stk
stable
stk
Construction Overview
Basic Examples
Video Tutorials
Molecules
Building Block
Constructed Molecule
Functional Groups
Functional Group Factories
Key Makers
Reactions
Reaction Factories
Writers
Topology Graphs
Topology Graph Components
Polymers
Small Molecules
Organic & Metal-Organic Cages
Covalent Organic Frameworks
Metal Complexes
Host Guest Complex
Macrocycle
[n]Rotaxane
Adding Topology Graphs
Optimizers
Molecular Databases
Molecule
Constructed Molecule
Value
Evolutionary Algorithm
Overview
Basic Example
Intermediate Example
Fitness Calculators
Fitness Normalizers
Selection
Mutation
Crossover
Plotting
Modules
Modules
stk
Index
Edit on GitHub
Index
A
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B
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C
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D
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E
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F
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G
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H
|
I
|
K
|
L
|
M
|
N
|
O
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P
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R
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S
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T
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U
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V
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W
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X
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Y
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Z
A
AboveAverage (class in stk)
Ac (class in stk)
Add (class in stk)
Ag (class in stk)
Al (class in stk)
Alcohol (class in stk)
AlcoholFactory (class in stk)
Aldehyde (class in stk)
AldehydeFactory (class in stk)
Alkene (class in stk)
Alkyne (class in stk)
Am (class in stk)
Amide (class in stk)
AmideFactory (class in stk)
AngledVertex (class in stk.cage)
Ar (class in stk)
As (class in stk)
At (class in stk)
Atom (class in stk)
AtomInfo (class in stk)
Au (class in stk)
AxleVertex (class in stk.rotaxane)
B
B (class in stk)
Ba (class in stk)
Batch (class in stk)
BatchKey (in module stk)
Be (class in stk)
Best (class in stk)
Bh (class in stk)
Bi (class in stk)
BiDentateLigandVertex (class in stk.metal_complex)
BidentateSquarePlanar (class in stk.metal_complex)
Bk (class in stk)
Bond (class in stk)
BondInfo (class in stk)
BoronicAcid (class in stk)
BoronicAcidFactory (class in stk)
Br (class in stk)
Bromo (class in stk)
BromoFactory (class in stk)
BuildingBlock (class in stk)
C
C (class in stk)
Ca (class in stk)
Cage (class in stk.cage)
CarboxylicAcid (class in stk)
CarboxylicAcidFactory (class in stk)
Cd (class in stk)
Ce (class in stk)
Cf (class in stk)
CisProtectedSquarePlanar (class in stk.metal_complex)
Cl (class in stk)
clone() (stk.Ac method)
(stk.Ag method)
(stk.Al method)
(stk.Alcohol method)
(stk.Aldehyde method)
(stk.Alkene method)
(stk.Alkyne method)
(stk.Am method)
(stk.Amide method)
(stk.Ar method)
(stk.As method)
(stk.At method)
(stk.Atom method)
(stk.Au method)
(stk.B method)
(stk.Ba method)
(stk.Be method)
(stk.Bh method)
(stk.Bi method)
(stk.Bk method)
(stk.Bond method)
(stk.BoronicAcid method)
(stk.Br method)
(stk.Bromo method)
(stk.BuildingBlock method)
(stk.C method)
(stk.Ca method)
(stk.cage.AngledVertex method)
(stk.cage.Cage method)
(stk.cage.EightPlusSixteen method)
(stk.cage.EightPlusTwelve method)
(stk.cage.FivePlusTen method)
(stk.cage.FourPlusEight method)
(stk.cage.FourPlusFour method)
(stk.cage.FourPlusSix method)
(stk.cage.FourPlusSix2 method)
(stk.cage.LinearVertex method)
(stk.cage.M12L24 method)
(stk.cage.M24L48 method)
(stk.cage.M2L4Lantern method)
(stk.cage.M3L3Triangle method)
(stk.cage.M3L6 method)
(stk.cage.M4L4Square method)
(stk.cage.M4L4Tetrahedron method)
(stk.cage.M4L6Tetrahedron method)
(stk.cage.M4L6TetrahedronSpacer method)
(stk.cage.M4L8 method)
(stk.cage.M6L12Cube method)
(stk.cage.M6L2L3Prism method)
(stk.cage.M8L6Cube method)
(stk.cage.NonLinearVertex method)
(stk.cage.OnePlusOne method)
(stk.cage.SixPlusEight method)
(stk.cage.SixPlusNine method)
(stk.cage.SixPlusTwelve method)
(stk.cage.TenPlusTwenty method)
(stk.cage.ThreePlusSix method)
(stk.cage.TwelvePlusThirty method)
(stk.cage.TwentyPlusThirty method)
(stk.cage.TwoPlusFour method)
(stk.cage.TwoPlusThree method)
(stk.cage.TwoPlusTwo method)
(stk.cage.UnaligningVertex method)
(stk.CarboxylicAcid method)
(stk.Cd method)
(stk.Ce method)
(stk.Cf method)
(stk.Cl method)
(stk.Cm method)
(stk.Cn method)
(stk.Co method)
(stk.cof.Cof method)
(stk.cof.Hexagonal method)
(stk.cof.Honeycomb method)
(stk.cof.Kagome method)
(stk.cof.LinearVertex method)
(stk.cof.LinkerlessHoneycomb method)
(stk.cof.NonLinearVertex method)
(stk.cof.PeriodicHexagonal method)
(stk.cof.PeriodicHoneycomb method)
(stk.cof.PeriodicKagome method)
(stk.cof.PeriodicLinkerlessHoneycomb method)
(stk.cof.PeriodicSquare method)
(stk.cof.Square method)
(stk.cof.UnaligningVertex method)
(stk.ConstructedMolecule method)
(stk.ConstructionState method)
(stk.Cr method)
(stk.Cs method)
(stk.Cu method)
(stk.Db method)
(stk.Dibromo method)
(stk.Difluoro method)
(stk.Diol method)
(stk.Ds method)
(stk.Dy method)
(stk.Edge method)
(stk.Er method)
(stk.Es method)
(stk.Eu method)
(stk.F method)
(stk.Fe method)
(stk.Fl method)
(stk.Fluoro method)
(stk.Fm method)
(stk.Fr method)
(stk.FunctionalGroup method)
(stk.Ga method)
(stk.Gd method)
(stk.Ge method)
(stk.GenericFunctionalGroup method)
(stk.GraphState method)
(stk.H method)
(stk.He method)
(stk.Hf method)
(stk.Hg method)
(stk.Ho method)
(stk.host_guest.Complex method)
(stk.host_guest.GuestVertex method)
(stk.host_guest.HostVertex method)
(stk.Hs method)
(stk.I method)
(stk.In method)
(stk.Iodo method)
(stk.Ir method)
(stk.K method)
(stk.Kr method)
(stk.La method)
(stk.Li method)
(stk.Lr method)
(stk.Lu method)
(stk.Lv method)
(stk.macrocycle.CycleVertex method)
(stk.macrocycle.Macrocycle method)
(stk.Mc method)
(stk.Md method)
(stk.metal_complex.BiDentateLigandVertex method)
(stk.metal_complex.BidentateSquarePlanar method)
(stk.metal_complex.CisProtectedSquarePlanar method)
(stk.metal_complex.MetalComplex method)
(stk.metal_complex.MetalVertex method)
(stk.metal_complex.MonoDentateLigandVertex method)
(stk.metal_complex.Octahedral method)
(stk.metal_complex.OctahedralDelta method)
(stk.metal_complex.OctahedralLambda method)
(stk.metal_complex.Paddlewheel method)
(stk.metal_complex.Porphyrin method)
(stk.metal_complex.SquarePlanar method)
(stk.Mg method)
(stk.Mn method)
(stk.Mo method)
(stk.Molecule method)
(stk.MoleculeState method)
(stk.Mt method)
(stk.N method)
(stk.Na method)
(stk.Nb method)
(stk.Nd method)
(stk.Ne method)
(stk.Nh method)
(stk.Ni method)
(stk.No method)
(stk.Np method)
(stk.O method)
(stk.Og method)
(stk.Os method)
(stk.P method)
(stk.Pa method)
(stk.Pb method)
(stk.Pd method)
(stk.PeriodicInfo method)
(stk.Pm method)
(stk.Po method)
(stk.polymer.HeadVertex method)
(stk.polymer.Linear method)
