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 attribute) 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 attribute) center_types (hoobas.Build.Builder attribute) change_units() (hoobas.SimulationDomain.Domain method) (hoobas.SimulationDomain.Lattice method) charge_list (hoobas.Build.Builder attribute) 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 attribute) 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_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)

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 attribute)

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

O

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

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 attribute)

Polyaniline (class in hoobas.LinearChain) PolymerBySequence (class in hoobas.LinearChain) PolyStyreneSulfonateChain (class in hoobas.LinearChain) PolystyreneSulfonateMonomer (class in hoobas.LinearChain) potential (hoobas.Composite.TopologyType attribute) 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_to_salt_CPeter() (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 attribute) swap_ends() (hoobas.LinearChain.DNA3SPNChain method) sys_box (hoobas.Build.Builder attribute)

T

Tetrahedron (class in hoobas.GenShape) 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)

X

XY_rotate() (hoobas.LinearChain.LinearChain method)