stk
Molecules
BuildingBlock
BuildingBlock.__init__()
BuildingBlock.clone()
BuildingBlock.get_atomic_positions()
BuildingBlock.get_atoms()
BuildingBlock.get_bonds()
BuildingBlock.get_canonical_atom_ids()
BuildingBlock.get_centroid()
BuildingBlock.get_core_atom_ids()
BuildingBlock.get_direction()
BuildingBlock.get_functional_groups()
BuildingBlock.get_maximum_diameter()
BuildingBlock.get_num_atoms()
BuildingBlock.get_num_bonds()
BuildingBlock.get_num_functional_groups()
BuildingBlock.get_num_placers()
BuildingBlock.get_placer_ids()
BuildingBlock.get_plane_normal()
BuildingBlock.get_position_matrix()
BuildingBlock.init()
BuildingBlock.init_from_file()
BuildingBlock.init_from_molecule()
BuildingBlock.init_from_rdkit_mol()
BuildingBlock.init_from_vabene_molecule()
BuildingBlock.to_rdkit_mol()
BuildingBlock.with_canonical_atom_ordering()
BuildingBlock.with_centroid()
BuildingBlock.with_displacement()
BuildingBlock.with_functional_groups()
BuildingBlock.with_position_matrix()
BuildingBlock.with_rotation_about_axis()
BuildingBlock.with_rotation_between_vectors()
BuildingBlock.with_rotation_to_minimize_angle()
BuildingBlock.with_structure_from_file()
BuildingBlock.write()
ConstructedMolecule
ConstructedMolecule.__init__()
ConstructedMolecule.clone()
ConstructedMolecule.get_atom_infos()
ConstructedMolecule.get_atomic_positions()
ConstructedMolecule.get_atoms()
ConstructedMolecule.get_bond_infos()
ConstructedMolecule.get_bonds()
ConstructedMolecule.get_building_blocks()
ConstructedMolecule.get_canonical_atom_ids()
ConstructedMolecule.get_centroid()
ConstructedMolecule.get_direction()
ConstructedMolecule.get_maximum_diameter()
ConstructedMolecule.get_num_atoms()
ConstructedMolecule.get_num_bonds()
ConstructedMolecule.get_num_building_block()
ConstructedMolecule.get_plane_normal()
ConstructedMolecule.get_position_matrix()
ConstructedMolecule.init()
ConstructedMolecule.init_from_construction_result()
ConstructedMolecule.to_rdkit_mol()
ConstructedMolecule.with_canonical_atom_ordering()
ConstructedMolecule.with_centroid()
ConstructedMolecule.with_displacement()
ConstructedMolecule.with_position_matrix()
ConstructedMolecule.with_rotation_about_axis()
ConstructedMolecule.with_rotation_between_vectors()
ConstructedMolecule.with_rotation_to_minimize_angle()
ConstructedMolecule.with_structure_from_file()
ConstructedMolecule.write()
Alcohol
Alcohol.__init__()
Alcohol.clone()
Alcohol.get_atom()
Alcohol.get_atom_ids()
Alcohol.get_atoms()
Alcohol.get_bonder_ids()
Alcohol.get_bonders()
Alcohol.get_core_atom_ids()
Alcohol.get_deleter_ids()
Alcohol.get_deleters()
Alcohol.get_hydrogen()
Alcohol.get_num_bonders()
Alcohol.get_oxygen()
Alcohol.get_placer_ids()
Alcohol.with_atoms()
Alcohol.with_ids()
Aldehyde
Aldehyde.__init__()
Aldehyde.clone()
Aldehyde.get_atom()
Aldehyde.get_atom_ids()
Aldehyde.get_atoms()
Aldehyde.get_bonder_ids()
Aldehyde.get_bonders()
Aldehyde.get_carbon()
Aldehyde.get_core_atom_ids()
Aldehyde.get_deleter_ids()
Aldehyde.get_deleters()
Aldehyde.get_hydrogen()
Aldehyde.get_num_bonders()
Aldehyde.get_oxygen()
Aldehyde.get_placer_ids()
Aldehyde.with_atoms()
Aldehyde.with_ids()
Alkene
Alkene.__init__()
Alkene.clone()
Alkene.get_atom1()
Alkene.get_atom2()
Alkene.get_atom3()
Alkene.get_atom4()
Alkene.get_atom_ids()
Alkene.get_atoms()
Alkene.get_bonder_ids()
Alkene.get_bonders()
Alkene.get_carbon1()
Alkene.get_carbon2()
Alkene.get_core_atom_ids()
Alkene.get_deleter_ids()
Alkene.get_deleters()
Alkene.get_num_bonders()
Alkene.get_placer_ids()
Alkene.with_atoms()
Alkene.with_ids()
Alkyne
Alkyne.__init__()
Alkyne.clone()
Alkyne.get_atom1()
