baggianalysis
0.2.0b1.dev9+g42a7eac.d20210823
The core module
Particle-related classes
Topology-related classes and utility functions
Configuration parsers
Configuration exporters
Filters
Trajectory classes
Observables
Neighbour finders
The utils module
Writing a parser
Writing a function to parse custom topologies
baggianalysis
»
Index
Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
_
_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_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.ParticleSet method)
analyse_and_print() (baggianalysis.core.MSD method)
analyse_particle_set() (baggianalysis.core.FormFactor method)
analyse_system() (baggianalysis.core.BondOrderParameters method)
(baggianalysis.core.ClusterList method)
(baggianalysis.core.ConvexHull method)
(baggianalysis.core.FormFactor 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.ConvexHull method)
(baggianalysis.core.FormFactor method)
(baggianalysis.core.MSD method)
(baggianalysis.core.PoreSize method)
(baggianalysis.core.RDF method)
(baggianalysis.core.StructureFactor method)
angles() (baggianalysis.core.Topology property)
apply() (baggianalysis.core.Topology method)
area() (baggianalysis.core.ConvexHullResult property)
(baggianalysis.core.ConvexHullTriangle method)
available_index() (baggianalysis.core.System method)
average_velocity() (baggianalysis.core.ParticleSet 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
charge() (baggianalysis.core.Particle property)
(baggianalysis.core.ParticleSet method)
charges() (baggianalysis.core.ParticleSet method)
clear_b_factors() (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)
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)
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)
GroParser (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)
initialise_from_filelist() (baggianalysis.core.BaseTrajectory method)
initialise_from_folder() (baggianalysis.core.BaseTrajectory method)
initialise_from_trajectory_file() (baggianalysis.core.BaseTrajectory method)
L
LAMMPSDataFileExporter (class in baggianalysis.core)
LAMMPSDataFileParser (class in baggianalysis.core)
LAMMPSDumpParser (class in baggianalysis.core)
LazyTrajectory (class in baggianalysis.core)
LJKAParser (class in baggianalysis.core)
M
make_copy() (baggianalysis.core.Particle 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)
OxDNAParser (class in baggianalysis.core)
P
parse_LAMMPS_topology() (in module baggianalysis.core)
parse_microgel_bondfile() (in module baggianalysis.core)
Particle (class in baggianalysis.core)
particle_by_id() (baggianalysis.core.ParticleSet method)
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)
Q
q_modules() (baggianalysis.core.DestructuredStructureFactor property)
R
radius() (baggianalysis.core.PoreSize method)
RDF (class in baggianalysis.core)
reindex_particles() (baggianalysis.core.System 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.ConvexHull method)
(baggianalysis.core.FormFactor method)
(baggianalysis.core.MSD method)
(baggianalysis.core.PoreSize method)
(baggianalysis.core.RDF method)
(baggianalysis.core.StructureFactor method)
result() (baggianalysis.core.BondOrderParameters method)
(baggianalysis.core.ClusterList method)
(baggianalysis.core.ConvexHull method)
(baggianalysis.core.FormFactor method)
(baggianalysis.core.MSD method)
(baggianalysis.core.PoreSize method)
(baggianalysis.core.RDF method)
(baggianalysis.core.StructureFactor method)
S
SANNFinder (class in baggianalysis.core)
SANNFinder.SymmetryPolicy (class in baggianalysis.core)
set_b_factors() (baggianalysis.core.StructureFactor method)
set_include_system() (baggianalysis.core.BaseTrajectory method)
set_neighbours() (baggianalysis.core.NeighbourFinder method)
set_orientation_inserter() (baggianalysis.core.OxDNAParser method)
set_topology() (baggianalysis.core.BaseParser 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)
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)
velocities() (baggianalysis.core.ParticleSet method)
velocity() (baggianalysis.core.Particle property)
vertices() (baggianalysis.core.ConvexHullResult property)
volume() (baggianalysis.core.ConvexHullResult property)
(baggianalysis.core.ConvexHullTriangle method)
W
write() (baggianalysis.core.BaseExporter method)
write_topology() (baggianalysis.core.BaseExporter method)
write_trajectory() (baggianalysis.core.BaseExporter method)