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stk

  • Construction Overview
    • Introduction
    • Topology Graph
    • Building Blocks
  • Basic Examples
    • Creating Building Blocks
    • Specifying Multiple Functional Groups
    • Constructing Molecules
    • Using Built-in Optimizers During Construction
    • Using RDKit to Optimize Molecular Structures
    • Writing Molecular Files
    • Placing and Retrieving Molecules From a Database
      • Requirements
      • Molecules and Building Blocks
      • Constructed Molecules
    • Placing and Retrieving Molecular Property Values From a Database
      • Requirements
      • Storing Values
    • Specifying Functional Groups Individually
    • Changing Bonder and Deleter Atoms in Functional Group Factories
    • Handling Molecules with Metal Atoms and Dative Bonds
    • Making Keys for Molecules with Dative Bonds
    • Creating New Topology Graphs with Existing Vertices
    • Extending stk
  • Video Tutorials
    • Basics of stk
    • Functional Groups in stk
    • Cage Building
    • Hierarchical Construction with stk
    • Using stko with stk
    • Databases and stk-vis in stk
    • Host-Guest Conformers with stk

Molecules

  • Building Block
  • 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()
  • Constructed Molecule
  • 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()
  • Functional Group
    • Alcohol
    • 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
      • 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
      • 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
      • 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
      • 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()
    • Boronic Acid
    • 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
      • 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()
    • Carboxylic Acid
    • 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()
    • Dibormo
    • 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
      • 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
      • 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
      • 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()
    • Generic Functional Group
    • 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
      • 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()
    • Primary Amino
    • 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()
    • Ring Amine
    • 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()
    • Secondary Amino
    • 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()
    • Single Atom
    • 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
      • 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
      • 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()
  • Functional Group Factory
    • Alcohol Factory
    • AlcoholFactory
      • AlcoholFactory.__init__()
      • AlcoholFactory.get_functional_groups()
    • Aldehyde Factory
    • AldehydeFactory
      • AldehydeFactory.__init__()
      • AldehydeFactory.get_functional_groups()
    • Amide Factory
    • AmideFactory
      • AmideFactory.__init__()
      • AmideFactory.get_functional_groups()
    • Boronic Acid Factory
    • BoronicAcidFactory
      • BoronicAcidFactory.__init__()
      • BoronicAcidFactory.get_functional_groups()
    • Bromo Factory
    • BromoFactory
      • BromoFactory.__init__()
      • BromoFactory.get_functional_groups()
    • Carboxylic Acid Factory
    • CarboxylicAcidFactory
      • CarboxylicAcidFactory.__init__()
      • CarboxylicAcidFactory.get_functional_groups()
    • Dibromo Factory
    • DibromoFactory