(stk.polymer.LinearVertex method)
(stk.polymer.TailVertex method)
(stk.polymer.TerminalVertex method)
(stk.polymer.UnaligningVertex method)
(stk.Pr method)
(stk.PrimaryAmino method)
(stk.Pt method)
(stk.Pu method)
(stk.Ra method)
(stk.Rb method)
(stk.Re method)
(stk.Rf method)
(stk.Rg method)
(stk.Rh method)
(stk.RingAmine method)
(stk.Rn method)
(stk.rotaxane.AxleVertex method)
(stk.rotaxane.CycleVertex method)
(stk.rotaxane.NRotaxane method)
(stk.Ru method)
(stk.S method)
(stk.Sb method)
(stk.Sc method)
(stk.Se method)
(stk.SecondaryAmino method)
(stk.Sg method)
(stk.Si method)
(stk.SingleAtom method)
(stk.Sm method)
(stk.small.CoreVertex method)
(stk.small.NCore method)
(stk.small.SubstituentVertex method)
(stk.Sn method)
(stk.Sr method)
(stk.Ta method)
(stk.Tb method)
(stk.Tc method)
(stk.Te method)
(stk.Th method)
(stk.Thioacid method)
(stk.Thiol method)
(stk.Ti method)
(stk.Tl method)
(stk.Tm method)
(stk.TopologyGraph method)
(stk.Ts method)
(stk.U method)
(stk.V method)
(stk.Vertex method)
(stk.W method)
(stk.Xe method)
(stk.Y method)
(stk.Yb method)
(stk.Zn method)
(stk.Zr method)
Cm (class in stk)
Cn (class in stk)
Co (class in stk)
Cof (class in stk.cof)
Collapser (class in stk)
Complex (class in stk.host_guest)
construct() (stk.cage.Cage method)
(stk.cage.EightPlusSixteen method)
(stk.cage.EightPlusTwelve method)
(stk.cage.FivePlusTen method)
(stk.cage.FourPlusEight method)
(stk.cage.FourPlusFour method)
(stk.cage.FourPlusSix method)
(stk.cage.FourPlusSix2 method)
(stk.cage.M12L24 method)
(stk.cage.M24L48 method)
(stk.cage.M2L4Lantern method)
(stk.cage.M3L3Triangle method)
(stk.cage.M3L6 method)
(stk.cage.M4L4Square method)
(stk.cage.M4L4Tetrahedron method)
(stk.cage.M4L6Tetrahedron method)
(stk.cage.M4L6TetrahedronSpacer method)
(stk.cage.M4L8 method)
(stk.cage.M6L12Cube method)
(stk.cage.M6L2L3Prism method)
(stk.cage.M8L6Cube method)
(stk.cage.OnePlusOne method)
(stk.cage.SixPlusEight method)
(stk.cage.SixPlusNine method)
(stk.cage.SixPlusTwelve method)
(stk.cage.TenPlusTwenty method)
(stk.cage.ThreePlusSix method)
(stk.cage.TwelvePlusThirty method)
(stk.cage.TwentyPlusThirty method)
(stk.cage.TwoPlusFour method)
(stk.cage.TwoPlusThree method)
(stk.cage.TwoPlusTwo method)
(stk.cof.Cof method)
(stk.cof.Hexagonal method)
(stk.cof.Honeycomb method)
(stk.cof.Kagome method)
(stk.cof.LinkerlessHoneycomb method)
(stk.cof.PeriodicHexagonal method)
(stk.cof.PeriodicHoneycomb method)
(stk.cof.PeriodicKagome method)
(stk.cof.PeriodicLinkerlessHoneycomb method)
(stk.cof.PeriodicSquare method)
(stk.cof.Square method)
(stk.host_guest.Complex method)
(stk.macrocycle.Macrocycle method)
(stk.metal_complex.BidentateSquarePlanar method)
(stk.metal_complex.CisProtectedSquarePlanar method)
(stk.metal_complex.MetalComplex method)
(stk.metal_complex.Octahedral method)
(stk.metal_complex.OctahedralDelta method)
(stk.metal_complex.OctahedralLambda method)
(stk.metal_complex.Paddlewheel method)
(stk.metal_complex.Porphyrin method)
(stk.metal_complex.SquarePlanar method)
(stk.polymer.Linear method)
(stk.rotaxane.NRotaxane method)
(stk.small.NCore method)
(stk.TopologyGraph method)
ConstructedMolecule (class in stk)
ConstructedMoleculeDatabase (class in stk)
ConstructedMoleculeDejsonizer (class in stk)
ConstructedMoleculeJsonizer (class in stk)
ConstructedMoleculeMongoDb (class in stk)
ConstructionResult (class in stk)
ConstructionState (class in stk)
CoreVertex (class in stk.small)
Cr (class in stk)
cross() (stk.GeneticRecombination method)
(stk.MoleculeCrosser method)
(stk.RandomCrosser method)
CrossoverRecord (class in stk)
Cs (class in stk)
Cu (class in stk)
CycleVertex (class in stk.macrocycle)
(class in stk.rotaxane)
D
DativeReaction (class in stk)
DativeReactionFactory (class in stk)
Db (class in stk)
Dibromo (class in stk)
DibromoFactory (class in stk)
Difluoro (class in stk)
DifluoroFactory (class in stk)
Diol (class in stk)
DiolFactory (class in stk)
DivideByMean (class in stk)
Ds (class in stk)
Dy (class in stk)
E
Edge (class in stk)
(in module stk.cof)
EdgeGroup (class in stk)
EightPlusSixteen (class in stk.cage)
EightPlusTwelve (class in stk.cage)
Er (class in stk)
Es (class in stk)
Eu (class in stk)
EvolutionaryAlgorithm (class in stk)
F
F (class in stk)
Fe (class in stk)
FilterBatches (class in stk)
FilterMolecules (class in stk)
FitnessCalculator (class in stk)
FitnessFunction (class in stk)
FitnessNormalizer (class in stk)
FitnessValues (class in stk)
FivePlusTen (class in stk.cage)
Fl (class in stk)
Fluoro (class in stk)
FluoroFactory (class in stk)
Fm (class in stk)
FourPlusEight (class in stk.cage)
FourPlusFour (class in stk.cage)
FourPlusSix (class in stk.cage)
FourPlusSix2 (class in stk.cage)
Fr (class in stk)
from_json() (stk.ConstructedMoleculeDejsonizer method)
(stk.MoleculeDejsonizer method)
FunctionalGroup (class in stk)
FunctionalGroupFactory (class in stk)
G
Ga (class in stk)
Gd (class in stk)
Ge (class in stk)
Generation (class in stk)
GenericFunctionalGroup (class in stk)
GenericReactionFactory (class in stk)
GeneticRecombination (class in stk)
get() (stk.ConstructedMoleculeDatabase method)
(stk.ConstructedMoleculeMongoDb method)
(stk.MoleculeDatabase method)
(stk.MoleculeMongoDb method)
(stk.ValueDatabase method)
(stk.ValueMongoDb method)
get_a() (stk.PeriodicInfo method)
get_acute_vector() (in module stk)
get_aligner_edge() (stk.cage.AngledVertex method)
(stk.cage.LinearVertex method)
(stk.cage.NonLinearVertex method)
(stk.cage.UnaligningVertex method)
(stk.cof.LinearVertex method)
(stk.cof.NonLinearVertex method)
(stk.cof.UnaligningVertex method)
get_all() (stk.ConstructedMoleculeDatabase method)
(stk.ConstructedMoleculeMongoDb method)
(stk.MoleculeDatabase method)
(stk.MoleculeMongoDb method)
get_alpha() (stk.PeriodicInfo method)
get_atom() (stk.Alcohol method)
(stk.Aldehyde method)
(stk.Amide method)
(stk.AtomInfo method)
(stk.BoronicAcid method)
(stk.Bromo method)
(stk.CarboxylicAcid method)
(stk.Fluoro method)
(stk.Iodo method)
(stk.PrimaryAmino method)
(stk.SingleAtom method)
(stk.Thioacid method)
(stk.Thiol method)
get_atom1() (stk.Alkene method)
(stk.Alkyne method)
(stk.Bond method)
(stk.Dibromo method)
(stk.Difluoro method)
(stk.Diol method)
(stk.SecondaryAmino method)
get_atom2() (stk.Alkene method)
(stk.Alkyne method)
(stk.Bond method)
(stk.Dibromo method)
(stk.Difluoro method)
(stk.Diol method)
(stk.SecondaryAmino method)
get_atom3() (stk.Alkene method)
get_atom4() (stk.Alkene method)
get_atom_ids() (stk.Alcohol method)
(stk.Aldehyde method)
(stk.Alkene method)
(stk.Alkyne method)
(stk.Amide method)
(stk.BoronicAcid method)
(stk.Bromo method)
(stk.CarboxylicAcid method)
(stk.Dibromo method)
(stk.Difluoro method)
(stk.Diol method)
(stk.Fluoro method)
(stk.FunctionalGroup method)
(stk.GenericFunctionalGroup method)
(stk.Iodo method)
(stk.PrimaryAmino method)
(stk.RingAmine method)
(stk.SecondaryAmino method)
(stk.SingleAtom method)
(stk.Thioacid method)
(stk.Thiol method)
get_atom_infos() (stk.ConstructedMolecule method)
(stk.ConstructionResult method)
(stk.ConstructionState method)
(stk.MoleculeState method)
