.ExplorationData.ExplorationData property) (molpher.core.ExplorationTree.ExplorationTree property) target molecule target_source (molpher.algorithms.antidecoys.pathfinder.AntidecoysPathFinder attribute) (molpher.algorithms.bidirectional.pathfinder.BidirectionalPathFinder attribute) target_source_min (molpher.algorithms.antidecoys.pathfinder.AntidecoysPathFinder attribute) (molpher.algorithms.bidirectional.pathfinder.BidirectionalPathFinder attribute) tearDown() (molpher.core.tests.test_api.TestAPI method) testAddAtomOperator() (molpher.core.tests.test_api.TestAPI method) testAddBondOperator() (molpher.core.tests.test_api.TestAPI method) TestAPI (class in molpher.core.tests.test_api) testAtomLibrary() (molpher.core.tests.test_api.TestAPI method) testContractBondOperator() (molpher.core.tests.test_api.TestAPI method) testExplorationData() (molpher.core.tests.test_api.TestAPI method) testInterlayAtomOperator() (molpher.core.tests.test_api.TestAPI method) testMolpher() (molpher.core.tests.test_api.TestAPI method) testMolpherAtom() (molpher.core.tests.test_api.TestAPI method)

testMolpherMol() (molpher.core.tests.test_api.TestAPI method) testMorphingOperator() (molpher.core.tests.test_api.TestAPI method) testMutateAtomOperator() (molpher.core.tests.test_api.TestAPI method) testRemoveBondOperator() (molpher.core.tests.test_api.TestAPI method) testRerouteBondOperator() (molpher.core.tests.test_api.TestAPI method) testTree() (molpher.core.tests.test_api.TestAPI method) thread_count (molpher.core.ExplorationTree.ExplorationTree property) timeit() (in module molpher.algorithms.functions) traverse() (molpher.core.ExplorationTree.ExplorationTree method) (molpher.swig_wrappers.core.ExplorationTree method) TraverseCallback (class in molpher.swig_wrappers.core) TraverseOper (class in molpher.core.operations.TraverseOper) (class in molpher.swig_wrappers.core) tree (molpher.core.MolpherMol.MolpherMol property) (molpher.core.operations.TreeOperation.TreeOperation property) tree operation tree snapshot tree_params (molpher.algorithms.settings.Settings attribute) TreeOperation (class in molpher.core.operations.TreeOperation) (class in molpher.swig_wrappers.core)

U

update() (molpher.swig_wrappers.core.ExplorationTree method)

update_target() (in module molpher.algorithms.antidecoys.utils)

V

verbose (molpher.algorithms.antidecoys.pathfinder.AntidecoysPathFinder attribute) (molpher.algorithms.bidirectional.pathfinder.BidirectionalPathFinder attribute) (molpher.algorithms.settings.Settings attribute)

virtual screening

W

WEIGHT (molpher.swig_wrappers.core.FilterMorphsOper attribute) weight_max (molpher.core.ExplorationData.ExplorationData property)

weight_min (molpher.core.ExplorationData.ExplorationData property) wrappers (in module molpher)

X

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