Index

_

__call__() (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.SortMorphsOper method) (molpher.swig_wrappers.core.TraverseCallback method) (molpher.swig_wrappers.core.TraverseOper method) (molpher.swig_wrappers.core.TreeOperation method)

A

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

ALL (molpher.swig_wrappers.core.FilterMorphsOper attribute) asData() (molpher.core.ExplorationTree.ExplorationTree method) (molpher.swig_wrappers.core.ExplorationTree method)

B

BidirectionalPathFinder (class in molpher.examples.bidirectional)

C

Callback (class in molpher.core.ExplorationTree) 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.examples.classic) close_produce (molpher.core.ExplorationData.ExplorationData 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) DUPLICATES (molpher.swig_wrappers.core.FilterMorphsOper attribute)

E

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) filterMorphs() (molpher.swig_wrappers.core.ExplorationTree method) FilterMorphsOper (class in molpher.core.operations.FilterMorphsOper) (class in molpher.swig_wrappers.core) FindClosest (class in molpher.examples.bidirectional) 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

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.bidirectional) (in module molpher.examples.classic) (in module molpher.examples.experiment) MAX_DERIVATIONS (molpher.swig_wrappers.core.FilterMorphsOper attribute) max_morphs_total (molpher.core.ExplorationData.ExplorationData attribute) molecular fingerprint molecular morphing Molpher molpher (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.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.bidirectional (module) molpher.examples.classic (module) molpher.examples.experiment (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.experiment)

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)

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.examples.classic.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)

R

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) 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) 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) SortMorphsOper (class in molpher.core.operations.SortMorphsOper) (class in molpher.swig_wrappers.core) source (molpher.core.ExplorationData.ExplorationData attribute) source molecule SYNTHESIS (molpher.swig_wrappers.core.FilterMorphsOper attribute)

T

target (molpher.core.ExplorationData.ExplorationData attribute) target molecule, [1] 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.examples.bidirectional) (in module molpher.examples.classic) 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 attribute) (molpher.core.operations.TreeOperation.TreeOperation attribute) tree operation tree snapshot TreeOperation (class in molpher.core.operations.TreeOperation) (class in molpher.swig_wrappers.core)

U

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

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

XML template