Alkyne.get_atom2()
Alkyne.get_atom_ids()
Alkyne.get_atoms()
Alkyne.get_bonder_ids()
Alkyne.get_bonders()
Alkyne.get_carbon1()
Alkyne.get_carbon2()
Alkyne.get_core_atom_ids()
Alkyne.get_deleter_ids()
Alkyne.get_deleters()
Alkyne.get_num_bonders()
Alkyne.get_placer_ids()
Alkyne.with_atoms()
Alkyne.with_ids()
Amide
Amide.__init__()
Amide.clone()
Amide.get_atom()
Amide.get_atom_ids()
Amide.get_atoms()
Amide.get_bonder_ids()
Amide.get_bonders()
Amide.get_carbon()
Amide.get_core_atom_ids()
Amide.get_deleter_ids()
Amide.get_deleters()
Amide.get_hydrogen1()
Amide.get_hydrogen2()
Amide.get_nitrogen()
Amide.get_num_bonders()
Amide.get_oxygen()
Amide.get_placer_ids()
Amide.with_atoms()
Amide.with_ids()
BoronicAcid
BoronicAcid.__init__()
BoronicAcid.clone()
BoronicAcid.get_atom()
BoronicAcid.get_atom_ids()
BoronicAcid.get_atoms()
BoronicAcid.get_bonder_ids()
BoronicAcid.get_bonders()
BoronicAcid.get_boron()
BoronicAcid.get_core_atom_ids()
BoronicAcid.get_deleter_ids()
BoronicAcid.get_deleters()
BoronicAcid.get_hydrogen1()
BoronicAcid.get_hydrogen2()
BoronicAcid.get_num_bonders()
BoronicAcid.get_oxygen1()
BoronicAcid.get_oxygen2()
BoronicAcid.get_placer_ids()
BoronicAcid.with_atoms()
BoronicAcid.with_ids()
Bromo
Bromo.__init__()
Bromo.clone()
Bromo.get_atom()
Bromo.get_atom_ids()
Bromo.get_atoms()
Bromo.get_bonder_ids()
Bromo.get_bonders()
Bromo.get_bromine()
Bromo.get_core_atom_ids()
Bromo.get_deleter_ids()
Bromo.get_deleters()
Bromo.get_num_bonders()
Bromo.get_placer_ids()
Bromo.with_atoms()
Bromo.with_ids()
CarboxylicAcid
CarboxylicAcid.__init__()
CarboxylicAcid.clone()
CarboxylicAcid.get_atom()
CarboxylicAcid.get_atom_ids()
CarboxylicAcid.get_atoms()
CarboxylicAcid.get_bonder_ids()
CarboxylicAcid.get_bonders()
CarboxylicAcid.get_carbon()
CarboxylicAcid.get_core_atom_ids()
CarboxylicAcid.get_deleter_ids()
CarboxylicAcid.get_deleters()
CarboxylicAcid.get_hydrogen()
CarboxylicAcid.get_num_bonders()
CarboxylicAcid.get_oxygen1()
CarboxylicAcid.get_oxygen2()
CarboxylicAcid.get_placer_ids()
CarboxylicAcid.with_atoms()
CarboxylicAcid.with_ids()
Dibromo
Dibromo.__init__()
Dibromo.clone()
Dibromo.get_atom1()
Dibromo.get_atom2()
Dibromo.get_atom_ids()
Dibromo.get_atoms()
Dibromo.get_bonder_ids()
Dibromo.get_bonders()
Dibromo.get_bromine1()
Dibromo.get_bromine2()
Dibromo.get_core_atom_ids()
Dibromo.get_deleter_ids()
Dibromo.get_deleters()
Dibromo.get_num_bonders()
Dibromo.get_placer_ids()
Dibromo.with_atoms()
Dibromo.with_ids()
Difluoro
Difluoro.__init__()
Difluoro.clone()
Difluoro.get_atom1()
Difluoro.get_atom2()
Difluoro.get_atom_ids()
Difluoro.get_atoms()
Difluoro.get_bonder_ids()
Difluoro.get_bonders()
Difluoro.get_core_atom_ids()
Difluoro.get_deleter_ids()
Difluoro.get_deleters()
Difluoro.get_fluorine1()
Difluoro.get_fluorine2()
Difluoro.get_num_bonders()
Difluoro.get_placer_ids()
Difluoro.with_atoms()
Difluoro.with_ids()
Diol
Diol.__init__()
Diol.clone()
Diol.get_atom1()
Diol.get_atom2()
Diol.get_atom_ids()
Diol.get_atoms()
Diol.get_bonder_ids()
Diol.get_bonders()
Diol.get_core_atom_ids()
Diol.get_deleter_ids()
Diol.get_deleters()
Diol.get_hydrogen1()
Diol.get_hydrogen2()
Diol.get_num_bonders()
Diol.get_oxygen1()
Diol.get_oxygen2()
Diol.get_placer_ids()
Diol.with_atoms()
Diol.with_ids()
Fluoro
Fluoro.__init__()
Fluoro.clone()
Fluoro.get_atom()
Fluoro.get_atom_ids()
Fluoro.get_atoms()
Fluoro.get_bonder_ids()
Fluoro.get_bonders()
Fluoro.get_core_atom_ids()
Fluoro.get_deleter_ids()
Fluoro.get_deleters()
Fluoro.get_fluorine()
Fluoro.get_num_bonders()
Fluoro.get_placer_ids()
Fluoro.with_atoms()
Fluoro.with_ids()
GenericFunctionalGroup