get_atomic_number() (stk.Ac method)
(stk.Ag method)
(stk.Al method)
(stk.Am method)
(stk.Ar method)
(stk.As method)
(stk.At method)
(stk.Atom method)
(stk.Au method)
(stk.B method)
(stk.Ba method)
(stk.Be method)
(stk.Bh method)
(stk.Bi method)
(stk.Bk method)
(stk.Br method)
(stk.C method)
(stk.Ca method)
(stk.Cd method)
(stk.Ce method)
(stk.Cf method)
(stk.Cl method)
(stk.Cm method)
(stk.Cn method)
(stk.Co method)
(stk.Cr method)
(stk.Cs method)
(stk.Cu method)
(stk.Db method)
(stk.Ds method)
(stk.Dy method)
(stk.Er method)
(stk.Es method)
(stk.Eu method)
(stk.F method)
(stk.Fe method)
(stk.Fl method)
(stk.Fm method)
(stk.Fr method)
(stk.Ga method)
(stk.Gd method)
(stk.Ge method)
(stk.H method)
(stk.He method)
(stk.Hf method)
(stk.Hg method)
(stk.Ho method)
(stk.Hs method)
(stk.I method)
(stk.In method)
(stk.Ir method)
(stk.K method)
(stk.Kr method)
(stk.La method)
(stk.Li method)
(stk.Lr method)
(stk.Lu method)
(stk.Lv method)
(stk.Mc method)
(stk.Md method)
(stk.Mg method)
(stk.Mn method)
(stk.Mo method)
(stk.Mt method)
(stk.N method)
(stk.Na method)
(stk.Nb method)
(stk.Nd method)
(stk.Ne method)
(stk.Nh method)
(stk.Ni method)
(stk.No method)
(stk.Np method)
(stk.O method)
(stk.Og method)
(stk.Os method)
(stk.P method)
(stk.Pa method)
(stk.Pb method)
(stk.Pd method)
(stk.Pm method)
(stk.Po method)
(stk.Pr method)
(stk.Pt method)
(stk.Pu method)
(stk.Ra method)
(stk.Rb method)
(stk.Re method)
(stk.Rf method)
(stk.Rg method)
(stk.Rh method)
(stk.Rn method)
(stk.Ru method)
(stk.S method)
(stk.Sb method)
(stk.Sc method)
(stk.Se method)
(stk.Sg method)
(stk.Si method)
(stk.Sm method)
(stk.Sn method)
(stk.Sr method)
(stk.Ta method)
(stk.Tb method)
(stk.Tc method)
(stk.Te method)
(stk.Th method)
(stk.Ti method)
(stk.Tl method)
(stk.Tm method)
(stk.Ts method)
(stk.U method)
(stk.V method)
(stk.W method)
(stk.Xe method)
(stk.Y method)
(stk.Yb method)
(stk.Zn method)
(stk.Zr method)
get_atomic_positions() (stk.BuildingBlock method)
(stk.ConstructedMolecule method)
(stk.Molecule method)
get_atoms() (stk.Alcohol method)
(stk.Aldehyde method)
(stk.Alkene method)
(stk.Alkyne method)
(stk.Amide method)
(stk.BoronicAcid method)
(stk.Bromo method)
(stk.BuildingBlock method)
(stk.CarboxylicAcid method)
(stk.ConstructedMolecule method)
(stk.ConstructionResult method)
(stk.ConstructionState method)
(stk.Dibromo method)
(stk.Difluoro method)
(stk.Diol method)
(stk.Fluoro method)
(stk.FunctionalGroup method)
(stk.GenericFunctionalGroup method)
(stk.Iodo method)
(stk.Molecule method)
(stk.MoleculeState method)
(stk.PrimaryAmino method)
(stk.RingAmine method)
(stk.SecondaryAmino method)
(stk.SingleAtom method)
(stk.Thioacid method)
(stk.Thiol method)
get_b() (stk.PeriodicInfo method)
get_beta() (stk.PeriodicInfo method)
get_bond() (stk.BondInfo method)
get_bond_infos() (stk.ConstructedMolecule method)
(stk.ConstructionResult method)
(stk.ConstructionState method)
(stk.MoleculeState method)
get_bonder_ids() (stk.Alcohol method)
(stk.Aldehyde method)
(stk.Alkene method)
(stk.Alkyne method)
(stk.Amide method)
(stk.BoronicAcid method)
(stk.Bromo method)
(stk.CarboxylicAcid method)
(stk.Dibromo method)
(stk.Difluoro method)
(stk.Diol method)
(stk.Fluoro method)
(stk.GenericFunctionalGroup method)
(stk.Iodo method)
(stk.PrimaryAmino method)
(stk.SecondaryAmino method)
(stk.SingleAtom method)
(stk.Thioacid method)
(stk.Thiol method)
get_bonders() (stk.Alcohol method)
(stk.Aldehyde method)
(stk.Alkene method)
(stk.Alkyne method)
(stk.Amide method)
(stk.BoronicAcid method)
(stk.Bromo method)
(stk.CarboxylicAcid method)
(stk.Dibromo method)
(stk.Difluoro method)
(stk.Diol method)
(stk.Fluoro method)
(stk.GenericFunctionalGroup method)
(stk.Iodo method)
(stk.PrimaryAmino method)
(stk.SecondaryAmino method)
(stk.SingleAtom method)
(stk.Thioacid method)
(stk.Thiol method)
get_bonds() (stk.BuildingBlock method)
(stk.ConstructedMolecule method)
(stk.ConstructionResult method)
(stk.ConstructionState method)
(stk.Molecule method)
(stk.MoleculeState method)
get_boron() (stk.BoronicAcid method)
get_bromine() (stk.Bromo method)
get_bromine1() (stk.Dibromo method)
get_bromine2() (stk.Dibromo method)
get_building_block() (stk.AtomInfo method)
(stk.BondInfo method)
(stk.ConstructionState method)
(stk.GraphState method)
(stk.host_guest.Guest method)
get_building_block_atom() (stk.AtomInfo method)
get_building_block_id() (stk.AtomInfo method)
(stk.BondInfo method)
get_building_blocks() (stk.cage.Cage method)
(stk.cage.EightPlusSixteen method)
(stk.cage.EightPlusTwelve method)
(stk.cage.FivePlusTen method)
(stk.cage.FourPlusEight method)
(stk.cage.FourPlusFour method)
(stk.cage.FourPlusSix method)
(stk.cage.FourPlusSix2 method)
(stk.cage.M12L24 method)
(stk.cage.M24L48 method)
(stk.cage.M2L4Lantern method)
(stk.cage.M3L3Triangle method)
(stk.cage.M3L6 method)
(stk.cage.M4L4Square method)
(stk.cage.M4L4Tetrahedron method)
(stk.cage.M4L6Tetrahedron method)
(stk.cage.M4L6TetrahedronSpacer method)
(stk.cage.M4L8 method)
(stk.cage.M6L12Cube method)
(stk.cage.M6L2L3Prism method)
(stk.cage.M8L6Cube method)
(stk.cage.OnePlusOne method)
(stk.cage.SixPlusEight method)
(stk.cage.SixPlusNine method)
(stk.cage.SixPlusTwelve method)
(stk.cage.TenPlusTwenty method)
(stk.cage.ThreePlusSix method)
(stk.cage.TwelvePlusThirty method)
(stk.cage.TwentyPlusThirty method)
(stk.cage.TwoPlusFour method)
(stk.cage.TwoPlusThree method)
(stk.cage.TwoPlusTwo method)
(stk.cof.Cof method)
(stk.cof.Hexagonal method)
(stk.cof.Honeycomb method)
(stk.cof.Kagome method)
(stk.cof.LinkerlessHoneycomb method)
(stk.cof.PeriodicHexagonal method)
(stk.cof.PeriodicHoneycomb method)
(stk.cof.PeriodicKagome method)
(stk.cof.PeriodicLinkerlessHoneycomb method)
(stk.cof.PeriodicSquare method)
(stk.cof.Square method)
(stk.ConstructedMolecule method)
(stk.ConstructionResult method)
(stk.ConstructionState method)
(stk.GraphState method)
(stk.host_guest.Complex method)
(stk.macrocycle.Macrocycle method)
(stk.metal_complex.BidentateSquarePlanar method)
(stk.metal_complex.CisProtectedSquarePlanar method)
(stk.metal_complex.MetalComplex method)
(stk.metal_complex.Octahedral method)
(stk.metal_complex.OctahedralDelta method)
(stk.metal_complex.OctahedralLambda method)
(stk.metal_complex.Paddlewheel method)
(stk.metal_complex.Porphyrin method)
(stk.metal_complex.SquarePlanar method)
(stk.polymer.Linear method)
(stk.rotaxane.NRotaxane method)
(stk.small.NCore method)
(stk.TopologyGraph method)
get_c() (stk.PeriodicInfo method)
get_canonical_atom_ids() (stk.BuildingBlock method)
(stk.ConstructedMolecule method)
(stk.Molecule method)
get_carbon() (stk.Aldehyde method)
(stk.Amide method)
(stk.CarboxylicAcid method)
(stk.Thioacid method)
get_carbon1() (stk.Alkene method)
(stk.Alkyne method)
(stk.RingAmine method)
get_carbon2() (stk.Alkene method)
(stk.Alkyne method)
(stk.RingAmine method)
get_carbon3() (stk.RingAmine method)
get_cell() (stk.cage.AngledVertex method)
(stk.cage.LinearVertex method)
(stk.cage.NonLinearVertex method)
(stk.cage.UnaligningVertex method)
(stk.cof.LinearVertex method)
(stk.cof.NonLinearVertex method)
