Index

_

_parse_file() (baggianalysis.core.BaseParser method)

A

add_angle() (baggianalysis.core.Topology method) add_bond() (baggianalysis.core.Topology method) add_bonded_angle() (baggianalysis.core.Particle method) add_bonded_dihedral() (baggianalysis.core.Particle method) add_bonded_neighbour() (baggianalysis.core.Particle method) add_chain_bonds() (baggianalysis.core.Topology method) add_dihedral() (baggianalysis.core.Topology method) add_filter() (baggianalysis.core.BaseTrajectory method) add_neighbour() (baggianalysis.core.Particle method) add_orientation_vector() (baggianalysis.core.Particle method) add_particle() (baggianalysis.core.CellLists method) (baggianalysis.core.ParticleSet method) analyse_and_print() (baggianalysis.core.CollectiveISF method) (baggianalysis.core.MSD method) (baggianalysis.core.ParticleAutocorrelation method) (baggianalysis.core.SelfISF method) analyse_particle_set() (baggianalysis.core.FormFactor method) (baggianalysis.core.GyrationRadius method) analyse_system() (baggianalysis.core.BondOrderParameters method) (baggianalysis.core.ClusterList method) (baggianalysis.core.ConvexHull method) (baggianalysis.core.FormFactor method) (baggianalysis.core.GyrationRadius method) (baggianalysis.core.PoreSize method) (baggianalysis.core.RDF method) (baggianalysis.core.StructureFactor method)

analyse_trajectory() (baggianalysis.core.BondOrderParameters method) (baggianalysis.core.ClusterList method) (baggianalysis.core.CollectiveISF method) (baggianalysis.core.ConvexHull method) (baggianalysis.core.FormFactor method) (baggianalysis.core.GyrationRadius method) (baggianalysis.core.MSD method) (baggianalysis.core.ParticleAutocorrelation method) (baggianalysis.core.PoreSize method) (baggianalysis.core.RDF method) (baggianalysis.core.SelfISF method) (baggianalysis.core.StructureFactor method) angles() (baggianalysis.core.Topology property) angular_velocity() (baggianalysis.core.Particle property) apply() (baggianalysis.core.Topology method) area() (baggianalysis.core.ConvexHullResult property) (baggianalysis.core.ConvexHullTriangle method) available_index() (baggianalysis.core.System method)

B

BaseExporter (class in baggianalysis.core) BaseFilter (class in baggianalysis.core) BaseParser (class in baggianalysis.core) BaseTrajectory (class in baggianalysis.core) bonded_angles() (baggianalysis.core.Particle property)

bonded_dihedrals() (baggianalysis.core.Particle property) bonded_neighbours() (baggianalysis.core.Particle property) BondOrderParameters (class in baggianalysis.core) bonds() (baggianalysis.core.Topology property) box() (baggianalysis.core.System property) bring_particles_in_box() (baggianalysis.core.System method)

C

CellLists (class in baggianalysis.core) charge() (baggianalysis.core.Particle property) (baggianalysis.core.ParticleSet method) charges() (baggianalysis.core.ParticleSet method) clear_b_factors() (baggianalysis.core.FormFactor method) (baggianalysis.core.StructureFactor method) ClusterList (class in baggianalysis.core) clusters() (baggianalysis.core.ClusterList property) (baggianalysis.core.Topology property) Cogli1Exporter (class in baggianalysis.core)

Cogli1Particle (class in baggianalysis.core) CollectiveISF (class in baggianalysis.core) color() (baggianalysis.core.Cogli1Particle property) com() (baggianalysis.core.ParticleSet method) ConvexHull (class in baggianalysis.core) ConvexHullResult (class in baggianalysis.core) ConvexHullTriangle (class in baggianalysis.core) copy_topology_from() (baggianalysis.core.System method) cos_contribs() (baggianalysis.core.DestructuredStructureFactor property) CutoffFinder (class in baggianalysis.core)

D

Default (class in baggianalysis.core.oxDNA_topology) destructured_from_system() (baggianalysis.core.StructureFactor method)

DestructuredStructureFactor (class in baggianalysis.core) dihedrals() (baggianalysis.core.Topology property) disable_checks() (baggianalysis.core.Topology method)

E

empty_copy() (baggianalysis.core.System method)

enable_checks() (baggianalysis.core.Topology method)

F

filter() (baggianalysis.core.BaseFilter method) FilterByFunction (class in baggianalysis.core) FilterById (class in baggianalysis.core) FilterByReducingToCOM (class in baggianalysis.core) FilterByType (class in baggianalysis.core)

FixedNumberFinder (class in baggianalysis.core) FixParticlePath (class in baggianalysis.core) FormFactor (class in baggianalysis.core) frames() (baggianalysis.core.FullTrajectory property) FullTrajectory (class in baggianalysis.core)