GenericFunctionalGroup.__init__()
GenericFunctionalGroup.clone()
GenericFunctionalGroup.get_atom_ids()
GenericFunctionalGroup.get_atoms()
GenericFunctionalGroup.get_bonder_ids()
GenericFunctionalGroup.get_bonders()
GenericFunctionalGroup.get_core_atom_ids()
GenericFunctionalGroup.get_deleter_ids()
GenericFunctionalGroup.get_deleters()
GenericFunctionalGroup.get_num_bonders()
GenericFunctionalGroup.get_placer_ids()
GenericFunctionalGroup.with_atoms()
GenericFunctionalGroup.with_ids()
Iodo
Iodo.__init__()
Iodo.clone()
Iodo.get_atom()
Iodo.get_atom_ids()
Iodo.get_atoms()
Iodo.get_bonder_ids()
Iodo.get_bonders()
Iodo.get_core_atom_ids()
Iodo.get_deleter_ids()
Iodo.get_deleters()
Iodo.get_iodine()
Iodo.get_num_bonders()
Iodo.get_placer_ids()
Iodo.with_atoms()
Iodo.with_ids()
PrimaryAmino
PrimaryAmino.__init__()
PrimaryAmino.clone()
PrimaryAmino.get_atom()
PrimaryAmino.get_atom_ids()
PrimaryAmino.get_atoms()
PrimaryAmino.get_bonder_ids()
PrimaryAmino.get_bonders()
PrimaryAmino.get_core_atom_ids()
PrimaryAmino.get_deleter_ids()
PrimaryAmino.get_deleters()
PrimaryAmino.get_hydrogen1()
PrimaryAmino.get_hydrogen2()
PrimaryAmino.get_nitrogen()
PrimaryAmino.get_num_bonders()
PrimaryAmino.get_placer_ids()
PrimaryAmino.with_atoms()
PrimaryAmino.with_ids()
RingAmine
RingAmine.__init__()
RingAmine.clone()
RingAmine.get_atom_ids()
RingAmine.get_atoms()
RingAmine.get_carbon1()
RingAmine.get_carbon2()
RingAmine.get_carbon3()
RingAmine.get_core_atom_ids()
RingAmine.get_hydrogen1()
RingAmine.get_hydrogen2()
RingAmine.get_hydrogen3()
RingAmine.get_nitrogen()
RingAmine.get_placer_ids()
RingAmine.with_atoms()
RingAmine.with_ids()
SecondaryAmino
SecondaryAmino.__init__()
SecondaryAmino.clone()
SecondaryAmino.get_atom1()
SecondaryAmino.get_atom2()
SecondaryAmino.get_atom_ids()
SecondaryAmino.get_atoms()
SecondaryAmino.get_bonder_ids()
SecondaryAmino.get_bonders()
SecondaryAmino.get_core_atom_ids()
SecondaryAmino.get_deleter_ids()
SecondaryAmino.get_deleters()
SecondaryAmino.get_hydrogen()
SecondaryAmino.get_nitrogen()
SecondaryAmino.get_num_bonders()
SecondaryAmino.get_placer_ids()
SecondaryAmino.with_atoms()
SecondaryAmino.with_ids()
SingleAtom
SingleAtom.__init__()
SingleAtom.clone()
SingleAtom.get_atom()
SingleAtom.get_atom_ids()
SingleAtom.get_atoms()
SingleAtom.get_bonder_ids()
SingleAtom.get_bonders()
SingleAtom.get_core_atom_ids()
SingleAtom.get_deleter_ids()
SingleAtom.get_deleters()
SingleAtom.get_num_bonders()
SingleAtom.get_placer_ids()
SingleAtom.with_atoms()
SingleAtom.with_ids()
Thioacid
Thioacid.__init__()
Thioacid.clone()
Thioacid.get_atom()
Thioacid.get_atom_ids()
Thioacid.get_atoms()
Thioacid.get_bonder_ids()
Thioacid.get_bonders()
Thioacid.get_carbon()
Thioacid.get_core_atom_ids()
Thioacid.get_deleter_ids()
Thioacid.get_deleters()
Thioacid.get_hydrogen()
Thioacid.get_num_bonders()
Thioacid.get_oxygen()
Thioacid.get_placer_ids()
Thioacid.get_sulfur()
Thioacid.with_atoms()
Thioacid.with_ids()
Thiol
Thiol.__init__()
Thiol.clone()
Thiol.get_atom()
Thiol.get_atom_ids()
Thiol.get_atoms()
Thiol.get_bonder_ids()
Thiol.get_bonders()
Thiol.get_core_atom_ids()
Thiol.get_deleter_ids()
Thiol.get_deleters()
Thiol.get_hydrogen()
Thiol.get_num_bonders()
Thiol.get_placer_ids()
Thiol.get_sulfur()
Thiol.with_atoms()
Thiol.with_ids()
FunctionalGroup
FunctionalGroup.__init__()
FunctionalGroup.clone()
FunctionalGroup.get_atom_ids()
FunctionalGroup.get_atoms()
FunctionalGroup.get_core_atom_ids()
FunctionalGroup.get_placer_ids()
FunctionalGroup.with_atoms()
FunctionalGroup.with_ids()
AlcoholFactory
AlcoholFactory.__init__()
AlcoholFactory.get_functional_groups()