      • DibromoFactory.__init__()
      • DibromoFactory.get_functional_groups()
    • Difluoro Factory
    • DifluoroFactory
      • DifluoroFactory.__init__()
      • DifluoroFactory.get_functional_groups()
    • Diol Factory
    • DiolFactory
      • DiolFactory.__init__()
      • DiolFactory.get_functional_groups()
    • Fluoro Factory
    • FluoroFactory
      • FluoroFactory.__init__()
      • FluoroFactory.get_functional_groups()
    • Iodo Factory
    • IodoFactory
      • IodoFactory.__init__()
      • IodoFactory.get_functional_groups()
    • Primary Amino Factory
    • PrimaryAminoFactory
      • PrimaryAminoFactory.__init__()
      • PrimaryAminoFactory.get_functional_groups()
    • Ring Amine Factory
    • RingAmineFactory
      • RingAmineFactory.__init__()
      • RingAmineFactory.get_functional_groups()
    • Secondary Amino Factory
    • SecondaryAminoFactory
      • SecondaryAminoFactory.__init__()
      • SecondaryAminoFactory.get_functional_groups()
    • SMARTS Functional Group Factory
    • SmartsFunctionalGroupFactory
      • SmartsFunctionalGroupFactory.__init__()
      • SmartsFunctionalGroupFactory.get_functional_groups()
    • Terminal Alkene Factory
    • TerminalAlkeneFactory
      • TerminalAlkeneFactory.__init__()
      • TerminalAlkeneFactory.get_functional_groups()
    • Terminal Alkyne Factory
    • TerminalAlkyneFactory
      • TerminalAlkyneFactory.__init__()
      • TerminalAlkyneFactory.get_functional_groups()
    • Thioacid Factory
    • ThioacidFactory
      • ThioacidFactory.__init__()
      • ThioacidFactory.get_functional_groups()
    • Thiol Factory
    • ThiolFactory
      • ThiolFactory.__init__()
      • ThiolFactory.get_functional_groups()
  • FunctionalGroupFactory
    • FunctionalGroupFactory.get_functional_groups()
  • Molecule Key Maker
    • InChI
    • Inchi
      • Inchi.__init__()
      • Inchi.get_key()
      • Inchi.get_key_name()
    • InChIKey
    • InchiKey
      • InchiKey.__init__()
      • InchiKey.get_key()
      • InchiKey.get_key_name()
    • SMILES
    • Smiles
      • Smiles.__init__()
      • Smiles.get_key()
      • Smiles.get_key_name()
  • MoleculeKeyMaker
    • MoleculeKeyMaker.__init__()
    • MoleculeKeyMaker.get_key()
    • MoleculeKeyMaker.get_key_name()
  • Reaction
    • One-One Reaction
    • OneOneReaction
      • OneOneReaction.__init__()
      • OneOneReaction.get_result()
    • One-Two Reaction
    • OneTwoReaction
      • OneTwoReaction.__init__()
      • OneTwoReaction.get_result()
    • Ring Amine Reaction
    • RingAmineReaction
      • RingAmineReaction.__init__()
      • RingAmineReaction.get_result()
    • Two-Two Reaction
    • TwoTwoReaction
      • TwoTwoReaction.__init__()
      • TwoTwoReaction.get_result()
    • Dative Reaction
    • DativeReaction
      • DativeReaction.__init__()
      • DativeReaction.get_result()
  • Reaction
    • Reaction.get_result()
  • Reaction Factory
    • Generic Reaction Factory
    • GenericReactionFactory
      • GenericReactionFactory.__init__()
      • GenericReactionFactory.get_reaction()
    • Dative Reaction Factory
    • DativeReactionFactory
      • DativeReactionFactory.__init__()
      • DativeReactionFactory.get_reaction()
  • ReactionFactory
    • ReactionFactory.get_reaction()
  • Writers
    • Mol Writer
    • MolWriter
      • MolWriter.to_string()
      • MolWriter.write()
    • PDB Writer
    • PdbWriter
      • PdbWriter.to_string()
      • PdbWriter.write()
    • Turbomole Writer
    • TurbomoleWriter
      • TurbomoleWriter.to_string()
      • TurbomoleWriter.write()
    • XYZ Writer
    • XyzWriter
      • XyzWriter.to_string()
      • XyzWriter.write()