(stk.cof.UnaligningVertex method)
(stk.host_guest.GuestVertex method)
(stk.host_guest.HostVertex method)
(stk.macrocycle.CycleVertex method)
(stk.metal_complex.BiDentateLigandVertex method)
(stk.metal_complex.MetalVertex method)
(stk.metal_complex.MonoDentateLigandVertex method)
(stk.polymer.HeadVertex method)
(stk.polymer.LinearVertex method)
(stk.polymer.TailVertex method)
(stk.polymer.TerminalVertex method)
(stk.polymer.UnaligningVertex method)
(stk.rotaxane.AxleVertex method)
(stk.rotaxane.CycleVertex method)
(stk.small.CoreVertex method)
(stk.small.SubstituentVertex method)
(stk.Vertex method)
get_cell_matrix() (stk.PeriodicInfo method)
get_centroid() (stk.BuildingBlock method)
(stk.ConstructedMolecule method)
(stk.Molecule method)
get_charge() (stk.Ac method)
(stk.Ag method)
(stk.Al method)
(stk.Am method)
(stk.Ar method)
(stk.As method)
(stk.At method)
(stk.Atom method)
(stk.Au method)
(stk.B method)
(stk.Ba method)
(stk.Be method)
(stk.Bh method)
(stk.Bi method)
(stk.Bk method)
(stk.Br method)
(stk.C method)
(stk.Ca method)
(stk.Cd method)
(stk.Ce method)
(stk.Cf method)
(stk.Cl method)
(stk.Cm method)
(stk.Cn method)
(stk.Co method)
(stk.Cr method)
(stk.Cs method)
(stk.Cu method)
(stk.Db method)
(stk.Ds method)
(stk.Dy method)
(stk.Er method)
(stk.Es method)
(stk.Eu method)
(stk.F method)
(stk.Fe method)
(stk.Fl method)
(stk.Fm method)
(stk.Fr method)
(stk.Ga method)
(stk.Gd method)
(stk.Ge method)
(stk.H method)
(stk.He method)
(stk.Hf method)
(stk.Hg method)
(stk.Ho method)
(stk.Hs method)
(stk.I method)
(stk.In method)
(stk.Ir method)
(stk.K method)
(stk.Kr method)
(stk.La method)
(stk.Li method)
(stk.Lr method)
(stk.Lu method)
(stk.Lv method)
(stk.Mc method)
(stk.Md method)
(stk.Mg method)
(stk.Mn method)
(stk.Mo method)
(stk.Mt method)
(stk.N method)
(stk.Na method)
(stk.Nb method)
(stk.Nd method)
(stk.Ne method)
(stk.Nh method)
(stk.Ni method)
(stk.No method)
(stk.Np method)
(stk.O method)
(stk.Og method)
(stk.Os method)
(stk.P method)
(stk.Pa method)
(stk.Pb method)
(stk.Pd method)
(stk.Pm method)
(stk.Po method)
(stk.Pr method)
(stk.Pt method)
(stk.Pu method)
(stk.Ra method)
(stk.Rb method)
(stk.Re method)
(stk.Rf method)
(stk.Rg method)
(stk.Rh method)
(stk.Rn method)
(stk.Ru method)
(stk.S method)
(stk.Sb method)
(stk.Sc method)
(stk.Se method)
(stk.Sg method)
(stk.Si method)
(stk.Sm method)
(stk.Sn method)
(stk.Sr method)
(stk.Ta method)
(stk.Tb method)
(stk.Tc method)
(stk.Te method)
(stk.Th method)
(stk.Ti method)
(stk.Tl method)
(stk.Tm method)
(stk.Ts method)
(stk.U method)
(stk.V method)
(stk.W method)
(stk.Xe method)
(stk.Y method)
(stk.Yb method)
(stk.Zn method)
(stk.Zr method)
get_core_atom_ids() (stk.Alcohol method)
(stk.Aldehyde method)
(stk.Alkene method)
(stk.Alkyne method)
(stk.Amide method)
(stk.BoronicAcid method)
(stk.Bromo method)
(stk.BuildingBlock method)
(stk.CarboxylicAcid method)
(stk.Dibromo method)
(stk.Difluoro method)
(stk.Diol method)
(stk.Fluoro method)
(stk.FunctionalGroup method)
(stk.GenericFunctionalGroup method)
(stk.Iodo method)
(stk.PrimaryAmino method)
(stk.RingAmine method)
(stk.SecondaryAmino method)
(stk.SingleAtom method)
(stk.Thioacid method)
(stk.Thiol method)
get_crosser_name() (stk.CrossoverRecord method)
get_crossover_records() (stk.Generation method)
get_deleted_atoms() (stk.ReactionResult method)
get_deleted_bonds() (stk.ReactionResult method)
get_deleter_ids() (stk.Alcohol method)
(stk.Aldehyde method)
(stk.Alkene method)
(stk.Alkyne method)
(stk.Amide method)
(stk.BoronicAcid method)
(stk.Bromo method)
(stk.CarboxylicAcid method)
(stk.Dibromo method)
(stk.Difluoro method)
(stk.Diol method)
(stk.Fluoro method)
(stk.GenericFunctionalGroup method)
(stk.Iodo method)
(stk.PrimaryAmino method)
(stk.SecondaryAmino method)
(stk.SingleAtom method)
(stk.Thioacid method)
(stk.Thiol method)
get_deleters() (stk.Alcohol method)
(stk.Aldehyde method)
(stk.Alkene method)
(stk.Alkyne method)
(stk.Amide method)
(stk.BoronicAcid method)
(stk.Bromo method)
(stk.CarboxylicAcid method)
(stk.Dibromo method)
(stk.Difluoro method)
(stk.Diol method)
(stk.Fluoro method)
(stk.GenericFunctionalGroup method)
(stk.Iodo method)
(stk.PrimaryAmino method)
(stk.SecondaryAmino method)
(stk.SingleAtom method)
(stk.Thioacid method)
(stk.Thiol method)
get_direction() (stk.BuildingBlock method)
(stk.ConstructedMolecule method)
(stk.Molecule method)
get_displacement() (stk.host_guest.Guest method)
get_edge() (stk.ConstructionState method)
(stk.GraphState method)
get_edge_group_functional_groups() (stk.ConstructionState method)
(stk.MoleculeState method)
get_edge_ids() (stk.EdgeGroup method)
get_edges() (stk.ConstructionState method)
(stk.GraphState method)
get_end_vector() (stk.host_guest.Guest method)
get_fitness_value() (stk.Batch method)
(stk.FitnessCalculator method)
(stk.FitnessFunction method)
(stk.PropertyVector method)
get_fitness_values() (stk.Generation method)
get_flip() (stk.macrocycle.CycleVertex method)
(stk.polymer.HeadVertex method)
(stk.polymer.LinearVertex method)
(stk.polymer.TailVertex method)
(stk.polymer.TerminalVertex method)
(stk.polymer.UnaligningVertex method)
(stk.rotaxane.CycleVertex method)
get_fluorine() (stk.Fluoro method)
get_fluorine1() (stk.Difluoro method)
get_fluorine2() (stk.Difluoro method)
get_functional_groups() (stk.AlcoholFactory method)
(stk.AldehydeFactory method)
(stk.AmideFactory method)
(stk.BoronicAcidFactory method)
(stk.BromoFactory method)
(stk.BuildingBlock method)
(stk.CarboxylicAcidFactory method)
(stk.DibromoFactory method)
(stk.DifluoroFactory method)
(stk.DiolFactory method)
(stk.FluoroFactory method)
(stk.FunctionalGroupFactory method)
(stk.IodoFactory method)
(stk.PrimaryAminoFactory method)
(stk.RingAmineFactory method)
(stk.SecondaryAminoFactory method)
(stk.SmartsFunctionalGroupFactory method)
(stk.TerminalAlkeneFactory method)
(stk.TerminalAlkyneFactory method)
(stk.ThioacidFactory method)
(stk.ThiolFactory method)
get_gamma() (stk.PeriodicInfo method)
get_generations() (stk.EvolutionaryAlgorithm method)
get_hydrogen() (stk.Alcohol method)
(stk.Aldehyde method)
(stk.CarboxylicAcid method)
(stk.SecondaryAmino method)
(stk.Thioacid method)
(stk.Thiol method)
get_hydrogen1() (stk.Amide method)
(stk.BoronicAcid method)
(stk.Diol method)
(stk.PrimaryAmino method)
(stk.RingAmine method)
get_hydrogen2() (stk.Amide method)
(stk.BoronicAcid method)
(stk.Diol method)
(stk.PrimaryAmino method)
(stk.RingAmine method)
get_hydrogen3() (stk.RingAmine method)
get_id() (stk.Ac method)
(stk.Ag method)
(stk.Al method)
(stk.Am method)
(stk.Ar method)
(stk.As method)
(stk.At method)
(stk.Atom method)
(stk.Au method)
(stk.B method)
(stk.Ba method)
(stk.Be method)
(stk.Bh method)
(stk.Bi method)
(stk.Bk method)
(stk.Br method)
(stk.C method)
(stk.Ca method)
(stk.cage.AngledVertex method)
(stk.cage.LinearVertex method)
(stk.cage.NonLinearVertex method)
(stk.cage.UnaligningVertex method)
(stk.Cd method)
(stk.Ce method)
(stk.Cf method)
(stk.Cl method)
(stk.Cm method)
(stk.Cn method)
(stk.Co method)
(stk.cof.LinearVertex method)
(stk.cof.NonLinearVertex method)