AldehydeFactory
AldehydeFactory.__init__()
AldehydeFactory.get_functional_groups()
AmideFactory
AmideFactory.__init__()
AmideFactory.get_functional_groups()
BoronicAcidFactory
BoronicAcidFactory.__init__()
BoronicAcidFactory.get_functional_groups()
BromoFactory
BromoFactory.__init__()
BromoFactory.get_functional_groups()
CarboxylicAcidFactory
CarboxylicAcidFactory.__init__()
CarboxylicAcidFactory.get_functional_groups()
DibromoFactory
DibromoFactory.__init__()
DibromoFactory.get_functional_groups()
DifluoroFactory
DifluoroFactory.__init__()
DifluoroFactory.get_functional_groups()
DiolFactory
DiolFactory.__init__()
DiolFactory.get_functional_groups()
FluoroFactory
FluoroFactory.__init__()
FluoroFactory.get_functional_groups()
IodoFactory
IodoFactory.__init__()
IodoFactory.get_functional_groups()
PrimaryAminoFactory
PrimaryAminoFactory.__init__()
PrimaryAminoFactory.get_functional_groups()
RingAmineFactory
RingAmineFactory.__init__()
RingAmineFactory.get_functional_groups()
SecondaryAminoFactory
SecondaryAminoFactory.__init__()
SecondaryAminoFactory.get_functional_groups()
SmartsFunctionalGroupFactory
SmartsFunctionalGroupFactory.__init__()
SmartsFunctionalGroupFactory.get_functional_groups()
TerminalAlkeneFactory
TerminalAlkeneFactory.__init__()
TerminalAlkeneFactory.get_functional_groups()
TerminalAlkyneFactory
TerminalAlkyneFactory.__init__()
TerminalAlkyneFactory.get_functional_groups()
ThioacidFactory
ThioacidFactory.__init__()
ThioacidFactory.get_functional_groups()
ThiolFactory
ThiolFactory.__init__()
ThiolFactory.get_functional_groups()
FunctionalGroupFactory
FunctionalGroupFactory.get_functional_groups()
Inchi
Inchi.__init__()
Inchi.get_key()
Inchi.get_key_name()
InchiKey
InchiKey.__init__()
InchiKey.get_key()
InchiKey.get_key_name()
Smiles
Smiles.__init__()
Smiles.get_key()
Smiles.get_key_name()
MoleculeKeyMaker
MoleculeKeyMaker.__init__()
MoleculeKeyMaker.get_key()
MoleculeKeyMaker.get_key_name()
OneOneReaction
OneOneReaction.__init__()
OneOneReaction.get_result()
OneTwoReaction
OneTwoReaction.__init__()
OneTwoReaction.get_result()
RingAmineReaction
RingAmineReaction.__init__()
RingAmineReaction.get_result()
TwoTwoReaction
TwoTwoReaction.__init__()
TwoTwoReaction.get_result()
DativeReaction
DativeReaction.__init__()
DativeReaction.get_result()
Reaction
Reaction.get_result()
GenericReactionFactory
GenericReactionFactory.__init__()
GenericReactionFactory.get_reaction()
DativeReactionFactory
DativeReactionFactory.__init__()
DativeReactionFactory.get_reaction()
ReactionFactory
ReactionFactory.get_reaction()
MolWriter
MolWriter.to_string()
MolWriter.write()
PdbWriter
PdbWriter.to_string()
PdbWriter.write()
TurbomoleWriter
TurbomoleWriter.to_string()
TurbomoleWriter.write()
XyzWriter
XyzWriter.to_string()
XyzWriter.write()
Topology Graphs
Linear
Linear.__init__()
Linear.clone()
Linear.construct()
Linear.get_building_blocks()
Linear.get_num_building_block()
Linear.with_building_blocks()
OnePlusOne
OnePlusOne.__init__()
OnePlusOne.clone()
OnePlusOne.construct()
OnePlusOne.get_building_blocks()
OnePlusOne.get_num_building_block()
OnePlusOne.with_building_blocks()
OnePlusOneVertex
OnePlusOneVertex.__init__()
OnePlusOneVertex.clone()
OnePlusOneVertex.get_aligner_edge()
OnePlusOneVertex.get_cell()
OnePlusOneVertex.get_id()
OnePlusOneVertex.get_position()
OnePlusOneVertex.init_at_center()
OnePlusOneVertex.map_functional_groups_to_edges()
OnePlusOneVertex.place_building_block()
OnePlusOneVertex.use_neighbor_placement()
OnePlusOneVertex.with_aligner_edge()
OnePlusOneVertex.with_position()
OnePlusOneVertex.with_scale()