Topology Graphs

  • Polymers
    • Linear
    • Linear
      • Linear.__init__()
      • Linear.clone()
      • Linear.construct()
      • Linear.get_building_blocks()
      • Linear.get_num_building_block()
      • Linear.with_building_blocks()
  • Cage
    • Organic
      • One Plus One
      • 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()
      • Two Plus Two
      • TwoPlusTwo
        • TwoPlusTwo.__init__()
        • TwoPlusTwo.clone()
        • TwoPlusTwo.construct()
        • TwoPlusTwo.get_building_blocks()
        • TwoPlusTwo.get_num_building_block()
        • TwoPlusTwo.with_building_blocks()
      • Two Plus Three
      • TwoPlusThree
        • TwoPlusThree.__init__()
        • TwoPlusThree.clone()
        • TwoPlusThree.construct()
        • TwoPlusThree.get_building_blocks()
        • TwoPlusThree.get_num_building_block()
        • TwoPlusThree.with_building_blocks()
      • Two Plus Four
      • TwoPlusFour
        • TwoPlusFour.__init__()
        • TwoPlusFour.clone()
        • TwoPlusFour.construct()
        • TwoPlusFour.get_building_blocks()
        • TwoPlusFour.get_num_building_block()
        • TwoPlusFour.with_building_blocks()
      • Three Plus Six
      • ThreePlusSix
        • ThreePlusSix.__init__()
        • ThreePlusSix.clone()
        • ThreePlusSix.construct()
        • ThreePlusSix.get_building_blocks()
        • ThreePlusSix.get_num_building_block()
        • ThreePlusSix.with_building_blocks()
      • Four Plus Four
      • FourPlusFour
        • FourPlusFour.__init__()
        • FourPlusFour.clone()
        • FourPlusFour.construct()
        • FourPlusFour.get_building_blocks()
        • FourPlusFour.get_num_building_block()
        • FourPlusFour.with_building_blocks()
      • Four Plus Six
      • FourPlusSix
        • FourPlusSix.__init__()
        • FourPlusSix.clone()
        • FourPlusSix.construct()
        • FourPlusSix.get_building_blocks()
        • FourPlusSix.get_num_building_block()
        • FourPlusSix.with_building_blocks()
      • Four Plus Six 2
      • FourPlusSix2
        • FourPlusSix2.__init__()
        • FourPlusSix2.clone()
        • FourPlusSix2.construct()
        • FourPlusSix2.get_building_blocks()
        • FourPlusSix2.get_num_building_block()
        • FourPlusSix2.with_building_blocks()
      • Four Plus Eight
      • FourPlusEight
        • FourPlusEight.__init__()
        • FourPlusEight.clone()
        • FourPlusEight.construct()
        • FourPlusEight.get_building_blocks()
        • FourPlusEight.get_num_building_block()
        • FourPlusEight.with_building_blocks()
      • Five Plus Ten
      • FivePlusTen
        • FivePlusTen.__init__()
        • FivePlusTen.clone()
        • FivePlusTen.construct()
        • FivePlusTen.get_building_blocks()
        • FivePlusTen.get_num_building_block()
        • FivePlusTen.with_building_blocks()
      • Six Plus Eight
      • SixPlusEight
        • SixPlusEight.__init__()
        • SixPlusEight.clone()
        • SixPlusEight.construct()
        • SixPlusEight.get_building_blocks()
        • SixPlusEight.get_num_building_block()
        • SixPlusEight.with_building_blocks()
      • Six Plus Nine
      • SixPlusNine
        • SixPlusNine.__init__()
        • SixPlusNine.clone()
        • SixPlusNine.construct()
        • SixPlusNine.get_building_blocks()
        • SixPlusNine.get_num_building_block()
        • SixPlusNine.with_building_blocks()
      • Six Plus Twelve
      • SixPlusTwelve
        • SixPlusTwelve.__init__()
        • SixPlusTwelve.clone()
        • SixPlusTwelve.construct()
        • SixPlusTwelve.get_building_blocks()
        • SixPlusTwelve.get_num_building_block()
        • SixPlusTwelve.with_building_blocks()
