Index

A | B | C | D | E | F | G | I | L | M | N | O | P | R | S | T | V | W

A

add() (pydmga.container.Container method)

(pydmga.draw.render.Render method)

add_arc() (pydmga.draw.render.SphereArcs method)

add_arcs() (pydmga.draw.render.GreatArcs method)

add_by_coords() (pydmga.container.Container method)

add_cutting_plane_arc() (pydmga.draw.render.SphereArcs method)

add_raw() (pydmga.container.Container method)

add_side() (pydmga.draw.render.ConvexPolygons method)

add_side_point() (pydmga.draw.render.ConvexPolygons method)

add_side_points() (pydmga.draw.render.ConvexPolygons method)

add_vertex() (pydmga.draw.render.ConvexPolygons method)

(pydmga.draw.render.GreatArcs method)
(pydmga.draw.render.PointCloud method)

add_vertices() (pydmga.draw.render.ConvexPolygons method)

(pydmga.draw.render.GreatArcs method)
(pydmga.draw.render.PointCloud method)

adjust_area() (pydmga.geometry.CastCylinderGeometry method)

(pydmga.geometry.Geometry method)

adjust_volume() (pydmga.geometry.Geometry method)

advance() (pydmga.draw.geometry.ArrayInput method)

(pydmga.draw.geometry.Input method)
(pydmga.draw.geometry.MultiFileInput method)

AlphaShape (class in pydmga.shape)

AlphaShapeCell (class in pydmga.shape)

AlphaShapeCellIterator (class in pydmga.shape)

AlphaSimplex (class in pydmga.shape)

area() (pydmga.model.Cell method)

(pydmga.model.CellSide method)

ArrayInput (class in pydmga.draw.geometry)

as_ball() (pydmga.io.pdb.PDBRecord method)

as_coords() (pydmga.io.pdb.PDBRecord method)

(pydmga.model.CellEdge method)
(pydmga.model.CellEdgesCollection method)
(pydmga.model.CellSide method)
(pydmga.model.CellSidesCollection method)
(pydmga.model.CellVertex method)
(pydmga.model.CellVertexCollection method)

as_dict() (pydmga.shape.AlphaSimplex method)

as_dict_short() (pydmga.shape.AlphaSimplex method)

as_list() (pydmga.model.CellSide method)

as_pair() (pydmga.model.CellEdge method)

as_pair_coords() (pydmga.model.CellEdge method)

as_particle() (pydmga.io.pdb.PDBRecord method)

as_tuple() (pydmga.model.CellEdge method)

(pydmga.model.CellVertex method)
(pydmga.shape.AlphaSimplex method)

Asset (class in pydmga.draw.render)

attach_to() (pydmga.draw.render.Asset method)

(pydmga.draw.render.ConvexPolygons method)
(pydmga.draw.render.GreatArcs method)
(pydmga.draw.render.Lines method)
(pydmga.draw.render.Outline method)
(pydmga.draw.render.PointCloud method)
(pydmga.draw.render.Primitive method)
(pydmga.draw.render.SphereArcs method)

B

Ball (class in pydmga.draw.geometry)
BLACK_HALF (pydmga.draw.render.Color attribute)
BLACK_OPAQUE (pydmga.draw.render.Color attribute)
BLACK_QUARTER (pydmga.draw.render.Color attribute)
BLUE10_HALF (pydmga.draw.render.Color attribute)
BLUE10_OPAQUE (pydmga.draw.render.Color attribute)
BLUE10_QUARTER (pydmga.draw.render.Color attribute)
BLUE20_HALF (pydmga.draw.render.Color attribute)
BLUE20_OPAQUE (pydmga.draw.render.Color attribute)
BLUE20_QUARTER (pydmga.draw.render.Color attribute)
BLUE30_HALF (pydmga.draw.render.Color attribute)
BLUE30_OPAQUE (pydmga.draw.render.Color attribute)
BLUE30_QUARTER (pydmga.draw.render.Color attribute)
BLUE40_HALF (pydmga.draw.render.Color attribute)
BLUE40_OPAQUE (pydmga.draw.render.Color attribute)
BLUE40_QUARTER (pydmga.draw.render.Color attribute)
BLUE50_HALF (pydmga.draw.render.Color attribute)
BLUE50_OPAQUE (pydmga.draw.render.Color attribute)

