Index

A

add_bonds_colloids() (hoobas.Build.Bias method) add_einstein_crystal_lattice() (hoobas.Build.Bias method) add_ions() (hoobas.Build.Builder method) add_layer() (hoobas.Build.Builder method) (hoobas.SimulationDomain.Lattice method) add_line() (hoobas.SimulationDomain.Lattice method) add_N_ext_obj() (hoobas.Build.Builder method) add_particles_on_lattice() (hoobas.SimulationDomain.Lattice method)

add_random_positions() (hoobas.SimulationDomain.Domain method) add_rho_molar_ions() (hoobas.Build.Builder method) add_shell() (hoobas.GenShape.PdbProtein method) add_species() (hoobas.Layers.LayeredTiling method) (hoobas.Layers.Multilayer method) aggregate_rigid_tuples() (hoobas.Build.HOOMDBuilder method) Angle (class in hoobas.Composite) AngleType (class in hoobas.Composite) AttachmentSite (class in hoobas.Composite)

B

Bead (class in hoobas.CGBead) bead_types() (hoobas.Build.Builder property) BeadList (class in hoobas.Composite) BeadMonomer (class in hoobas.LinearChain)

Bias (class in hoobas.Build) Bond (class in hoobas.Composite) BondType (class in hoobas.Composite) build() (hoobas.GenShape.PdbProtein method) Builder (class in hoobas.Build)

C

center_tags() (hoobas.Build.Builder property) center_types() (hoobas.Build.Builder property) change_units() (hoobas.SimulationDomain.Domain method) (hoobas.SimulationDomain.Lattice method) charge_list() (hoobas.Build.Builder property) charge_to_types_per_rigid_body() (hoobas.Build.HOOMDBuilder method) Colloid (class in hoobas.Colloid) ComplexColloid (class in hoobas.Colloid)

CompositeObject (class in hoobas.Composite) Constraint (class in hoobas.Composite) copy_ext_obj() (hoobas.Build.Builder method) correct_pnum_body_lists() (hoobas.Build.HOOMDBuilder method) CrossBuilder (class in hoobas.Build) Cube (class in hoobas.GenShape) cut_to_dimensions() (hoobas.SimulationDomain.Lattice method) Cylinder (class in hoobas.GenShape)

D

d_hkl() (hoobas.SimulationDomain.Lattice static method) deferred() (in module hoobas.Composite) denormalize() (hoobas.Build.Electrostatics method) Dihedral (class in hoobas.Composite) DihedralType (class in hoobas.Composite)

direct_lattice_vectors() (hoobas.SimulationDomain.Domain property) distance() (hoobas.Composite.TopologyType static method) DNA3SPNChain (class in hoobas.LinearChain) DNAChain (class in hoobas.LinearChain) Domain (class in hoobas.SimulationDomain)

E

Electrostatics (class in hoobas.Build) ElongatedRhombicDodecahedron (class in hoobas.GenShape) EmptyBox (class in hoobas.SimulationDomain) EmptyCube (class in hoobas.SimulationDomain)

EmptyHexagonalPrism (class in hoobas.SimulationDomain) enforce_PBC() (hoobas.Build.Builder method) enforce_XYPBC() (hoobas.Build.Builder method) ESPResSOppBuilder (class in hoobas.Build) export_pdb() (hoobas.Build.FileWriter method)

F

FileWriter (class in hoobas.Build) fix_remaining_charge() (hoobas.Build.Builder method)

force_layer_thickness() (hoobas.Layers.Multilayer method) FromComposite (class in hoobas.Colloid)

G

generate_crystal_slab() (hoobas.SimulationDomain.Lattice method) GenericBlockRingPolymer (class in hoobas.LinearChain) GenericPolymer (class in hoobas.LinearChain) GenericRingPolymer (class in hoobas.LinearChain)

get_N_idx() (hoobas.GenShape.shape method) get_pair() (hoobas.MartiniModels.MartiniForceMappings static method) get_pair_polarizable() (hoobas.MartiniModels.MartiniForceMappings static method) get_subgraph() (hoobas.Composite.CompositeObject method) get_type_charge_product() (hoobas.Build.Electrostatics method)

H

hoobas (module) hoobas.Build (module) hoobas.CGBead (module) hoobas.Colloid (module) hoobas.Composite (module)

hoobas.GenShape (module) hoobas.Layers (module) hoobas.LinearChain (module) hoobas.MartiniModels (module) hoobas.SimulationDomain (module) HOOMDBuilder (class in hoobas.Build)

I

import_mbuild() (hoobas.Composite.CompositeObject static method) import_snapshot() (hoobas.Build.HOOMDBuilder method)

