Index

_

__call__() (molpher.algorithms.antidecoys.pathfinder.AntidecoysPathFinder method) (molpher.algorithms.bidirectional.pathfinder.BidirectionalPathFinder method) (molpher.algorithms.classic.pathfinder.ClassicPathFinder 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) (molpher.algorithms.classic.pathfinder.ClassicPathFinder 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) (molpher.algorithms.classic.pathfinder.ClassicPathFinder attribute)

A

accept_max (molpher.core.ExplorationData.ExplorationData attribute) accept_min (molpher.core.ExplorationData.ExplorationData attribute) 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)

B

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

C

Callback (class in molpher.core.operations.TraverseOper) candidate morphs candidates (molpher.core.ExplorationTree.ExplorationTree attribute) candidates_mask (molpher.core.ExplorationTree.ExplorationTree attribute) 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 attribute)

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) 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 attribute) dist_to_target (molpher.core.MolpherMol.MolpherMol attribute)

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

E

environment variable CMAKE_INSTALL_PREFIX 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 attribute) far_produce (molpher.core.ExplorationData.ExplorationData attribute) 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) 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_closest (molpher.algorithms.classic.pathfinder.ClassicPathFinder attribute) 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 attribute)

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)

G

GatherAntiFPScores (class in molpher.algorithms.antidecoys.custom_opers) generateMorphs() (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 attribute) gens_without_improvement (molpher.core.MolpherMol.MolpherMol attribute) 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) 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) getMaxAcceptableMolecularWeight() (molpher.swig_wrappers.core.ExplorationData method) getMinAcceptableMolecularWeight() (molpher.swig_wrappers.core.ExplorationData method) getMolecularWeight() (molpher.swig_wrappers.core.MolpherMol method) getParentSMILES() (molpher.swig_wrappers.core.MolpherMol 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) historic_descendents (molpher.core.MolpherMol.MolpherMol attribute)

HISTORIC_DESCENDENTS (molpher.swig_wrappers.core.FilterMorphsOper attribute)

I

is_valid (molpher.core.ExplorationData.ExplorationData attribute)

L

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

load_data_from (C++ function) load_SAScore() (in module molpher)

M

main() (in module molpher.examples.basics) (in module molpher.examples.basics_alg) (in module molpher.examples.bidirectional) (in module molpher.examples.classic) MAX_DERIVATIONS (molpher.swig_wrappers.core.FilterMorphsOper attribute) max_iters (molpher.algorithms.settings.Settings attribute) max_morphs_total (molpher.core.ExplorationData.ExplorationData attribute) 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) molecular fingerprint molecular morphing Molpher molpher (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.MolpherMol (module) molpher.core.operations (module), [1] 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.basics (module) molpher.examples.basics_alg (module) molpher.examples.bidirectional (module) molpher.examples.classic (module) molpher.swig_wrappers (module) MolpherMol (class in molpher.core.MolpherMol) (class in molpher.swig_wrappers.core) morph morph generation morphing iteration morphing parameters MyFilterMorphs (class in molpher.examples.basics_alg)

N

non-producing molecule

non_producing_survive (molpher.core.ExplorationData.ExplorationData attribute)

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 attribute) out (molpher.algorithms.antidecoys.custom_opers.GatherAntiFPScores attribute)

P

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

path_found (molpher.core.ExplorationTree.ExplorationTree attribute) 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

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 (molpher.core.MolpherMol.MolpherMol attribute) 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) 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) (molpher.algorithms.classic.pathfinder.ClassicPathFinder attribute) setTree() (molpher.swig_wrappers.core.TreeOperation method) setUp() (molpher.core.tests.test_api.TestPythonAPI method) similarity (molpher.core.ExplorationData.ExplorationData attribute) similarity measure smiles (molpher.core.MolpherMol.MolpherMol attribute) 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 attribute) 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) SYNTHESIS (molpher.swig_wrappers.core.FilterMorphsOper attribute)

T

target (molpher.algorithms.antidecoys.pathfinder.AntidecoysPathFinder attribute) (molpher.algorithms.settings.Settings attribute) (molpher.core.ExplorationData.ExplorationData attribute) target molecule, [1] 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.TestPythonAPI method) testExplorationData() (molpher.core.tests.test_api.TestPythonAPI method) testMolpherMol() (molpher.core.tests.test_api.TestPythonAPI method) testMorphing() (molpher.core.tests.test_api.TestPythonAPI method) testOperations() (molpher.core.tests.test_api.TestPythonAPI method) TestPythonAPI (class in molpher.core.tests.test_api) testTree() (molpher.core.tests.test_api.TestPythonAPI method)

thread_count (molpher.core.ExplorationTree.ExplorationTree attribute) 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.algorithms.classic.pathfinder.ClassicPathFinder attribute) (molpher.core.MolpherMol.MolpherMol attribute) (molpher.core.operations.TreeOperation.TreeOperation attribute) 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)

W

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

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

X

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