BLUE50_QUARTER (pydmga.draw.render.Color attribute)
BLUE60_HALF (pydmga.draw.render.Color attribute)
BLUE60_OPAQUE (pydmga.draw.render.Color attribute)
BLUE60_QUARTER (pydmga.draw.render.Color attribute)
BLUE70_HALF (pydmga.draw.render.Color attribute)
BLUE70_OPAQUE (pydmga.draw.render.Color attribute)
BLUE70_QUARTER (pydmga.draw.render.Color attribute)
BLUE80_HALF (pydmga.draw.render.Color attribute)
BLUE80_OPAQUE (pydmga.draw.render.Color attribute)
BLUE80_QUARTER (pydmga.draw.render.Color attribute)
BLUE90_HALF (pydmga.draw.render.Color attribute)
BLUE90_OPAQUE (pydmga.draw.render.Color attribute)
BLUE90_QUARTER (pydmga.draw.render.Color attribute)
BLUE_HALF (pydmga.draw.render.Color attribute)
BLUE_OPAQUE (pydmga.draw.render.Color attribute)
BLUE_QUARTER (pydmga.draw.render.Color attribute)
border_arcs() (pydmga.shape.SASACell method)
BoxGeometry (class in pydmga.geometry)

C

cast_to_sphere() (pydmga.draw.render.OnSpherePrimitive method)
CastCylinderGeometry (class in pydmga.geometry)
CastOrthoPlaneGeometry (class in pydmga.geometry)
CastPlaneGeometry (class in pydmga.geometry)
CastSphereGeometry (class in pydmga.geometry)
Cell (class in pydmga.model)
CellEdge (class in pydmga.model)
CellEdgesCollection (class in pydmga.model)
CellEdgesIterator (class in pydmga.model)
CellSide (class in pydmga.model)
CellSideIterator (class in pydmga.model)
CellSidesCollection (class in pydmga.model)
CellSidesIterator (class in pydmga.model)

CellVertex (class in pydmga.model)

CellVertexCollection (class in pydmga.model)

CellVertexIterator (class in pydmga.model)

clear() (pydmga.draw.render.Render method)

Color (class in pydmga.draw.render)

connect() (pydmga.draw.render.GreatArcs method)

Container (class in pydmga.container)

ContainerIterator (class in pydmga.container)

ConvexPolygons (class in pydmga.draw.render)

cross() (pydmga.draw.render.OnSpherePrimitive method)

cube() (in module pydmga.draw.assets)

current_frame() (pydmga.draw.geometry.ArrayInput method)

(pydmga.draw.geometry.Input method)
(pydmga.draw.geometry.MultiFileInput method)

D

Diagram (class in pydmga.diagram)
diagram_part() (pydmga.shape.AlphaSimplex method)
DiagramIterator (class in pydmga.diagram)
DIM_EDGE (pydmga.shape.AlphaSimplex attribute)
DIM_SIDE (pydmga.shape.AlphaSimplex attribute)

DIM_VERTEX (pydmga.shape.AlphaSimplex attribute)
dist() (pydmga.draw.gen.TrajectoryGenerator method)
distance() (pydmga.draw.render.OnSpherePrimitive method)
doOutput() (pydmga.draw.gen.TrajectoryGenerator method)
dot() (pydmga.draw.render.OnSpherePrimitive method)

E

excluded_area() (pydmga.shape.SASACell method)

excluded_volume() (pydmga.shape.SASACell method)

F

find() (pydmga.container.Container method)
first() (pydmga.model.CellEdge method)
first_coords() (pydmga.model.CellEdge method)

first_frame() (pydmga.draw.geometry.ArrayInput method)