TwoPlusTwo
TwoPlusTwo.__init__()
TwoPlusTwo.clone()
TwoPlusTwo.construct()
TwoPlusTwo.get_building_blocks()
TwoPlusTwo.get_num_building_block()
TwoPlusTwo.with_building_blocks()
TwoPlusThree
TwoPlusThree.__init__()
TwoPlusThree.clone()
TwoPlusThree.construct()
TwoPlusThree.get_building_blocks()
TwoPlusThree.get_num_building_block()
TwoPlusThree.with_building_blocks()
TwoPlusFour
TwoPlusFour.__init__()
TwoPlusFour.clone()
TwoPlusFour.construct()
TwoPlusFour.get_building_blocks()
TwoPlusFour.get_num_building_block()
TwoPlusFour.with_building_blocks()
ThreePlusSix
ThreePlusSix.__init__()
ThreePlusSix.clone()
ThreePlusSix.construct()
ThreePlusSix.get_building_blocks()
ThreePlusSix.get_num_building_block()
ThreePlusSix.with_building_blocks()
FourPlusFour
FourPlusFour.__init__()
FourPlusFour.clone()
FourPlusFour.construct()
FourPlusFour.get_building_blocks()
FourPlusFour.get_num_building_block()
FourPlusFour.with_building_blocks()
FourPlusSix
FourPlusSix.__init__()
FourPlusSix.clone()
FourPlusSix.construct()
FourPlusSix.get_building_blocks()
FourPlusSix.get_num_building_block()
FourPlusSix.with_building_blocks()
FourPlusSix2
FourPlusSix2.__init__()
FourPlusSix2.clone()
FourPlusSix2.construct()
FourPlusSix2.get_building_blocks()
FourPlusSix2.get_num_building_block()
FourPlusSix2.with_building_blocks()
FourPlusEight
FourPlusEight.__init__()
FourPlusEight.clone()
FourPlusEight.construct()
FourPlusEight.get_building_blocks()
FourPlusEight.get_num_building_block()
FourPlusEight.with_building_blocks()
FivePlusTen
FivePlusTen.__init__()
FivePlusTen.clone()
FivePlusTen.construct()
FivePlusTen.get_building_blocks()
FivePlusTen.get_num_building_block()
FivePlusTen.with_building_blocks()
SixPlusEight
SixPlusEight.__init__()
SixPlusEight.clone()
SixPlusEight.construct()
SixPlusEight.get_building_blocks()
SixPlusEight.get_num_building_block()
SixPlusEight.with_building_blocks()
SixPlusNine
SixPlusNine.__init__()
SixPlusNine.clone()
SixPlusNine.construct()
SixPlusNine.get_building_blocks()
SixPlusNine.get_num_building_block()
SixPlusNine.with_building_blocks()
SixPlusTwelve
SixPlusTwelve.__init__()
SixPlusTwelve.clone()
SixPlusTwelve.construct()
SixPlusTwelve.get_building_blocks()
SixPlusTwelve.get_num_building_block()
SixPlusTwelve.with_building_blocks()
EightPlusTwelve
EightPlusTwelve.__init__()
EightPlusTwelve.clone()
EightPlusTwelve.construct()
EightPlusTwelve.get_building_blocks()
EightPlusTwelve.get_num_building_block()
EightPlusTwelve.with_building_blocks()
EightPlusSixteen
EightPlusSixteen.__init__()
EightPlusSixteen.clone()
EightPlusSixteen.construct()
EightPlusSixteen.get_building_blocks()
EightPlusSixteen.get_num_building_block()
EightPlusSixteen.with_building_blocks()
TenPlusTwenty
TenPlusTwenty.__init__()
TenPlusTwenty.clone()
TenPlusTwenty.construct()
TenPlusTwenty.get_building_blocks()
TenPlusTwenty.get_num_building_block()
TenPlusTwenty.with_building_blocks()
TwelvePlusThirty
TwelvePlusThirty.__init__()
TwelvePlusThirty.clone()
TwelvePlusThirty.construct()
TwelvePlusThirty.get_building_blocks()
TwelvePlusThirty.get_num_building_block()
TwelvePlusThirty.with_building_blocks()
TwentyPlusThirty
TwentyPlusThirty.__init__()
TwentyPlusThirty.clone()
TwentyPlusThirty.construct()
TwentyPlusThirty.get_building_blocks()
TwentyPlusThirty.get_num_building_block()
TwentyPlusThirty.with_building_blocks()
M2L4Lantern
M2L4Lantern.__init__()
M2L4Lantern.clone()
M2L4Lantern.construct()
M2L4Lantern.get_building_blocks()
M2L4Lantern.get_num_building_block()
M2L4Lantern.with_building_blocks()
M3L3Triangle
M3L3Triangle.__init__()
M3L3Triangle.clone()