      • Eight Plus Twelve
      • EightPlusTwelve
        • EightPlusTwelve.__init__()
        • EightPlusTwelve.clone()
        • EightPlusTwelve.construct()
        • EightPlusTwelve.get_building_blocks()
        • EightPlusTwelve.get_num_building_block()
        • EightPlusTwelve.with_building_blocks()
      • Eight Plus Sixteen
      • EightPlusSixteen
        • EightPlusSixteen.__init__()
        • EightPlusSixteen.clone()
        • EightPlusSixteen.construct()
        • EightPlusSixteen.get_building_blocks()
        • EightPlusSixteen.get_num_building_block()
        • EightPlusSixteen.with_building_blocks()
      • Ten Plus Twenty
      • TenPlusTwenty
        • TenPlusTwenty.__init__()
        • TenPlusTwenty.clone()
        • TenPlusTwenty.construct()
        • TenPlusTwenty.get_building_blocks()
        • TenPlusTwenty.get_num_building_block()
        • TenPlusTwenty.with_building_blocks()
      • Twelve Plus Thirty
      • TwelvePlusThirty
        • TwelvePlusThirty.__init__()
        • TwelvePlusThirty.clone()
        • TwelvePlusThirty.construct()
        • TwelvePlusThirty.get_building_blocks()
        • TwelvePlusThirty.get_num_building_block()
        • TwelvePlusThirty.with_building_blocks()
      • Twenty Plus Thirty
      • TwentyPlusThirty
        • TwentyPlusThirty.__init__()
        • TwentyPlusThirty.clone()
        • TwentyPlusThirty.construct()
        • TwentyPlusThirty.get_building_blocks()
        • TwentyPlusThirty.get_num_building_block()
        • TwentyPlusThirty.with_building_blocks()
    • Metal-Organic
      • M2L4 Lantern
      • M2L4Lantern
        • M2L4Lantern.__init__()
        • M2L4Lantern.clone()
        • M2L4Lantern.construct()
        • M2L4Lantern.get_building_blocks()
        • M2L4Lantern.get_num_building_block()
        • M2L4Lantern.with_building_blocks()
      • M3L3 Triangle
      • M3L3Triangle
        • M3L3Triangle.__init__()
        • M3L3Triangle.clone()
        • M3L3Triangle.construct()
        • M3L3Triangle.get_building_blocks()
        • M3L3Triangle.get_num_building_block()
        • M3L3Triangle.with_building_blocks()
      • M3L6
      • M3L6
        • M3L6.__init__()
        • M3L6.clone()
        • M3L6.construct()
        • M3L6.get_building_blocks()
        • M3L6.get_num_building_block()
        • M3L6.with_building_blocks()
      • M4L4 Square
      • M4L4Square
        • M4L4Square.__init__()
        • M4L4Square.clone()
        • M4L4Square.construct()
        • M4L4Square.get_building_blocks()
        • M4L4Square.get_num_building_block()
        • M4L4Square.with_building_blocks()
      • M4L4 Tetrahedron
      • M4L4Tetrahedron
        • M4L4Tetrahedron.__init__()
        • M4L4Tetrahedron.clone()
        • M4L4Tetrahedron.construct()
        • M4L4Tetrahedron.get_building_blocks()
        • M4L4Tetrahedron.get_num_building_block()
        • M4L4Tetrahedron.with_building_blocks()
      • M4L6 Tetrahedron with Spacer
      • M4L6TetrahedronSpacer
        • M4L6TetrahedronSpacer.__init__()
        • M4L6TetrahedronSpacer.clone()
        • M4L6TetrahedronSpacer.construct()
        • M4L6TetrahedronSpacer.get_building_blocks()
        • M4L6TetrahedronSpacer.get_num_building_block()
        • M4L6TetrahedronSpacer.with_building_blocks()
      • M4L6 Tetrahedron
      • M4L6Tetrahedron
        • M4L6Tetrahedron.__init__()
        • M4L6Tetrahedron.clone()
        • M4L6Tetrahedron.construct()
        • M4L6Tetrahedron.get_building_blocks()
        • M4L6Tetrahedron.get_num_building_block()
        • M4L6Tetrahedron.with_building_blocks()
      • M4L8
      • M4L8
        • M4L8.__init__()
        • M4L8.clone()
        • M4L8.construct()
        • M4L8.get_building_blocks()