G

GenericOxDNAExporter (class in baggianalysis.core) get_cell() (baggianalysis.core.CellLists method)

GroParser (class in baggianalysis.core) GyrationRadius (class in baggianalysis.core)

H

has_bonded_neighbour() (baggianalysis.core.Particle method)

has_neighbour() (baggianalysis.core.Particle method)

I

id_exists() (baggianalysis.core.ParticleSet method) include_bonded_neighbours() (baggianalysis.core.NeighbourFinder method) index() (baggianalysis.core.Particle property) indexes() (baggianalysis.core.ParticleSet method) init() (baggianalysis.core.WaveVectorList method)

init_cells() (baggianalysis.core.CellLists method) initialise_from_filelist() (baggianalysis.core.BaseTrajectory method) initialise_from_folder() (baggianalysis.core.BaseTrajectory method) initialise_from_trajectory_file() (baggianalysis.core.BaseTrajectory method) is_overlap() (baggianalysis.core.CellLists method)

L

LAMMPS_cogli() (in module baggianalysis.converters) LAMMPS_cogli_command_line() (in module baggianalysis.converters) LAMMPSDataFileExporter (class in baggianalysis.core) LAMMPSDataFileParser (class in baggianalysis.core)

LAMMPSDumpParser (class in baggianalysis.core) LAMMPSTrajectory() (in module baggianalysis.traj) LazyTrajectory (class in baggianalysis.core) LJKAParser (class in baggianalysis.core)

M

make_copy() (baggianalysis.core.Particle method) (baggianalysis.core.ParticleSet method) make_empty_topology() (baggianalysis.core.Topology static method) make_system() (baggianalysis.core.BaseParser method) make_topology_from_file() (baggianalysis.core.Topology static method) make_topology_from_system() (baggianalysis.core.Topology static method)

MapParticles (class in baggianalysis.core) mass() (baggianalysis.core.Particle property) (baggianalysis.core.ParticleSet method) masses() (baggianalysis.core.ParticleSet method) molecule() (baggianalysis.core.Particle property) molecules() (baggianalysis.core.System method) MSD (class in baggianalysis.core)

N

N() (baggianalysis.core.oxDNA_topology.Default method) (baggianalysis.core.ParticleSet method) N_A() (baggianalysis.core.oxDNA_topology.Default method) N_arms() (baggianalysis.core.oxDNA_topology.TSP method) N_monomers_per_arm() (baggianalysis.core.oxDNA_topology.TSP method) N_stars() (baggianalysis.core.oxDNA_topology.TSP method) name() (baggianalysis.core.ParticleSet property) (baggianalysis.core.SANNFinder.SymmetryPolicy property)

NeighbourFinder (class in baggianalysis.core) neighbours() (baggianalysis.core.Particle property) next_frame() (baggianalysis.core.BaseTrajectory method) NO_ACTION (baggianalysis.core.SANNFinder attribute) (baggianalysis.core.SANNFinder.SymmetryPolicy attribute) normal() (baggianalysis.core.ConvexHullTriangle property) normalise_molecules() (baggianalysis.core.System method)

O

orientation_vectors() (baggianalysis.core.Particle property) other() (baggianalysis.core.ParticleBond method) oxDNA_cogli() (in module baggianalysis.converters) oxDNA_cogli_command_line() (in module baggianalysis.converters)

oxDNA_LAMMPS() (in module baggianalysis.converters) oxDNA_LAMMPS_command_line() (in module baggianalysis.converters) OxDNAParser (class in baggianalysis.core) OxDNATrajectory() (in module baggianalysis.traj)

P

parse_LAMMPS_topology() (in module baggianalysis.core) parse_microgel_bondfile() (in module baggianalysis.core) parse_polymer_bondfile() (in module baggianalysis.core) Particle (class in baggianalysis.core) particle_by_id() (baggianalysis.core.ParticleSet method) ParticleAngle (class in baggianalysis.core) ParticleAutocorrelation (class in baggianalysis.core) ParticleBond (class in baggianalysis.core) ParticleDihedral (class in baggianalysis.core) particles() (baggianalysis.core.ParticleSet method) (baggianalysis.core.TopologyAngle property) (baggianalysis.core.TopologyBond property) (baggianalysis.core.TopologyDihedral property)

ParticleSet (class in baggianalysis.core) PatchyParticlesParser (class in baggianalysis.core) PoreSize (class in baggianalysis.core) position() (baggianalysis.core.Particle property) positions() (baggianalysis.core.ParticleSet method) print_bondfile() (in module baggianalysis.utils) print_detailed_polymer_topology() (in module baggianalysis.utils)

Q

q_modules() (baggianalysis.core.DestructuredStructureFactor property) (baggianalysis.core.WaveVectorList method)

q_vectors() (baggianalysis.core.WaveVectorList property)