M3L3Triangle.construct()
M3L3Triangle.get_building_blocks()
M3L3Triangle.get_num_building_block()
M3L3Triangle.with_building_blocks()
M3L6
M3L6.__init__()
M3L6.clone()
M3L6.construct()
M3L6.get_building_blocks()
M3L6.get_num_building_block()
M3L6.with_building_blocks()
M4L4Square
M4L4Square.__init__()
M4L4Square.clone()
M4L4Square.construct()
M4L4Square.get_building_blocks()
M4L4Square.get_num_building_block()
M4L4Square.with_building_blocks()
M4L4Tetrahedron
M4L4Tetrahedron.__init__()
M4L4Tetrahedron.clone()
M4L4Tetrahedron.construct()
M4L4Tetrahedron.get_building_blocks()
M4L4Tetrahedron.get_num_building_block()
M4L4Tetrahedron.with_building_blocks()
M4L6TetrahedronSpacer
M4L6TetrahedronSpacer.__init__()
M4L6TetrahedronSpacer.clone()
M4L6TetrahedronSpacer.construct()
M4L6TetrahedronSpacer.get_building_blocks()
M4L6TetrahedronSpacer.get_num_building_block()
M4L6TetrahedronSpacer.with_building_blocks()
M4L6Tetrahedron
M4L6Tetrahedron.__init__()
M4L6Tetrahedron.clone()
M4L6Tetrahedron.construct()
M4L6Tetrahedron.get_building_blocks()
M4L6Tetrahedron.get_num_building_block()
M4L6Tetrahedron.with_building_blocks()
M4L8
M4L8.__init__()
M4L8.clone()
M4L8.construct()
M4L8.get_building_blocks()
M4L8.get_num_building_block()
M4L8.with_building_blocks()
M6L2L3Prism
M6L2L3Prism.__init__()
M6L2L3Prism.clone()
M6L2L3Prism.construct()
M6L2L3Prism.get_building_blocks()
M6L2L3Prism.get_num_building_block()
M6L2L3Prism.with_building_blocks()
M6L12Cube
M6L12Cube.__init__()
M6L12Cube.clone()
M6L12Cube.construct()
M6L12Cube.get_building_blocks()
M6L12Cube.get_num_building_block()
M6L12Cube.with_building_blocks()
M8L6Cube
M8L6Cube.__init__()
M8L6Cube.clone()
M8L6Cube.construct()
M8L6Cube.get_building_blocks()
M8L6Cube.get_num_building_block()
M8L6Cube.with_building_blocks()
M12L24
M12L24.__init__()
M12L24.clone()
M12L24.construct()
M12L24.get_building_blocks()
M12L24.get_num_building_block()
M12L24.with_building_blocks()
M24L48
M24L48.__init__()
M24L48.clone()
M24L48.construct()
M24L48.get_building_blocks()
M24L48.get_num_building_block()
M24L48.with_building_blocks()
Cage
Cage.__init__()
Cage.clone()
Cage.construct()
Cage.get_building_blocks()
Cage.get_num_building_block()
Cage.with_building_blocks()
OverlyOccupiedVertexError
OverlyOccupiedVertexError.add_note()
OverlyOccupiedVertexError.args
OverlyOccupiedVertexError.with_traceback()
UnoccupiedVertexError
UnoccupiedVertexError.add_note()
UnoccupiedVertexError.args
UnoccupiedVertexError.with_traceback()
Hexagonal
Hexagonal.__init__()
Hexagonal.clone()
Hexagonal.construct()
Hexagonal.get_building_blocks()
Hexagonal.get_num_building_block()
Hexagonal.with_building_blocks()
Honeycomb
Honeycomb.__init__()
Honeycomb.clone()
Honeycomb.construct()
Honeycomb.get_building_blocks()
Honeycomb.get_num_building_block()
Honeycomb.with_building_blocks()
Kagome
Kagome.__init__()
Kagome.clone()
Kagome.construct()
Kagome.get_building_blocks()
Kagome.get_num_building_block()
Kagome.with_building_blocks()
LinkerlessHoneycomb
LinkerlessHoneycomb.__init__()
LinkerlessHoneycomb.clone()
LinkerlessHoneycomb.construct()
LinkerlessHoneycomb.get_building_blocks()
LinkerlessHoneycomb.get_num_building_block()
LinkerlessHoneycomb.with_building_blocks()
Square
Square.__init__()
Square.clone()
Square.construct()
Square.get_building_blocks()
Square.get_num_building_block()
Square.with_building_blocks()
PeriodicHexagonal
PeriodicHexagonal.__init__()
PeriodicHexagonal.clone()
PeriodicHexagonal.construct()
PeriodicHexagonal.get_building_blocks()
PeriodicHexagonal.get_num_building_block()
PeriodicHexagonal.with_building_blocks()