(pydmga.draw.geometry.Input method)
(pydmga.draw.geometry.MultiFileInput method)

frame_iterator_task() (pydmga.draw.render.VoroRender method)

G

Geometry (class in pydmga.geometry)

get() (pydmga.container.Container method)

get_all_cells() (pydmga.diagram.Diagram method)

get_cell() (pydmga.diagram.Diagram method)

(pydmga.shape.AlphaShape method)
(pydmga.shape.SASAShape method)
(pydmga.shape.Shape method)

get_cells() (pydmga.diagram.Diagram method)

(pydmga.shape.Shape method)

get_sides() (pydmga.model.Cell method)

get_sides_as_coords() (pydmga.model.Cell method)

go() (pydmga.draw.geometry.ArrayInput method)

(pydmga.draw.geometry.Input method)
(pydmga.draw.geometry.MultiFileInput method)

GRAY10_HALF (pydmga.draw.render.Color attribute)

GRAY10_OPAQUE (pydmga.draw.render.Color attribute)

GRAY10_QUARTER (pydmga.draw.render.Color attribute)

GRAY20_HALF (pydmga.draw.render.Color attribute)

GRAY20_OPAQUE (pydmga.draw.render.Color attribute)

GRAY20_QUARTER (pydmga.draw.render.Color attribute)

GRAY30_HALF (pydmga.draw.render.Color attribute)

GRAY30_OPAQUE (pydmga.draw.render.Color attribute)

GRAY30_QUARTER (pydmga.draw.render.Color attribute)

GRAY40_HALF (pydmga.draw.render.Color attribute)

GRAY40_OPAQUE (pydmga.draw.render.Color attribute)

GRAY40_QUARTER (pydmga.draw.render.Color attribute)

GRAY50_HALF (pydmga.draw.render.Color attribute)

GRAY50_OPAQUE (pydmga.draw.render.Color attribute)

GRAY50_QUARTER (pydmga.draw.render.Color attribute)

GRAY60_HALF (pydmga.draw.render.Color attribute)

GRAY60_OPAQUE (pydmga.draw.render.Color attribute)

GRAY60_QUARTER (pydmga.draw.render.Color attribute)

GRAY70_HALF (pydmga.draw.render.Color attribute)

GRAY70_OPAQUE (pydmga.draw.render.Color attribute)

GRAY70_QUARTER (pydmga.draw.render.Color attribute)

GRAY80_HALF (pydmga.draw.render.Color attribute)

GRAY80_OPAQUE (pydmga.draw.render.Color attribute)

GRAY80_QUARTER (pydmga.draw.render.Color attribute)

GRAY90_HALF (pydmga.draw.render.Color attribute)