(stk.cof.UnaligningVertex method)
(stk.Cr method)
(stk.Cs method)
(stk.Cu method)
(stk.Db method)
(stk.Ds method)
(stk.Dy method)
(stk.Edge method)
(stk.Er method)
(stk.Es method)
(stk.Eu method)
(stk.F method)
(stk.Fe method)
(stk.Fl method)
(stk.Fm method)
(stk.Fr method)
(stk.Ga method)
(stk.Gd method)
(stk.Ge method)
(stk.H method)
(stk.He method)
(stk.Hf method)
(stk.Hg method)
(stk.Ho method)
(stk.host_guest.GuestVertex method)
(stk.host_guest.HostVertex method)
(stk.Hs method)
(stk.I method)
(stk.In method)
(stk.Ir method)
(stk.K method)
(stk.Kr method)
(stk.La method)
(stk.Li method)
(stk.Lr method)
(stk.Lu method)
(stk.Lv method)
(stk.macrocycle.CycleVertex method)
(stk.Mc method)
(stk.Md method)
(stk.metal_complex.BiDentateLigandVertex method)
(stk.metal_complex.MetalVertex method)
(stk.metal_complex.MonoDentateLigandVertex method)
(stk.Mg method)
(stk.Mn method)
(stk.Mo method)
(stk.Mt method)
(stk.N method)
(stk.Na method)
(stk.Nb method)
(stk.Nd method)
(stk.Ne method)
(stk.Nh method)
(stk.Ni method)
(stk.No method)
(stk.Np method)
(stk.O method)
(stk.Og method)
(stk.Os method)
(stk.P method)
(stk.Pa method)
(stk.Pb method)
(stk.Pd method)
(stk.Pm method)
(stk.Po method)
(stk.polymer.HeadVertex method)
(stk.polymer.LinearVertex method)
(stk.polymer.TailVertex method)
(stk.polymer.TerminalVertex method)
(stk.polymer.UnaligningVertex method)
(stk.Pr method)
(stk.Pt method)
(stk.Pu method)
(stk.Ra method)
(stk.Rb method)
(stk.Re method)
(stk.Rf method)
(stk.Rg method)
(stk.Rh method)
(stk.Rn method)
(stk.rotaxane.AxleVertex method)
(stk.rotaxane.CycleVertex method)
(stk.Ru method)
(stk.S method)
(stk.Sb method)
(stk.Sc method)
(stk.Se method)
(stk.Sg method)
(stk.Si method)
(stk.Sm method)
(stk.small.CoreVertex method)
(stk.small.SubstituentVertex method)
(stk.Sn method)
(stk.Sr method)
(stk.Ta method)
(stk.Tb method)
(stk.Tc method)
(stk.Te method)
(stk.Th method)
(stk.Ti method)
(stk.Tl method)
(stk.Tm method)
(stk.Ts method)
(stk.U method)
(stk.V method)
(stk.Vertex method)
(stk.W method)
(stk.Xe method)
(stk.Y method)
(stk.Yb method)
(stk.Zn method)
(stk.Zr method)
get_identity_key() (stk.Batch method)
get_iodine() (stk.Iodo method)
get_key() (stk.Inchi method)
(stk.InchiKey method)
(stk.MoleculeKeyMaker method)
(stk.Smiles method)
get_key_name() (stk.Inchi method)
(stk.InchiKey method)
(stk.MoleculeKeyMaker method)
(stk.Smiles method)
get_lattice_constants() (stk.ConstructionState method)
(stk.GraphState method)
get_maximum_diameter() (stk.BuildingBlock method)
(stk.ConstructedMolecule method)
(stk.Molecule method)
get_molecule() (stk.MoleculeRecord method)
get_molecule_record() (stk.CrossoverRecord method)
(stk.MutationRecord method)
get_molecule_records() (stk.Generation method)
get_mutation_records() (stk.Generation method)
get_mutator_name() (stk.MutationRecord method)
get_new_atoms() (stk.ReactionResult method)
get_new_bonds() (stk.ReactionResult method)
get_nitrogen() (stk.Amide method)
(stk.PrimaryAmino method)
(stk.RingAmine method)
(stk.SecondaryAmino method)
get_num_atoms() (stk.BuildingBlock method)
(stk.ConstructedMolecule method)
(stk.Molecule method)
get_num_bonders() (stk.Alcohol method)
(stk.Aldehyde method)
(stk.Alkene method)
(stk.Alkyne method)
(stk.Amide method)
(stk.BoronicAcid method)
(stk.Bromo method)
(stk.CarboxylicAcid method)
(stk.Dibromo method)
(stk.Difluoro method)
(stk.Diol method)
(stk.Fluoro method)
(stk.GenericFunctionalGroup method)
(stk.Iodo method)
(stk.PrimaryAmino method)
(stk.SecondaryAmino method)
(stk.SingleAtom method)
(stk.Thioacid method)
(stk.Thiol method)
get_num_bonds() (stk.BuildingBlock method)
(stk.ConstructedMolecule method)
(stk.Molecule method)
get_num_building_block() (stk.cage.Cage method)
(stk.cage.EightPlusSixteen method)
(stk.cage.EightPlusTwelve method)
(stk.cage.FivePlusTen method)
(stk.cage.FourPlusEight method)
(stk.cage.FourPlusFour method)
(stk.cage.FourPlusSix method)
(stk.cage.FourPlusSix2 method)
(stk.cage.M12L24 method)
(stk.cage.M24L48 method)
(stk.cage.M2L4Lantern method)
(stk.cage.M3L3Triangle method)
(stk.cage.M3L6 method)
(stk.cage.M4L4Square method)
(stk.cage.M4L4Tetrahedron method)
(stk.cage.M4L6Tetrahedron method)
(stk.cage.M4L6TetrahedronSpacer method)
(stk.cage.M4L8 method)
(stk.cage.M6L12Cube method)
(stk.cage.M6L2L3Prism method)
(stk.cage.M8L6Cube method)
(stk.cage.OnePlusOne method)
(stk.cage.SixPlusEight method)
(stk.cage.SixPlusNine method)
(stk.cage.SixPlusTwelve method)
(stk.cage.TenPlusTwenty method)
(stk.cage.ThreePlusSix method)
(stk.cage.TwelvePlusThirty method)
(stk.cage.TwentyPlusThirty method)
(stk.cage.TwoPlusFour method)
(stk.cage.TwoPlusThree method)
(stk.cage.TwoPlusTwo method)
(stk.cof.Cof method)
(stk.cof.Hexagonal method)
(stk.cof.Honeycomb method)
(stk.cof.Kagome method)
(stk.cof.LinkerlessHoneycomb method)
(stk.cof.PeriodicHexagonal method)
(stk.cof.PeriodicHoneycomb method)
(stk.cof.PeriodicKagome method)
(stk.cof.PeriodicLinkerlessHoneycomb method)
(stk.cof.PeriodicSquare method)
(stk.cof.Square method)
(stk.ConstructedMolecule method)
(stk.ConstructionResult method)
(stk.ConstructionState method)
(stk.GraphState method)
(stk.host_guest.Complex method)
(stk.macrocycle.Macrocycle method)
(stk.metal_complex.BidentateSquarePlanar method)
(stk.metal_complex.CisProtectedSquarePlanar method)
(stk.metal_complex.MetalComplex method)
(stk.metal_complex.Octahedral method)
(stk.metal_complex.OctahedralDelta method)
(stk.metal_complex.OctahedralLambda method)
(stk.metal_complex.Paddlewheel method)
(stk.metal_complex.Porphyrin method)
(stk.metal_complex.SquarePlanar method)
(stk.polymer.Linear method)
(stk.rotaxane.NRotaxane method)
(stk.small.NCore method)
(stk.TopologyGraph method)
get_num_edges() (stk.ConstructionState method)
(stk.GraphState method)
get_num_functional_groups() (stk.BuildingBlock method)
get_num_placers() (stk.BuildingBlock method)
get_num_vertices() (stk.ConstructionState method)
(stk.GraphState method)
get_order() (stk.Bond method)
get_oxygen() (stk.Alcohol method)
(stk.Aldehyde method)
(stk.Amide method)
(stk.Thioacid method)
get_oxygen1() (stk.BoronicAcid method)
(stk.CarboxylicAcid method)
(stk.Diol method)
get_oxygen2() (stk.BoronicAcid method)
(stk.CarboxylicAcid method)
(stk.Diol method)
get_periodicity() (stk.Bond method)
(stk.Edge method)
get_placer_ids() (stk.Alcohol method)
(stk.Aldehyde method)
(stk.Alkene method)
(stk.Alkyne method)
(stk.Amide method)
(stk.BoronicAcid method)
(stk.Bromo method)
(stk.BuildingBlock method)
(stk.CarboxylicAcid method)
(stk.Dibromo method)
(stk.Difluoro method)
(stk.Diol method)
(stk.Fluoro method)
(stk.FunctionalGroup method)
(stk.GenericFunctionalGroup method)
(stk.Iodo method)
(stk.PrimaryAmino method)
(stk.RingAmine method)
(stk.SecondaryAmino method)
(stk.SingleAtom method)
(stk.Thioacid method)
(stk.Thiol method)
get_plane_normal() (stk.BuildingBlock method)
(stk.ConstructedMolecule method)
(stk.Molecule method)
get_plot_data() (stk.ProgressPlotter method)
get_position() (stk.cage.AngledVertex method)
(stk.cage.LinearVertex method)
(stk.cage.NonLinearVertex method)