PeriodicHoneycomb
PeriodicHoneycomb.__init__()
PeriodicHoneycomb.clone()
PeriodicHoneycomb.construct()
PeriodicHoneycomb.get_building_blocks()
PeriodicHoneycomb.get_num_building_block()
PeriodicHoneycomb.with_building_blocks()
PeriodicKagome
PeriodicKagome.__init__()
PeriodicKagome.clone()
PeriodicKagome.construct()
PeriodicKagome.get_building_blocks()
PeriodicKagome.get_num_building_block()
PeriodicKagome.with_building_blocks()
PeriodicLinkerlessHoneycomb
PeriodicLinkerlessHoneycomb.__init__()
PeriodicLinkerlessHoneycomb.clone()
PeriodicLinkerlessHoneycomb.construct()
PeriodicLinkerlessHoneycomb.get_building_blocks()
PeriodicLinkerlessHoneycomb.get_num_building_block()
PeriodicLinkerlessHoneycomb.with_building_blocks()
PeriodicSquare
PeriodicSquare.__init__()
PeriodicSquare.clone()
PeriodicSquare.construct()
PeriodicSquare.get_building_blocks()
PeriodicSquare.get_num_building_block()
PeriodicSquare.with_building_blocks()
Cof
Cof.__init__()
Cof.clone()
Cof.construct()
Cof.get_building_blocks()
Cof.get_num_building_block()
Cof.with_building_blocks()
Paddlewheel
Paddlewheel.__init__()
Paddlewheel.clone()
Paddlewheel.construct()
Paddlewheel.get_building_blocks()
Paddlewheel.get_num_building_block()
Paddlewheel.with_building_blocks()
Porphyrin
Porphyrin.__init__()
Porphyrin.clone()
Porphyrin.construct()
Porphyrin.get_building_blocks()
Porphyrin.get_num_building_block()
Porphyrin.with_building_blocks()
Octahedral
Octahedral.__init__()
Octahedral.clone()
Octahedral.construct()
Octahedral.get_building_blocks()
Octahedral.get_num_building_block()
Octahedral.with_building_blocks()
OctahedralLambda
OctahedralLambda.__init__()
OctahedralLambda.clone()
OctahedralLambda.construct()
OctahedralLambda.get_building_blocks()
OctahedralLambda.get_num_building_block()
OctahedralLambda.with_building_blocks()
OctahedralDelta
OctahedralDelta.__init__()
OctahedralDelta.clone()
OctahedralDelta.construct()
OctahedralDelta.get_building_blocks()
OctahedralDelta.get_num_building_block()
OctahedralDelta.with_building_blocks()
SquarePlanar
SquarePlanar.__init__()
SquarePlanar.clone()
SquarePlanar.construct()
SquarePlanar.get_building_blocks()
SquarePlanar.get_num_building_block()
SquarePlanar.with_building_blocks()
BidentateSquarePlanar
BidentateSquarePlanar.__init__()
BidentateSquarePlanar.clone()
BidentateSquarePlanar.construct()
BidentateSquarePlanar.get_building_blocks()
BidentateSquarePlanar.get_num_building_block()
BidentateSquarePlanar.with_building_blocks()
CisProtectedSquarePlanar
CisProtectedSquarePlanar.__init__()
CisProtectedSquarePlanar.clone()
CisProtectedSquarePlanar.construct()
CisProtectedSquarePlanar.get_building_blocks()
CisProtectedSquarePlanar.get_num_building_block()
CisProtectedSquarePlanar.with_building_blocks()
MetalComplex
MetalComplex.__init__()
MetalComplex.clone()
MetalComplex.construct()
MetalComplex.get_building_blocks()
MetalComplex.get_num_building_block()
MetalComplex.with_building_blocks()
Complex
Complex.__init__()
Complex.clone()
Complex.construct()
Complex.get_building_blocks()
Complex.get_num_building_block()
Complex.with_building_blocks()
Guest
Guest.__init__()
Guest.get_building_block()
Guest.get_displacement()
Guest.get_end_vector()
Guest.get_start_vector()
Macrocycle
Macrocycle.__init__()
Macrocycle.clone()
Macrocycle.construct()
Macrocycle.get_building_blocks()
Macrocycle.get_num_building_block()
Macrocycle.with_building_blocks()
NRotaxane
NRotaxane.__init__()
NRotaxane.clone()
NRotaxane.construct()
NRotaxane.get_building_blocks()
NRotaxane.get_num_building_block()
NRotaxane.with_building_blocks()