        • M4L8.get_num_building_block()
        • M4L8.with_building_blocks()
      • M6L2L3 Prism
      • M6L2L3Prism
        • M6L2L3Prism.__init__()
        • M6L2L3Prism.clone()
        • M6L2L3Prism.construct()
        • M6L2L3Prism.get_building_blocks()
        • M6L2L3Prism.get_num_building_block()
        • M6L2L3Prism.with_building_blocks()
      • M6L12 Cube
      • M6L12Cube
        • M6L12Cube.__init__()
        • M6L12Cube.clone()
        • M6L12Cube.construct()
        • M6L12Cube.get_building_blocks()
        • M6L12Cube.get_num_building_block()
        • M6L12Cube.with_building_blocks()
      • M8L6 Cube
      • M8L6Cube
        • M8L6Cube.__init__()
        • M8L6Cube.clone()
        • M8L6Cube.construct()
        • M8L6Cube.get_building_blocks()
        • M8L6Cube.get_num_building_block()
        • M8L6Cube.with_building_blocks()
      • M12L24
      • M12L24
        • M12L24.__init__()
        • M12L24.clone()
        • M12L24.construct()
        • M12L24.get_building_blocks()
        • M12L24.get_num_building_block()
        • M12L24.with_building_blocks()
      • M24L48
      • 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()
  • Covalent Organic Framework
    • Hexagonal
    • Hexagonal
      • Hexagonal.__init__()
      • Hexagonal.clone()
      • Hexagonal.construct()
      • Hexagonal.get_building_blocks()
      • Hexagonal.get_num_building_block()
      • Hexagonal.with_building_blocks()
    • Honeycomb
    • Honeycomb
      • Honeycomb.__init__()
      • Honeycomb.clone()
      • Honeycomb.construct()
      • Honeycomb.get_building_blocks()
      • Honeycomb.get_num_building_block()
      • Honeycomb.with_building_blocks()
    • Kagome
    • Kagome
      • Kagome.__init__()
      • Kagome.clone()
      • Kagome.construct()
      • Kagome.get_building_blocks()
      • Kagome.get_num_building_block()
      • Kagome.with_building_blocks()
    • Linkerless Honeycomb
    • LinkerlessHoneycomb
      • LinkerlessHoneycomb.__init__()
      • LinkerlessHoneycomb.clone()
      • LinkerlessHoneycomb.construct()
      • LinkerlessHoneycomb.get_building_blocks()
      • LinkerlessHoneycomb.get_num_building_block()
      • LinkerlessHoneycomb.with_building_blocks()
    • Square
    • Square
      • Square.__init__()
      • Square.clone()
      • Square.construct()
      • Square.get_building_blocks()
      • Square.get_num_building_block()
      • Square.with_building_blocks()
    • Periodic Hexagonal
    • PeriodicHexagonal
      • PeriodicHexagonal.__init__()
      • PeriodicHexagonal.clone()
      • PeriodicHexagonal.construct()
      • PeriodicHexagonal.get_building_blocks()
      • PeriodicHexagonal.get_num_building_block()
      • PeriodicHexagonal.with_building_blocks()
    • Periodic Honeycomb
    • PeriodicHoneycomb
      • PeriodicHoneycomb.__init__()
      • PeriodicHoneycomb.clone()
      • PeriodicHoneycomb.construct()
      • PeriodicHoneycomb.get_building_blocks()
      • PeriodicHoneycomb.get_num_building_block()
      • PeriodicHoneycomb.with_building_blocks()
    • Periodic Kagome
    • PeriodicKagome
      • PeriodicKagome.__init__()
      • PeriodicKagome.clone()
      • PeriodicKagome.construct()
      • PeriodicKagome.get_building_blocks()
      • PeriodicKagome.get_num_building_block()
      • PeriodicKagome.with_building_blocks()
    • Periodic Linkerless Honeycomb
    • PeriodicLinkerlessHoneycomb
      • PeriodicLinkerlessHoneycomb.__init__()
      • PeriodicLinkerlessHoneycomb.clone()
      • PeriodicLinkerlessHoneycomb.construct()
      • PeriodicLinkerlessHoneycomb.get_building_blocks()
      • PeriodicLinkerlessHoneycomb.get_num_building_block()
      • PeriodicLinkerlessHoneycomb.with_building_blocks()