(stk.cage.UnaligningVertex method)
(stk.cof.LinearVertex method)
(stk.cof.NonLinearVertex method)
(stk.cof.UnaligningVertex method)
(stk.Edge method)
(stk.host_guest.GuestVertex method)
(stk.host_guest.HostVertex method)
(stk.macrocycle.CycleVertex method)
(stk.metal_complex.BiDentateLigandVertex method)
(stk.metal_complex.MetalVertex method)
(stk.metal_complex.MonoDentateLigandVertex method)
(stk.polymer.HeadVertex method)
(stk.polymer.LinearVertex method)
(stk.polymer.TailVertex method)
(stk.polymer.TerminalVertex method)
(stk.polymer.UnaligningVertex method)
(stk.rotaxane.AxleVertex method)
(stk.rotaxane.CycleVertex method)
(stk.small.CoreVertex method)
(stk.small.SubstituentVertex method)
(stk.Vertex method)
get_position_matrix() (stk.BuildingBlock method)
(stk.ConstructedMolecule method)
(stk.ConstructionResult method)
(stk.ConstructionState method)
(stk.Molecule method)
(stk.MoleculeState method)
get_reaction() (stk.DativeReactionFactory method)
(stk.GenericReactionFactory method)
(stk.ReactionFactory method)
get_result() (stk.DativeReaction method)
(stk.OneOneReaction method)
(stk.OneTwoReaction method)
(stk.Reaction method)
(stk.RingAmineReaction method)
(stk.TwoTwoReaction method)
get_size() (stk.Batch method)
get_start_vector() (stk.host_guest.Guest method)
get_sulfur() (stk.Thioacid method)
(stk.Thiol method)
get_topology_graph() (stk.MoleculeRecord method)
get_vector_1() (stk.PeriodicInfo method)
get_vector_2() (stk.PeriodicInfo method)
get_vector_3() (stk.PeriodicInfo method)
get_vertex1_id() (stk.Edge method)
get_vertex2_id() (stk.Edge method)
get_vertex_alignments() (stk.cage.Cage method)
(stk.cage.EightPlusSixteen method)
(stk.cage.EightPlusTwelve method)
(stk.cage.FivePlusTen method)
(stk.cage.FourPlusEight method)
(stk.cage.FourPlusFour method)
(stk.cage.FourPlusSix method)
(stk.cage.FourPlusSix2 method)
(stk.cage.M12L24 method)
(stk.cage.M24L48 method)
(stk.cage.M2L4Lantern method)
(stk.cage.M3L3Triangle method)
(stk.cage.M3L6 method)
(stk.cage.M4L4Square method)
(stk.cage.M4L4Tetrahedron method)
(stk.cage.M4L6Tetrahedron method)
(stk.cage.M4L6TetrahedronSpacer method)
(stk.cage.M4L8 method)
(stk.cage.M6L12Cube method)
(stk.cage.M6L2L3Prism method)
(stk.cage.M8L6Cube method)
(stk.cage.OnePlusOne method)
(stk.cage.SixPlusEight method)
(stk.cage.SixPlusNine method)
(stk.cage.SixPlusTwelve method)
(stk.cage.TenPlusTwenty method)
(stk.cage.ThreePlusSix method)
(stk.cage.TwelvePlusThirty method)
(stk.cage.TwentyPlusThirty method)
(stk.cage.TwoPlusFour method)
(stk.cage.TwoPlusThree method)
(stk.cage.TwoPlusTwo method)
get_vertex_ids() (stk.Edge method)
get_vertices() (stk.ConstructionState method)
(stk.GraphState method)
GraphState (class in stk)
Guest (class in stk.host_guest)
GuestVertex (class in stk.host_guest)
H
H (class in stk)
He (class in stk)
HeadVertex (class in stk.polymer)
Hexagonal (class in stk.cof)
Hf (class in stk)
Hg (class in stk)
Ho (class in stk)
Honeycomb (class in stk.cof)
HostVertex (class in stk.host_guest)
Hs (class in stk)
I
I (class in stk)
In (class in stk)
Inchi (class in stk)
InchiKey (class in stk)
init() (stk.BuildingBlock class method)
(stk.ConstructedMolecule class method)
init_at_center() (stk.cage.AngledVertex class method)
(stk.cage.LinearVertex class method)
(stk.cage.NonLinearVertex class method)
(stk.cage.UnaligningVertex class method)
(stk.cof.LinearVertex class method)
(stk.cof.NonLinearVertex class method)
(stk.cof.UnaligningVertex class method)
init_at_shifted_center() (stk.cof.LinearVertex class method)
(stk.cof.NonLinearVertex class method)
(stk.cof.UnaligningVertex class method)
init_from_construction_result() (stk.ConstructedMolecule class method)
init_from_file() (stk.BuildingBlock class method)
init_from_molecule() (stk.BuildingBlock class method)
init_from_rdkit_mol() (stk.BuildingBlock class method)
init_from_vabene_molecule() (stk.BuildingBlock class method)
Iodo (class in stk)
IodoFactory (class in stk)
Ir (class in stk)
is_periodic() (stk.Bond method)
(stk.Edge method)
K
K (class in stk)
Kagome (class in stk.cof)
Kr (class in stk)
L
La (class in stk)
Li (class in stk)
Linear (class in stk.polymer)
LinearVertex (class in stk.cage)
(class in stk.cof)
(class in stk.polymer)
LinkerlessHoneycomb (class in stk.cof)
Lr (class in stk)
Lu (class in stk)
Lv (class in stk)
M
M12L24 (class in stk.cage)
M24L48 (class in stk.cage)
M2L4Lantern (class in stk.cage)
M3L3Triangle (class in stk.cage)
M3L6 (class in stk.cage)
M4L4Square (class in stk.cage)
M4L4Tetrahedron (class in stk.cage)
M4L6Tetrahedron (class in stk.cage)
M4L6TetrahedronSpacer (class in stk.cage)
M4L8 (class in stk.cage)
M6L12Cube (class in stk.cage)
M6L2L3Prism (class in stk.cage)
M8L6Cube (class in stk.cage)
Macrocycle (class in stk.macrocycle)
map_functional_groups_to_edges() (stk.cage.AngledVertex method)
(stk.cage.LinearVertex method)
(stk.cage.NonLinearVertex method)
(stk.cage.UnaligningVertex method)
(stk.cof.LinearVertex method)
(stk.cof.NonLinearVertex method)
(stk.cof.UnaligningVertex method)
(stk.host_guest.GuestVertex method)
(stk.host_guest.HostVertex method)
(stk.macrocycle.CycleVertex method)
(stk.metal_complex.BiDentateLigandVertex method)
(stk.metal_complex.MetalVertex method)
(stk.metal_complex.MonoDentateLigandVertex method)
(stk.polymer.HeadVertex method)
(stk.polymer.LinearVertex method)
(stk.polymer.TailVertex method)
(stk.polymer.TerminalVertex method)
(stk.polymer.UnaligningVertex method)
(stk.rotaxane.AxleVertex method)
(stk.rotaxane.CycleVertex method)
(stk.small.CoreVertex method)
(stk.small.SubstituentVertex method)
(stk.Vertex method)
Mc (class in stk)
MCHammer (class in stk)
Md (class in stk)
MetalComplex (class in stk.metal_complex)
MetalVertex (class in stk.metal_complex)
Mg (class in stk)
Mn (class in stk)
Mo (class in stk)
module
stk
stk.cage
stk.cof
stk.host_guest
stk.macrocycle
stk.metal_complex
stk.polymer
stk.rotaxane
stk.small
Molecule (class in stk)
MoleculeCrosser (class in stk)
MoleculeDatabase (class in stk)
MoleculeDejsonizer (class in stk)
MoleculeJsonizer (class in stk)
MoleculeKeyMaker (class in stk)
MoleculeMongoDb (class in stk)
MoleculeMutator (class in stk)
MoleculeRecord (class in stk)
MoleculeState (class in stk)
MolWriter (class in stk)
MonoDentateLigandVertex (class in stk.metal_complex)
Mt (class in stk)
Multiply (class in stk)
mutate() (stk.MoleculeMutator method)
(stk.RandomBuildingBlock method)
(stk.RandomMutator method)
(stk.RandomTopologyGraph method)
(stk.SimilarBuildingBlock method)
MutationRecord (class in stk)
N
N (class in stk)
Na (class in stk)
Nb (class in stk)
NCore (class in stk.small)
Nd (class in stk)
Ne (class in stk)
Nh (class in stk)
Ni (class in stk)
No (class in stk)
NonLinearVertex (class in stk.cage)
(class in stk.cof)
normalize() (stk.Add method)
(stk.DivideByMean method)
(stk.FitnessNormalizer method)
(stk.Multiply method)
(stk.NormalizerSequence method)
(stk.NullFitnessNormalizer method)
(stk.Power method)
(stk.ReplaceFitness method)
(stk.ShiftUp method)
(stk.Sum method)
normalize_vector() (in module stk)
