Index

_ | A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U | W | X

_

__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

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