    • Periodic Square
    • 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()
  • OverlyOccupiedVertexError
    • OverlyOccupiedVertexError.add_note()
    • OverlyOccupiedVertexError.args
    • OverlyOccupiedVertexError.with_traceback()
  • UnoccupiedVertexError
    • UnoccupiedVertexError.add_note()
    • UnoccupiedVertexError.args
    • UnoccupiedVertexError.with_traceback()
  • Metal Complex
    • Paddlewheel
    • Paddlewheel
      • Paddlewheel.__init__()
      • Paddlewheel.clone()
      • Paddlewheel.construct()
      • Paddlewheel.get_building_blocks()
      • Paddlewheel.get_num_building_block()
      • Paddlewheel.with_building_blocks()
    • Porphyrin
    • Porphyrin
      • Porphyrin.__init__()
      • Porphyrin.clone()
      • Porphyrin.construct()
      • Porphyrin.get_building_blocks()
      • Porphyrin.get_num_building_block()
      • Porphyrin.with_building_blocks()
    • Octahedral
    • Octahedral
      • Octahedral.__init__()
      • Octahedral.clone()
      • Octahedral.construct()
      • Octahedral.get_building_blocks()
      • Octahedral.get_num_building_block()
      • Octahedral.with_building_blocks()
    • Octahedral Lambda
    • OctahedralLambda
      • OctahedralLambda.__init__()
      • OctahedralLambda.clone()
      • OctahedralLambda.construct()
      • OctahedralLambda.get_building_blocks()
      • OctahedralLambda.get_num_building_block()
      • OctahedralLambda.with_building_blocks()
    • Octahedral Delta
    • OctahedralDelta
      • OctahedralDelta.__init__()
      • OctahedralDelta.clone()
      • OctahedralDelta.construct()
      • OctahedralDelta.get_building_blocks()
      • OctahedralDelta.get_num_building_block()
      • OctahedralDelta.with_building_blocks()
    • Square Planar
    • SquarePlanar
      • SquarePlanar.__init__()
      • SquarePlanar.clone()
      • SquarePlanar.construct()
      • SquarePlanar.get_building_blocks()
      • SquarePlanar.get_num_building_block()
      • SquarePlanar.with_building_blocks()
    • Bidentate Square Planar
    • BidentateSquarePlanar
      • BidentateSquarePlanar.__init__()
      • BidentateSquarePlanar.clone()
      • BidentateSquarePlanar.construct()
      • BidentateSquarePlanar.get_building_blocks()
      • BidentateSquarePlanar.get_num_building_block()
      • BidentateSquarePlanar.with_building_blocks()
    • Cis Protected Square Planar
    • 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()
  • Host Guest Complex
  • 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
    • Macrocycle.__init__()
    • Macrocycle.clone()
    • Macrocycle.construct()
    • Macrocycle.get_building_blocks()
    • Macrocycle.get_num_building_block()
    • Macrocycle.with_building_blocks()
  • [n]Rotaxane
  • NRotaxane
    • NRotaxane.__init__()
    • NRotaxane.clone()
    • NRotaxane.construct()
    • NRotaxane.get_building_blocks()
    • NRotaxane.get_num_building_block()
    • NRotaxane.with_building_blocks()
  • Topology Graph
  • TopologyGraph
    • TopologyGraph.__init__()
    • TopologyGraph.clone()
    • TopologyGraph.construct()
    • TopologyGraph.get_building_blocks()
    • TopologyGraph.get_num_building_block()
    • TopologyGraph.with_building_blocks()
  • Optimizer
    • Collapser
    • Collapser
      • Collapser.__init__()
      • Collapser.optimize()
    • Periodic Collapser
    • PeriodicCollapser
      • PeriodicCollapser.__init__()
      • PeriodicCollapser.optimize()
    • MCHammer
    • MCHammer
      • MCHammer.__init__()
      • MCHammer.optimize()
    • Spinner
    • Spinner
      • Spinner.__init__()
      • Spinner.optimize()
    • Null Optimizer
    • NullOptimizer
      • NullOptimizer.optimize()
  • Optimizer
    • Optimizer.optimize()