GRAY90_OPAQUE (pydmga.draw.render.Color attribute)
GRAY90_QUARTER (pydmga.draw.render.Color attribute)
GreatArcs (class in pydmga.draw.render)
GREEN10_HALF (pydmga.draw.render.Color attribute)
GREEN10_OPAQUE (pydmga.draw.render.Color attribute)
GREEN10_QUARTER (pydmga.draw.render.Color attribute)
GREEN20_HALF (pydmga.draw.render.Color attribute)
GREEN20_OPAQUE (pydmga.draw.render.Color attribute)
GREEN20_QUARTER (pydmga.draw.render.Color attribute)
GREEN30_HALF (pydmga.draw.render.Color attribute)
GREEN30_OPAQUE (pydmga.draw.render.Color attribute)
GREEN30_QUARTER (pydmga.draw.render.Color attribute)
GREEN40_HALF (pydmga.draw.render.Color attribute)
GREEN40_OPAQUE (pydmga.draw.render.Color attribute)
GREEN40_QUARTER (pydmga.draw.render.Color attribute)
GREEN50_HALF (pydmga.draw.render.Color attribute)
GREEN50_OPAQUE (pydmga.draw.render.Color attribute)
GREEN50_QUARTER (pydmga.draw.render.Color attribute)
GREEN60_HALF (pydmga.draw.render.Color attribute)
GREEN60_OPAQUE (pydmga.draw.render.Color attribute)
GREEN60_QUARTER (pydmga.draw.render.Color attribute)
GREEN70_HALF (pydmga.draw.render.Color attribute)
GREEN70_OPAQUE (pydmga.draw.render.Color attribute)
GREEN70_QUARTER (pydmga.draw.render.Color attribute)
GREEN80_HALF (pydmga.draw.render.Color attribute)
GREEN80_OPAQUE (pydmga.draw.render.Color attribute)
GREEN80_QUARTER (pydmga.draw.render.Color attribute)
GREEN90_HALF (pydmga.draw.render.Color attribute)
GREEN90_OPAQUE (pydmga.draw.render.Color attribute)
GREEN90_QUARTER (pydmga.draw.render.Color attribute)
GREEN_HALF (pydmga.draw.render.Color attribute)
GREEN_OPAQUE (pydmga.draw.render.Color attribute)
GREEN_QUARTER (pydmga.draw.render.Color attribute)

I

Input (class in pydmga.draw.geometry)

L

last_frame() (pydmga.draw.geometry.ArrayInput method)

(pydmga.draw.geometry.Input method)
(pydmga.draw.geometry.MultiFileInput method)

leap() (pydmga.draw.geometry.ArrayInput method)

(pydmga.draw.geometry.Input method)
(pydmga.draw.geometry.MultiFileInput method)

Lines (class in pydmga.draw.render)

M

max_alpha_threshold() (pydmga.shape.AlphaShape method)

(pydmga.shape.AlphaShapeCell method)

MultiFileInput (class in pydmga.draw.geometry)

N

next() (pydmga.container.ContainerIterator method)

(pydmga.diagram.DiagramIterator method)
(pydmga.model.CellEdgesIterator method)
(pydmga.model.CellSideIterator method)
(pydmga.model.CellSidesIterator method)
(pydmga.model.CellVertexIterator method)
(pydmga.shape.AlphaShapeCellIterator method)
(pydmga.shape.SASAContoursIterator method)
(pydmga.shape.ShapeIterator method)

normalize() (pydmga.draw.render.OnSpherePrimitive method)

O

on_boundary() (pydmga.geometry.BoxGeometry method)

(pydmga.geometry.CastCylinderGeometry method)
(pydmga.geometry.CastOrthoPlaneGeometry method)
(pydmga.geometry.CastSphereGeometry method)
(pydmga.geometry.Geometry method)
(pydmga.geometry.OrthogonalGeometry method)

OneFrame (class in pydmga.draw.geometry)

OnSpherePrimitive (class in pydmga.draw.render)

OrthogonalGeometry (class in pydmga.geometry)
Outline (class in pydmga.draw.render)

P

PDBRecord (class in pydmga.io.pdb)
PointCloud (class in pydmga.draw.render)
polygon_arcs() (pydmga.shape.SASACell method)
Position (class in pydmga.draw.geometry)
Primitive (class in pydmga.draw.render)
pydmga.__init__ (module)
pydmga.container (module)
pydmga.diagram (module)
pydmga.draw (module)

pydmga.draw.assets (module)
pydmga.draw.gen (module)
pydmga.draw.geometry (module)
pydmga.draw.render (module)
pydmga.geometry (module)
pydmga.io (module)
pydmga.io.pdb (module)
pydmga.model (module)
pydmga.shape (module)