normalized (stk.FitnessValues attribute)
NormalizerSequence (class in stk)
Np (class in stk)
NRotaxane (class in stk.rotaxane)
NullFitnessNormalizer (class in stk)
NullOptimizer (class in stk)
O
O (class in stk)
Octahedral (class in stk.metal_complex)
OctahedralDelta (class in stk.metal_complex)
OctahedralLambda (class in stk.metal_complex)
Og (class in stk)
OneOneReaction (class in stk)
OnePlusOne (class in stk.cage)
OneTwoReaction (class in stk)
optimize() (stk.Collapser method)
(stk.MCHammer method)
(stk.NullOptimizer method)
(stk.Optimizer method)
(stk.PeriodicCollapser method)
(stk.Spinner method)
Optimizer (class in stk)
Os (class in stk)
P
P (class in stk)
Pa (class in stk)
Paddlewheel (class in stk.metal_complex)
Pb (class in stk)
Pd (class in stk)
PdbWriter (class in stk)
PeriodicCollapser (class in stk)
PeriodicHexagonal (class in stk.cof)
PeriodicHoneycomb (class in stk.cof)
PeriodicInfo (class in stk)
PeriodicKagome (class in stk.cof)
PeriodicLinkerlessHoneycomb (class in stk.cof)
PeriodicSquare (class in stk.cof)
place_building_block() (stk.cage.AngledVertex method)
(stk.cage.LinearVertex method)
(stk.cage.NonLinearVertex method)
(stk.cage.UnaligningVertex method)
(stk.cof.LinearVertex method)
(stk.cof.NonLinearVertex method)
(stk.cof.UnaligningVertex method)
(stk.host_guest.GuestVertex method)
(stk.host_guest.HostVertex method)
(stk.macrocycle.CycleVertex method)
(stk.metal_complex.BiDentateLigandVertex method)
(stk.metal_complex.MetalVertex method)
(stk.metal_complex.MonoDentateLigandVertex method)
(stk.polymer.HeadVertex method)
(stk.polymer.LinearVertex method)
(stk.polymer.TailVertex method)
(stk.polymer.TerminalVertex method)
(stk.polymer.UnaligningVertex method)
(stk.rotaxane.AxleVertex method)
(stk.rotaxane.CycleVertex method)
(stk.small.CoreVertex method)
(stk.small.SubstituentVertex method)
(stk.Vertex method)
Pm (class in stk)
Po (class in stk)
Porphyrin (class in stk.metal_complex)
Power (class in stk)
Pr (class in stk)
PrimaryAmino (class in stk)
PrimaryAminoFactory (class in stk)
ProgressPlotter (class in stk)
PropertyVector (class in stk)
Pt (class in stk)
Pu (class in stk)
put() (stk.ConstructedMoleculeDatabase method)
(stk.ConstructedMoleculeMongoDb method)
(stk.MoleculeDatabase method)
(stk.MoleculeMongoDb method)
(stk.ValueDatabase method)
(stk.ValueMongoDb method)
R
Ra (class in stk)
RandomBuildingBlock (class in stk)
RandomCrosser (class in stk)
RandomMutator (class in stk)
RandomTopologyGraph (class in stk)
raw (stk.FitnessValues attribute)
Rb (class in stk)
Re (class in stk)
Reaction (class in stk)
ReactionFactory (class in stk)
ReactionResult (class in stk)
RemoveBatches (class in stk)
RemoveMolecules (class in stk)
ReplaceFitness (class in stk)
Rf (class in stk)
Rg (class in stk)
Rh (class in stk)
RingAmine (class in stk)
RingAmineFactory (class in stk)
RingAmineReaction (class in stk)
Rn (class in stk)
rotation_matrix_arbitrary_axis() (in module stk)
Roulette (class in stk)
Ru (class in stk)
S
S (class in stk)
Sb (class in stk)
Sc (class in stk)
Se (class in stk)
SecondaryAmino (class in stk)
SecondaryAminoFactory (class in stk)
select() (stk.AboveAverage method)
(stk.Best method)
(stk.FilterBatches method)
(stk.FilterMolecules method)
(stk.RemoveBatches method)
(stk.RemoveMolecules method)
(stk.Roulette method)
(stk.Selector method)
(stk.StochasticUniversalSampling method)
(stk.Tournament method)
(stk.Worst method)
SelectionPlotter (class in stk)
Selector (class in stk)
Sg (class in stk)
ShiftUp (class in stk)
Si (class in stk)
SimilarBuildingBlock (class in stk)
SingleAtom (class in stk)
SixPlusEight (class in stk.cage)
SixPlusNine (class in stk.cage)
SixPlusTwelve (class in stk.cage)
Sm (class in stk)
SmartsFunctionalGroupFactory (class in stk)
Smiles (class in stk)
Sn (class in stk)
Spinner (class in stk)
Square (class in stk.cof)
SquarePlanar (class in stk.metal_complex)
Sr (class in stk)
stk
module
stk.cage
module
stk.cof
module
stk.host_guest
module
stk.macrocycle
module
stk.metal_complex
module
stk.polymer
module
stk.rotaxane
module
stk.small
module
StochasticUniversalSampling (class in stk)
SubstituentVertex (class in stk.small)
Sum (class in stk)
T
Ta (class in stk)
TailVertex (class in stk.polymer)
Tb (class in stk)
Tc (class in stk)
Te (class in stk)
TenPlusTwenty (class in stk.cage)
TerminalAlkeneFactory (class in stk)
TerminalAlkyneFactory (class in stk)
TerminalVertex (class in stk.polymer)
Th (class in stk)
Thioacid (class in stk)
ThioacidFactory (class in stk)
Thiol (class in stk)
ThiolFactory (class in stk)
ThreePlusSix (class in stk.cage)
Ti (class in stk)
Tl (class in stk)
Tm (class in stk)
to_json() (stk.ConstructedMoleculeJsonizer method)
(stk.MoleculeJsonizer method)
to_rdkit_mol() (stk.BuildingBlock method)
(stk.ConstructedMolecule method)
(stk.Molecule method)
to_string() (stk.MolWriter method)
(stk.PdbWriter method)
(stk.TurbomoleWriter method)
(stk.XyzWriter method)
TopologyGraph (class in stk)
Tournament (class in stk)
Ts (class in stk)
TurbomoleWriter (class in stk)
TwelvePlusThirty (class in stk.cage)
TwentyPlusThirty (class in stk.cage)
TwoPlusFour (class in stk.cage)
TwoPlusThree (class in stk.cage)
TwoPlusTwo (class in stk.cage)
TwoTwoReaction (class in stk)
U
U (class in stk)
UnaligningVertex (class in stk.cage)
(class in stk.cof)
(class in stk.polymer)
use_neighbor_placement() (stk.cage.AngledVertex method)
(stk.cage.LinearVertex method)
(stk.cage.NonLinearVertex method)
(stk.cage.UnaligningVertex method)
V
V (class in stk)
ValueDatabase (class in stk)
ValueMongoDb (class in stk)
vector_angle() (in module stk)
Vertex (class in stk)
W
W (class in stk)
with_aligner_edge() (stk.cage.AngledVertex method)
(stk.cage.LinearVertex method)
(stk.cage.NonLinearVertex method)
(stk.cage.UnaligningVertex method)
with_atoms() (stk.Alcohol method)
(stk.Aldehyde method)
(stk.Alkene method)
(stk.Alkyne method)
(stk.Amide method)
(stk.Bond method)
(stk.BoronicAcid method)
(stk.Bromo method)
(stk.CarboxylicAcid method)
(stk.Dibromo method)
(stk.Difluoro method)
(stk.Diol method)
(stk.Fluoro method)
(stk.FunctionalGroup method)
(stk.GenericFunctionalGroup method)
(stk.Iodo method)
(stk.PrimaryAmino method)
(stk.RingAmine method)
(stk.SecondaryAmino method)
(stk.SingleAtom method)
(stk.Thioacid method)
(stk.Thiol method)
with_building_blocks() (stk.cage.Cage method)
(stk.cage.EightPlusSixteen method)
(stk.cage.EightPlusTwelve method)
(stk.cage.FivePlusTen method)
(stk.cage.FourPlusEight method)
(stk.cage.FourPlusFour method)
(stk.cage.FourPlusSix method)
(stk.cage.FourPlusSix2 method)
(stk.cage.M12L24 method)
(stk.cage.M24L48 method)
(stk.cage.M2L4Lantern method)
(stk.cage.M3L3Triangle method)
(stk.cage.M3L6 method)
(stk.cage.M4L4Square method)
(stk.cage.M4L4Tetrahedron method)
(stk.cage.M4L6Tetrahedron method)
(stk.cage.M4L6TetrahedronSpacer method)
(stk.cage.M4L8 method)
(stk.cage.M6L12Cube method)
(stk.cage.M6L2L3Prism method)
(stk.cage.M8L6Cube method)
(stk.cage.OnePlusOne method)
(stk.cage.SixPlusEight method)
(stk.cage.SixPlusNine method)
(stk.cage.SixPlusTwelve method)