Molecular Databases

  • Molecule Database
    • Molecule MongoDB
    • MoleculeMongoDb
      • MoleculeMongoDb.__init__()
      • MoleculeMongoDb.get()
      • MoleculeMongoDb.get_all()
      • MoleculeMongoDb.put()
  • MoleculeDatabase
    • MoleculeDatabase.get()
    • MoleculeDatabase.get_all()
    • MoleculeDatabase.put()
  • Constructed Molecule Database
    • Constructed Molecule MongoDB
    • ConstructedMoleculeMongoDb
      • ConstructedMoleculeMongoDb.__init__()
      • ConstructedMoleculeMongoDb.get()
      • ConstructedMoleculeMongoDb.get_all()
      • ConstructedMoleculeMongoDb.put()
  • ConstructedMoleculeDatabase
    • ConstructedMoleculeDatabase.get()
    • ConstructedMoleculeDatabase.get_all()
    • ConstructedMoleculeDatabase.put()
  • Value Database
    • Value MongoDB
    • ValueMongoDb
      • ValueMongoDb.__init__()
      • ValueMongoDb.get()
      • ValueMongoDb.put()
  • ValueDatabase
    • ValueDatabase.get()
    • ValueDatabase.put()

Evolutionary Algorithm

  • Evolutionary Algorithm
  • EvolutionaryAlgorithm
    • EvolutionaryAlgorithm.__init__()
    • EvolutionaryAlgorithm.get_generations()
  • Basic Example
    • Introduction
    • EA Components
    • Basic EA Loop
      • Adding a Database
    • Plotting the EA Progress
    • Review
    • Defining EA Components
      • Defining a Database
    • Final Version
  • Intermediate Example
    • Introduction
    • Defining a New Fitness Calculator
    • Defining a Fitness Normalizer
    • Caching Fitness Values
    • Plotting Selection
    • Final Version
  • Fitness Calculator
    • Fitness Calculator
    • FitnessFunction
      • FitnessFunction.__init__()
      • FitnessFunction.get_fitness_value()
    • Property Vector
    • PropertyVector
      • PropertyVector.__init__()
      • PropertyVector.get_fitness_value()
  • FitnessCalculator
    • FitnessCalculator.get_fitness_value()
  • Fitness Normalizer
    • Add
    • Add
      • Add.__init__()
      • Add.normalize()
    • Divide By Mean
    • DivideByMean
      • DivideByMean.__init__()
      • DivideByMean.normalize()
    • Multiply
    • Multiply
      • Multiply.__init__()
      • Multiply.normalize()
    • Normalizer Sequence
    • NormalizerSequence
      • NormalizerSequence.__init__()
      • NormalizerSequence.normalize()
    • Null Fitness Normalizer
    • NullFitnessNormalizer
      • NullFitnessNormalizer.normalize()
    • Power
    • Power
      • Power.__init__()
      • Power.normalize()
    • Replace Fitness
    • ReplaceFitness
      • ReplaceFitness.__init__()
      • ReplaceFitness.normalize()
    • Shift Up
    • ShiftUp
      • ShiftUp.__init__()
      • ShiftUp.normalize()
    • Sum
    • Sum
      • Sum.__init__()
      • Sum.normalize()
  • FitnessNormalizer
    • FitnessNormalizer.normalize()
  • Selector
    • Above Average
    • AboveAverage
      • AboveAverage.__init__()
      • AboveAverage.select()
    • Best
    • Best
      • Best.__init__()
      • Best.select()
    • Filter Batches
    • FilterBatches
      • FilterBatches.__init__()
      • FilterBatches.select()
    • Filter Molecules
    • FilterMolecules
      • FilterMolecules.__init__()
      • FilterMolecules.select()
    • Remove Batches
    • RemoveBatches
      • RemoveBatches.__init__()
      • RemoveBatches.select()
    • Remove Molecules
    • RemoveMolecules
      • RemoveMolecules.__init__()
      • RemoveMolecules.select()
    • Roulette
    • Roulette
      • Roulette.__init__()
      • Roulette.select()
    • Stochastic Universal Sampling
    • StochasticUniversalSampling
      • StochasticUniversalSampling.__init__()
      • StochasticUniversalSampling.select()
    • Tournament
    • Tournament
      • Tournament.__init__()
      • Tournament.select()
    • Worst
    • Worst
      • Worst.__init__()
      • Worst.select()
  • Selector
    • Selector.__init__()
    • Selector.select()
  • Mutation
    • Molecule Mutator
      • Random Building Block
      • RandomBuildingBlock
        • RandomBuildingBlock.__init__()
        • RandomBuildingBlock.mutate()
      • Random Topology Graph
      • RandomTopologyGraph
        • RandomTopologyGraph.__init__()
        • RandomTopologyGraph.mutate()
      • Similar Building Block
      • SimilarBuildingBlock
        • SimilarBuildingBlock.__init__()
        • SimilarBuildingBlock.mutate()
    • MoleculeMutator
      • MoleculeMutator.mutate()
    • Compound
      • Random Mutator
      • RandomMutator
        • RandomMutator.__init__()
        • RandomMutator.mutate()
  • Crossover
    • Molecule Crosser
      • Genetic Recombination
      • GeneticRecombination
        • GeneticRecombination.__init__()
        • GeneticRecombination.cross()
    • MoleculeCrosser
      • MoleculeCrosser.cross()
    • Compound
      • Random Crosser
      • RandomCrosser
        • RandomCrosser.__init__()
        • RandomCrosser.cross()
  • Plotting
    • Progress Plotter
    • ProgressPlotter
      • ProgressPlotter.__init__()
      • ProgressPlotter.get_plot_data()
      • ProgressPlotter.write()
    • Selection Plotter
    • SelectionPlotter
      • SelectionPlotter.__init__()

Modules

  • Modules
    • stk package
      • Subpackages
        • stk.databases package
        • stk.ea package
        • stk.molecular package
        • stk.serialization package
        • stk.utilities package
stk
  • Plotters
  • Edit on GitHub

Plotters

  • Progress Plotter
  • ProgressPlotter
    • ProgressPlotter.__init__()
    • ProgressPlotter.get_plot_data()
    • ProgressPlotter.write()
  • Selection Plotter
  • SelectionPlotter
    • SelectionPlotter.__init__()
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