TopologyGraph
TopologyGraph.__init__()
TopologyGraph.clone()
TopologyGraph.construct()
TopologyGraph.get_building_blocks()
TopologyGraph.get_num_building_block()
TopologyGraph.with_building_blocks()
Collapser
Collapser.__init__()
Collapser.optimize()
PeriodicCollapser
PeriodicCollapser.__init__()
PeriodicCollapser.optimize()
MCHammer
MCHammer.__init__()
MCHammer.optimize()
Spinner
Spinner.__init__()
Spinner.optimize()
NullOptimizer
NullOptimizer.optimize()
Optimizer
Optimizer.optimize()
Molecular Databases
MoleculeMongoDb
MoleculeMongoDb.__init__()
MoleculeMongoDb.get()
MoleculeMongoDb.get_all()
MoleculeMongoDb.put()
MoleculeDatabase
MoleculeDatabase.get()
MoleculeDatabase.get_all()
MoleculeDatabase.put()
ConstructedMoleculeMongoDb
ConstructedMoleculeMongoDb.__init__()
ConstructedMoleculeMongoDb.get()
ConstructedMoleculeMongoDb.get_all()
ConstructedMoleculeMongoDb.put()
ConstructedMoleculeDatabase
ConstructedMoleculeDatabase.get()
ConstructedMoleculeDatabase.get_all()
ConstructedMoleculeDatabase.put()
ValueMongoDb
ValueMongoDb.__init__()
ValueMongoDb.get()
ValueMongoDb.put()
ValueDatabase
ValueDatabase.get()
ValueDatabase.put()
Evolutionary Algorithm
EvolutionaryAlgorithm
EvolutionaryAlgorithm.__init__()
EvolutionaryAlgorithm.get_generations()
FitnessFunction
FitnessFunction.__init__()
FitnessFunction.get_fitness_value()
PropertyVector
PropertyVector.__init__()
PropertyVector.get_fitness_value()
FitnessCalculator
FitnessCalculator.get_fitness_value()
Add
Add.__init__()
Add.normalize()
DivideByMean
DivideByMean.__init__()
DivideByMean.normalize()
Multiply
Multiply.__init__()
Multiply.normalize()
NormalizerSequence
NormalizerSequence.__init__()
NormalizerSequence.normalize()
NullFitnessNormalizer
NullFitnessNormalizer.normalize()
Power
Power.__init__()
Power.normalize()
ReplaceFitness
ReplaceFitness.__init__()
ReplaceFitness.normalize()
ShiftUp
ShiftUp.__init__()
ShiftUp.normalize()
Sum
Sum.__init__()
Sum.normalize()
FitnessNormalizer
FitnessNormalizer.normalize()
AboveAverage
AboveAverage.__init__()
AboveAverage.select()
Best
Best.__init__()
Best.select()
FilterBatches
FilterBatches.__init__()
FilterBatches.select()
FilterMolecules
FilterMolecules.__init__()
FilterMolecules.select()
RemoveBatches
RemoveBatches.__init__()
RemoveBatches.select()
RemoveMolecules
RemoveMolecules.__init__()
RemoveMolecules.select()
Roulette
Roulette.__init__()
Roulette.select()
StochasticUniversalSampling
StochasticUniversalSampling.__init__()
StochasticUniversalSampling.select()
Tournament
Tournament.__init__()
Tournament.select()
Worst
Worst.__init__()
Worst.select()
Selector
Selector.__init__()
Selector.select()
RandomBuildingBlock
RandomBuildingBlock.__init__()
RandomBuildingBlock.mutate()
RandomTopologyGraph
RandomTopologyGraph.__init__()
RandomTopologyGraph.mutate()
SimilarBuildingBlock
SimilarBuildingBlock.__init__()
SimilarBuildingBlock.mutate()
MoleculeMutator
MoleculeMutator.mutate()
RandomMutator
RandomMutator.__init__()
RandomMutator.mutate()
GeneticRecombination
GeneticRecombination.__init__()
GeneticRecombination.cross()
MoleculeCrosser
MoleculeCrosser.cross()
RandomCrosser
RandomCrosser.__init__()
RandomCrosser.cross()
ProgressPlotter
ProgressPlotter.__init__()
ProgressPlotter.get_plot_data()
ProgressPlotter.write()
SelectionPlotter
SelectionPlotter.__init__()
Modules
HashableDict
HashableDict.clear()
HashableDict.copy()
HashableDict.fromkeys()
HashableDict.get()
HashableDict.items()
HashableDict.keys()
HashableDict.pop()
HashableDict.popitem()
HashableDict.setdefault()
HashableDict.update()
HashableDict.values()
get_any_value()