baggianalysis
0.0.2a1.dev24+gb8d84ed.d20210208
The core module
Particle-related classes
Topology-related classes and utility functions
Configuration parsers
Configuration exporters
Filters
Trajectory classes
Observables
Neighbour finders
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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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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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_neighbour() (baggianalysis.core.Particle method)
add_dihedral() (baggianalysis.core.Topology method)
add_filter() (baggianalysis.core.BaseTrajectory method)
add_neighbour() (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.ConvexHull method)
(baggianalysis.core.FormFactor method)
(baggianalysis.core.PoreSize method)
(baggianalysis.core.StructureFactor method)
analyse_trajectory() (baggianalysis.core.BondOrderParameters method)
(baggianalysis.core.ConvexHull method)
(baggianalysis.core.FormFactor method)
(baggianalysis.core.MSD method)
(baggianalysis.core.PoreSize method)
(baggianalysis.core.StructureFactor method)
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_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
clear_b_factors() (baggianalysis.core.StructureFactor method)
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
destructured_from_system() (baggianalysis.core.StructureFactor method)
DestructuredStructureFactor (class in baggianalysis.core)
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)
I
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_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)
molecule() (baggianalysis.core.Particle property)
molecules() (baggianalysis.core.System method)
MSD (class in baggianalysis.core)
N
N() (baggianalysis.core.ParticleSet 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)
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)
ParticleSet (class in baggianalysis.core)
PoreSize (class in baggianalysis.core)
position() (baggianalysis.core.Particle property)
positions() (baggianalysis.core.ParticleSet method)
Q
q_modules() (baggianalysis.core.DestructuredStructureFactor property)
R
radius() (baggianalysis.core.PoreSize method)
remove_particle() (baggianalysis.core.ParticleSet method)
remove_particle_by_id() (baggianalysis.core.ParticleSet method)
reset() (baggianalysis.core.BaseTrajectory method)
result() (baggianalysis.core.BondOrderParameters method)
(baggianalysis.core.ConvexHull method)
(baggianalysis.core.FormFactor method)
(baggianalysis.core.MSD method)
(baggianalysis.core.PoreSize 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_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)
triangles() (baggianalysis.core.ConvexHullResult property)
type() (baggianalysis.core.Particle property)
types() (baggianalysis.core.ParticleSet 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)