R

random() (in module pydmga.geometry)
readnext() (in module pydmga.io.pdb)
RED10_HALF (pydmga.draw.render.Color attribute)
RED10_OPAQUE (pydmga.draw.render.Color attribute)
RED10_QUARTER (pydmga.draw.render.Color attribute)
RED20_HALF (pydmga.draw.render.Color attribute)
RED20_OPAQUE (pydmga.draw.render.Color attribute)
RED20_QUARTER (pydmga.draw.render.Color attribute)
RED30_HALF (pydmga.draw.render.Color attribute)
RED30_OPAQUE (pydmga.draw.render.Color attribute)
RED30_QUARTER (pydmga.draw.render.Color attribute)
RED40_HALF (pydmga.draw.render.Color attribute)
RED40_OPAQUE (pydmga.draw.render.Color attribute)
RED40_QUARTER (pydmga.draw.render.Color attribute)
RED50_HALF (pydmga.draw.render.Color attribute)
RED50_OPAQUE (pydmga.draw.render.Color attribute)
RED50_QUARTER (pydmga.draw.render.Color attribute)

RED60_HALF (pydmga.draw.render.Color attribute)
RED60_OPAQUE (pydmga.draw.render.Color attribute)
RED60_QUARTER (pydmga.draw.render.Color attribute)
RED70_HALF (pydmga.draw.render.Color attribute)
RED70_OPAQUE (pydmga.draw.render.Color attribute)
RED70_QUARTER (pydmga.draw.render.Color attribute)
RED80_HALF (pydmga.draw.render.Color attribute)
RED80_OPAQUE (pydmga.draw.render.Color attribute)
RED80_QUARTER (pydmga.draw.render.Color attribute)
RED90_HALF (pydmga.draw.render.Color attribute)
RED90_OPAQUE (pydmga.draw.render.Color attribute)
RED90_QUARTER (pydmga.draw.render.Color attribute)
RED_HALF (pydmga.draw.render.Color attribute)
RED_OPAQUE (pydmga.draw.render.Color attribute)
RED_QUARTER (pydmga.draw.render.Color attribute)
Render (class in pydmga.draw.render)

S

sas_area() (pydmga.shape.SASACell method)

(pydmga.shape.SASAShape method)

sas_volume() (pydmga.shape.SASACell method)

(pydmga.shape.SASAShape method)

SASAArc (class in pydmga.shape)

SASACell (class in pydmga.shape)

SASAContoursIterator (class in pydmga.shape)

SASAShape (class in pydmga.shape)

second() (pydmga.model.CellEdge method)

second_coords() (pydmga.model.CellEdge method)

Shape (class in pydmga.shape)

shape() (pydmga.shape.AlphaShapeCell method)

(pydmga.shape.SASACell method)

ShapeIterator (class in pydmga.shape)

simulation() (pydmga.draw.gen.TrajectoryGenerator method)

size() (pydmga.container.Container method)

(pydmga.diagram.Diagram method)
(pydmga.model.CellEdgesCollection method)
(pydmga.model.CellSide method)
(pydmga.model.CellSidesCollection method)
(pydmga.model.CellVertexCollection method)
(pydmga.shape.AlphaShape method)
(pydmga.shape.SASAShape method)
(pydmga.shape.Shape method)

sphere() (in module pydmga.draw.assets)

SphereArcs (class in pydmga.draw.render)

start_side() (pydmga.draw.render.ConvexPolygons method)

startOutput() (pydmga.draw.gen.TrajectoryGenerator method)

stopOutput() (pydmga.draw.gen.TrajectoryGenerator method)

T

TrajectoryGenerator (class in pydmga.draw.gen)

transform() (pydmga.geometry.CastCylinderGeometry method)

(pydmga.geometry.CastOrthoPlaneGeometry method)
(pydmga.geometry.CastPlaneGeometry method)
(pydmga.geometry.CastSphereGeometry method)
(pydmga.geometry.Geometry method)

type() (pydmga.io.pdb.PDBRecord method)

V

volume() (pydmga.model.Cell method)

VoroRender (class in pydmga.draw.render)

W

WHITE_HALF (pydmga.draw.render.Color attribute)
WHITE_OPAQUE (pydmga.draw.render.Color attribute)

WHITE_QUARTER (pydmga.draw.render.Color attribute)