(stk.cage.TenPlusTwenty method)
(stk.cage.ThreePlusSix method)
(stk.cage.TwelvePlusThirty method)
(stk.cage.TwentyPlusThirty method)
(stk.cage.TwoPlusFour method)
(stk.cage.TwoPlusThree method)
(stk.cage.TwoPlusTwo method)
(stk.cof.Cof method)
(stk.cof.Hexagonal method)
(stk.cof.Honeycomb method)
(stk.cof.Kagome method)
(stk.cof.LinkerlessHoneycomb method)
(stk.cof.PeriodicHexagonal method)
(stk.cof.PeriodicHoneycomb method)
(stk.cof.PeriodicKagome method)
(stk.cof.PeriodicLinkerlessHoneycomb method)
(stk.cof.PeriodicSquare method)
(stk.cof.Square method)
(stk.host_guest.Complex method)
(stk.macrocycle.Macrocycle method)
(stk.metal_complex.BidentateSquarePlanar method)
(stk.metal_complex.CisProtectedSquarePlanar method)
(stk.metal_complex.MetalComplex method)
(stk.metal_complex.Octahedral method)
(stk.metal_complex.OctahedralDelta method)
(stk.metal_complex.OctahedralLambda method)
(stk.metal_complex.Paddlewheel method)
(stk.metal_complex.Porphyrin method)
(stk.metal_complex.SquarePlanar method)
(stk.polymer.Linear method)
(stk.rotaxane.NRotaxane method)
(stk.small.NCore method)
(stk.TopologyGraph method)
with_canonical_atom_ordering() (stk.BuildingBlock method)
(stk.ConstructedMolecule method)
(stk.Molecule method)
with_centroid() (stk.BuildingBlock method)
(stk.ConstructedMolecule method)
(stk.Molecule method)
with_displacement() (stk.BuildingBlock method)
(stk.ConstructedMolecule method)
(stk.Molecule method)
with_functional_groups() (stk.BuildingBlock method)
with_id() (stk.Ac method)
(stk.Ag method)
(stk.Al method)
(stk.Am method)
(stk.Ar method)
(stk.As method)
(stk.At method)
(stk.Atom method)
(stk.Au method)
(stk.B method)
(stk.Ba method)
(stk.Be method)
(stk.Bh method)
(stk.Bi method)
(stk.Bk method)
(stk.Br method)
(stk.C method)
(stk.Ca method)
(stk.Cd method)
(stk.Ce method)
(stk.Cf method)
(stk.Cl method)
(stk.Cm method)
(stk.Cn method)
(stk.Co method)
(stk.Cr method)
(stk.Cs method)
(stk.Cu method)
(stk.Db method)
(stk.Ds method)
(stk.Dy method)
(stk.Er method)
(stk.Es method)
(stk.Eu method)
(stk.F method)
(stk.Fe method)
(stk.Fl method)
(stk.Fm method)
(stk.Fr method)
(stk.Ga method)
(stk.Gd method)
(stk.Ge method)
(stk.H method)
(stk.He method)
(stk.Hf method)
(stk.Hg method)
(stk.Ho method)
(stk.Hs method)
(stk.I method)
(stk.In method)
(stk.Ir method)
(stk.K method)
(stk.Kr method)
(stk.La method)
(stk.Li method)
(stk.Lr method)
(stk.Lu method)
(stk.Lv method)
(stk.Mc method)
(stk.Md method)
(stk.Mg method)
(stk.Mn method)
(stk.Mo method)
(stk.Mt method)
(stk.N method)
(stk.Na method)
(stk.Nb method)
(stk.Nd method)
(stk.Ne method)
(stk.Nh method)
(stk.Ni method)
(stk.No method)
(stk.Np method)
(stk.O method)
(stk.Og method)
(stk.Os method)
(stk.P method)
(stk.Pa method)
(stk.Pb method)
(stk.Pd method)
(stk.Pm method)
(stk.Po method)
(stk.Pr method)
(stk.Pt method)
(stk.Pu method)
(stk.Ra method)
(stk.Rb method)
(stk.Re method)
(stk.Rf method)
(stk.Rg method)
(stk.Rh method)
(stk.Rn method)
(stk.Ru method)
(stk.S method)
(stk.Sb method)
(stk.Sc method)
(stk.Se method)
(stk.Sg method)
(stk.Si method)
(stk.Sm method)
(stk.Sn method)
(stk.Sr method)
(stk.Ta method)
(stk.Tb method)
(stk.Tc method)
(stk.Te method)
(stk.Th method)
(stk.Ti method)
(stk.Tl method)
(stk.Tm method)
(stk.Ts method)
(stk.U method)
(stk.V method)
(stk.W method)
(stk.Xe method)
(stk.Y method)
(stk.Yb method)
(stk.Zn method)
(stk.Zr method)
with_ids() (stk.Alcohol method)
(stk.Aldehyde method)
(stk.Alkene method)
(stk.Alkyne method)
(stk.Amide method)
(stk.Bond method)
(stk.BoronicAcid method)
(stk.Bromo method)
(stk.CarboxylicAcid method)
(stk.Dibromo method)
(stk.Difluoro method)
(stk.Diol method)
(stk.Fluoro method)
(stk.FunctionalGroup method)
(stk.GenericFunctionalGroup method)
(stk.Iodo method)
(stk.PrimaryAmino method)
(stk.RingAmine method)
(stk.SecondaryAmino method)
(stk.SingleAtom method)
(stk.Thioacid method)
(stk.Thiol method)
with_lattice_constants() (stk.ConstructionState method)
(stk.GraphState method)
with_placement_results() (stk.ConstructionState method)
(stk.MoleculeState method)
with_position() (stk.cage.AngledVertex method)
(stk.cage.LinearVertex method)
(stk.cage.NonLinearVertex method)
(stk.cage.UnaligningVertex method)
(stk.cof.LinearVertex method)
(stk.cof.NonLinearVertex method)
(stk.cof.UnaligningVertex method)
(stk.Edge method)
(stk.host_guest.GuestVertex method)
(stk.host_guest.HostVertex method)
(stk.macrocycle.CycleVertex method)
(stk.metal_complex.BiDentateLigandVertex method)
(stk.metal_complex.MetalVertex method)
(stk.metal_complex.MonoDentateLigandVertex method)
(stk.polymer.HeadVertex method)
(stk.polymer.LinearVertex method)
(stk.polymer.TailVertex method)
(stk.polymer.TerminalVertex method)
(stk.polymer.UnaligningVertex method)
(stk.rotaxane.AxleVertex method)
(stk.rotaxane.CycleVertex method)
(stk.small.CoreVertex method)
(stk.small.SubstituentVertex method)
(stk.Vertex method)
with_position_matrix() (stk.BuildingBlock method)
(stk.ConstructedMolecule method)
(stk.ConstructionState method)
(stk.Molecule method)
(stk.MoleculeState method)
with_reaction_results() (stk.ConstructionState method)
(stk.MoleculeState method)
with_rotation_about_axis() (stk.BuildingBlock method)
(stk.ConstructedMolecule method)
(stk.Molecule method)
with_rotation_between_vectors() (stk.BuildingBlock method)
(stk.ConstructedMolecule method)
(stk.Molecule method)
with_rotation_to_minimize_angle() (stk.BuildingBlock method)
(stk.ConstructedMolecule method)
(stk.Molecule method)
with_scale() (stk.cage.AngledVertex method)
(stk.cage.LinearVertex method)
(stk.cage.NonLinearVertex method)
(stk.cage.UnaligningVertex method)
(stk.cof.LinearVertex method)
(stk.cof.NonLinearVertex method)
(stk.cof.UnaligningVertex method)
(stk.Edge method)
(stk.host_guest.GuestVertex method)
(stk.host_guest.HostVertex method)
(stk.macrocycle.CycleVertex method)
(stk.metal_complex.BiDentateLigandVertex method)
(stk.metal_complex.MetalVertex method)
(stk.metal_complex.MonoDentateLigandVertex method)
(stk.polymer.HeadVertex method)
(stk.polymer.LinearVertex method)
(stk.polymer.TailVertex method)
(stk.polymer.TerminalVertex method)
(stk.polymer.UnaligningVertex method)
(stk.rotaxane.AxleVertex method)
(stk.rotaxane.CycleVertex method)
(stk.small.CoreVertex method)
(stk.small.SubstituentVertex method)
(stk.Vertex method)
with_structure_from_file() (stk.BuildingBlock method)
(stk.ConstructedMolecule method)
(stk.Molecule method)
with_use_neighbor_placement() (stk.cage.AngledVertex method)
(stk.cage.LinearVertex method)
(stk.cage.NonLinearVertex method)
(stk.cage.UnaligningVertex method)
with_vertices() (stk.ConstructionState method)
(stk.GraphState method)
Worst (class in stk)
write() (stk.BuildingBlock method)
(stk.ConstructedMolecule method)
(stk.Molecule method)
(stk.MolWriter method)
(stk.PdbWriter method)
(stk.ProgressPlotter method)
(stk.TurbomoleWriter method)
(stk.XyzWriter method)
X
Xe (class in stk)
XyzWriter (class in stk)
Y
Y (class in stk)
Yb (class in stk)
Z
Zn (class in stk)
Zr (class in stk)
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