R

radius() (baggianalysis.core.PoreSize method) RDF (class in baggianalysis.core) reindex_particles() (baggianalysis.core.System method) remove_bonded_neighbour() (baggianalysis.core.Particle method) remove_neighbour() (baggianalysis.core.Particle method) remove_particle() (baggianalysis.core.ParticleSet method) remove_particle_by_id() (baggianalysis.core.ParticleSet method) remove_unappliable_links() (baggianalysis.core.Topology method) rescale_lengths() (baggianalysis.core.System method) reset() (baggianalysis.core.BaseTrajectory method) (baggianalysis.core.BondOrderParameters method) (baggianalysis.core.ClusterList method) (baggianalysis.core.CollectiveISF method) (baggianalysis.core.ConvexHull method) (baggianalysis.core.FormFactor method) (baggianalysis.core.GyrationRadius method) (baggianalysis.core.MSD method) (baggianalysis.core.ParticleAutocorrelation method) (baggianalysis.core.PoreSize method) (baggianalysis.core.RDF method) (baggianalysis.core.SelfISF method) (baggianalysis.core.StructureFactor method)

result() (baggianalysis.core.BondOrderParameters method) (baggianalysis.core.ClusterList method) (baggianalysis.core.CollectiveISF method) (baggianalysis.core.ConvexHull method) (baggianalysis.core.FormFactor method) (baggianalysis.core.GyrationRadius method) (baggianalysis.core.MSD method) (baggianalysis.core.ParticleAutocorrelation method) (baggianalysis.core.PoreSize method) (baggianalysis.core.RDF method) (baggianalysis.core.SelfISF method) (baggianalysis.core.StructureFactor method)

S

SANNFinder (class in baggianalysis.core) SANNFinder.SymmetryPolicy (class in baggianalysis.core) select() (baggianalysis.core.ParticleSet method) SelfISF (class in baggianalysis.core) set_b_factors() (baggianalysis.core.FormFactor method) (baggianalysis.core.StructureFactor method) set_com() (baggianalysis.core.ParticleSet method) set_include_system() (baggianalysis.core.BaseTrajectory method) set_logging_mode() (in module baggianalysis.core) set_neighbours() (baggianalysis.core.NeighbourFinder method) set_orientation_inserter() (baggianalysis.core.OxDNAParser method) set_topology() (baggianalysis.core.BaseParser method)

shift() (baggianalysis.core.Particle method) show() (baggianalysis.core.Cogli1Particle property) sin_contribs() (baggianalysis.core.DestructuredStructureFactor property) size() (baggianalysis.core.Cogli1Particle property) sort_particles_by_id() (baggianalysis.core.ParticleSet method) StructureFactor (class in baggianalysis.core) SubtractCOM (class in baggianalysis.core) SYMMETRISE_BY_ADDING (baggianalysis.core.SANNFinder attribute) (baggianalysis.core.SANNFinder.SymmetryPolicy attribute) SYMMETRISE_BY_REMOVING (baggianalysis.core.SANNFinder attribute) (baggianalysis.core.SANNFinder.SymmetryPolicy attribute) System (class in baggianalysis.core)

T

time() (baggianalysis.core.System property) Topology (class in baggianalysis.core) topology() (baggianalysis.core.LAMMPSDataFileParser property) topology_from_LAMMPS_data_file() (in module baggianalysis.core) topology_parser() (baggianalysis.core.OxDNAParser method) TopologyAngle (class in baggianalysis.core) TopologyBond (class in baggianalysis.core) TopologyDihedral (class in baggianalysis.core)

triangles() (baggianalysis.core.ConvexHullResult property) TSP (class in baggianalysis.core.oxDNA_topology) type() (baggianalysis.core.oxDNA_topology.Default method) (baggianalysis.core.Particle property) (baggianalysis.core.TopologyAngle property) (baggianalysis.core.TopologyBond property) (baggianalysis.core.TopologyDihedral property) types() (baggianalysis.core.ParticleSet method)

U

use_topology() (baggianalysis.core.BaseParser method)

V

v1() (baggianalysis.core.ConvexHullTriangle property) v2() (baggianalysis.core.ConvexHullTriangle property) v3() (baggianalysis.core.ConvexHullTriangle property) value() (baggianalysis.core.SANNFinder.SymmetryPolicy property) velocities() (baggianalysis.core.ParticleSet method)

velocity() (baggianalysis.core.Particle property) (baggianalysis.core.ParticleSet method) vertices() (baggianalysis.core.ConvexHullResult property) volume() (baggianalysis.core.ConvexHullResult property) (baggianalysis.core.ConvexHullTriangle method)

W

WaveVectorList (class in baggianalysis.core) write() (baggianalysis.core.BaseExporter method)

write_topology() (baggianalysis.core.BaseExporter method) write_trajectory() (baggianalysis.core.BaseExporter method)