ImproperType (class in hoobas.Composite) ITPMartiniParser (class in hoobas.MartiniModels)

L

Lattice (class in hoobas.SimulationDomain) LayeredTiling (class in hoobas.Layers)

LinearChain (class in hoobas.LinearChain) link() (hoobas.Composite.TopologyTypeList method) load() (hoobas.Composite.CompositeObject static method)

M

make_set() (hoobas.Composite.TopologyTypeList method) map() (hoobas.MartiniModels.MMaps static method) map_from_default() (hoobas.MartiniModels.MMaps static method) MartiniChain (class in hoobas.MartiniModels) MartiniForceMappings (class in hoobas.MartiniModels) MartiniMappings (class in hoobas.MartiniModels) MartiniPolarizableWaterMolecule (class in hoobas.MartiniModels)

match_box_conventions() (hoobas.Build.openMMBuilder method) match_hoomd_box_conventions() (hoobas.Build.HOOMDBuilder method) merge() (hoobas.Composite.CompositeObject method) MetaBuilder (class in hoobas.Build) MMaps (class in hoobas.MartiniModels) MultiDisperseColloid (class in hoobas.Colloid) Multilayer (class in hoobas.Layers)

N

normal_to() (hoobas.SimulationDomain.Lattice static method) normalization() (hoobas.Build.Electrostatics property)

normalize() (hoobas.Build.Electrostatics method) num_beads() (hoobas.Build.Builder property)

O

obj_end_index() (hoobas.Build.Builder property) obj_start_index() (hoobas.Build.Builder property)

Octahedron (class in hoobas.GenShape) openMMBuilder (class in hoobas.Build) override() (hoobas.Composite.CompositeObject method)

P

pairlist_by_type() (hoobas.Build.ESPResSOppBuilder method) parse_input_lattice() (hoobas.SimulationDomain.Domain static method) parse_pdb_protein() (hoobas.GenShape.PdbProtein method) ParsingError PdbProtein (class in hoobas.GenShape) permittivity() (hoobas.Build.Electrostatics property)

Polyaniline (class in hoobas.LinearChain) PolymerBySequence (class in hoobas.LinearChain) PolyStyreneSulfonateChain (class in hoobas.LinearChain) PolystyreneSulfonateMonomer (class in hoobas.LinearChain) potential() (hoobas.Composite.TopologyType property) ProteinResidueCG (class in hoobas.GenShape)

Q

quadruplelist_by_type() (hoobas.Build.ESPResSOppBuilder method)

R

RandomPolymer (class in hoobas.LinearChain) read() (hoobas.Build.ESPResSOppBuilder method) relative_positions() (hoobas.Colloid.Colloid method) (hoobas.Colloid.FromComposite method)

remap() (hoobas.Composite.TopologyTypeList method) (hoobas.MartiniModels.MMaps static method) resolve_args() (hoobas.Composite.CompositeObject method) reverse_lookup() (hoobas.MartiniModels.MMaps static method) RhombicDodecahedron (class in hoobas.GenShape)

S

save() (hoobas.Composite.CompositeObject method) set_eps_salt_water() (hoobas.Build.Electrostatics method) set_eps_water_temperature() (hoobas.Build.Electrostatics method) set_geometric_quaternion() (hoobas.GenShape.shape method) set_rotation_function() (hoobas.Build.Builder method) set_snapshot() (hoobas.Build.HOOMDBuilder method) shape (class in hoobas.GenShape) ShellShape (class in hoobas.GenShape)

shift_pos() (hoobas.Build.Builder method) SimpleColloid (class in hoobas.Colloid) Sphere (class in hoobas.GenShape) SquareRod (class in hoobas.GenShape) sticky_end (hoobas.LinearChain.DNAChain attribute) surface_types() (hoobas.Build.Builder property) swap_ends() (hoobas.LinearChain.DNA3SPNChain method) sys_box() (hoobas.Build.Builder property)

T

Tetrahedron (class in hoobas.GenShape) thickness() (hoobas.LinearChain.LinearChain property) TopologyItem (class in hoobas.Composite) TopologyList (class in hoobas.Composite) TopologyType (class in hoobas.Composite) TopologyTypeList (class in hoobas.Composite)

transform() (hoobas.Composite.TopologyType method) (hoobas.Composite.TopologyTypeList method) (hoobas.Layers.Multilayer method) triplelist_by_type() (hoobas.Build.ESPResSOppBuilder method) TruncatedTetrahedron (class in hoobas.GenShape) type_from_default() (hoobas.MartiniModels.MMaps static method)

U

unlink() (hoobas.Composite.TopologyTypeList method)

W

write() (hoobas.Build.ESPResSOppBuilder method) (hoobas.Build.openMMBuilder method)