Index

Symbols

--focal-length cinemol command line option --include-hydrogens cinemol command line option --look cinemol command line option --resolution cinemol command line option --rotation-over-x-axis cinemol command line option --rotation-over-y-axis cinemol command line option --rotation-over-z-axis cinemol command line option --scale cinemol command line option --style cinemol command line option --verbosity cinemol command line option --version cinemol command line option

-fl cinemol command line option -hs cinemol command line option -l cinemol command line option -r cinemol command line option -rx cinemol command line option -ry cinemol command line option -rz cinemol command line option -s cinemol command line option -sc cinemol command line option -v cinemol command line option

A

add_node() (Scene method) arange() (in module cinemol.fitting) argmax() (in module cinemol.fitting)

argmin() (in module cinemol.fitting) Atom (class in cinemol.api) AtomColoringScheme (class in cinemol.style) AtomRadiusScheme (class in cinemol.style)

B

Bond (class in cinemol.api)

C

calculate_convex_hull() (in module cinemol.fitting) calculate_distance() (Point3D method) calculate_intersecting_nodes() (in module cinemol.model) calculate_view_box() (Scene method) Cartoon (class in cinemol.style) cinemol command line option --focal-length --include-hydrogens --look --resolution --rotation-over-x-axis --rotation-over-y-axis --rotation-over-z-axis --scale --style --verbosity --version -fl -hs -l -r -rx -ry -rz -s -sc -v INPUT OUTPUT

cinemol.api module cinemol.fitting module cinemol.geometry module cinemol.model module cinemol.parsers module cinemol.style module cinemol.svg module Circle2D (class in cinemol.svg) Circle3D (class in cinemol.geometry) Color (class in cinemol.style) CoreyPaulingKoltungAtomColor (class in cinemol.style) create_fill() (in module cinemol.model) create_random() (Vector3D class method) create_vector() (Point3D method) cross() (Point2D method) (Vector3D method) Cylinder (class in cinemol.geometry) cylinder_intersects_with_cylinder() (in module cinemol.geometry) CylinderCapType (class in cinemol.geometry)

D

Depiction (class in cinemol.style) diffuse() (Color method) distance_to_line() (in module cinemol.geometry) dot() (Vector3D method)

draw() (Scene method) draw_atoms_in_spacefilling_style() (in module cinemol.api) draw_bonds_in_tube_style() (in module cinemol.api) draw_bonds_in_wireframe_style() (in module cinemol.api) draw_molecule() (in module cinemol.api)

F

Fill (class in cinemol.style) FillStyle (class in cinemol.style)

filter_atoms_and_bonds() (in module cinemol.api) footer() (Svg method)

G

get_color() (AtomColoringScheme method) (CoreyPaulingKoltungAtomColor method) get_node_polygon_vertices() (in module cinemol.model) get_perpendicular_lines() (in module cinemol.geometry) get_points_on_circumference_circle_3d() (in module cinemol.geometry) get_points_on_line_3d() (in module cinemol.geometry)

get_points_on_surface_cap() (in module cinemol.geometry) get_points_on_surface_circle_3d() (in module cinemol.geometry) get_points_on_surface_cylinder() (in module cinemol.geometry) get_points_on_surface_sphere() (in module cinemol.geometry) Glossy (class in cinemol.style) gram_schmidt() (in module cinemol.geometry)

H

header() (Svg method)

I

INPUT cinemol command line option

L

length() (Vector3D method) Line2D (class in cinemol.svg)

Line3D (class in cinemol.geometry) LinearGradient (class in cinemol.style) Look (class in cinemol.api)

M

midpoint() (Point3D method) ModelCylinder (class in cinemol.model) ModelSphere (class in cinemol.model) ModelWire (class in cinemol.model) module cinemol.api cinemol.fitting cinemol.geometry cinemol.model cinemol.parsers cinemol.style cinemol.svg

multiply() (Vector3D method)

N

normalize() (Vector3D method)

O

OUTPUT cinemol command line option

P

parse_sdf() (in module cinemol.parsers) Plane3D (class in cinemol.geometry) Point2D (class in cinemol.geometry) Point3D (class in cinemol.geometry) point_is_inside_cylinder() (in module cinemol.geometry)

point_is_inside_sphere() (in module cinemol.geometry) Polygon2D (class in cinemol.svg) prepare_nodes_for_intersecting() (in module cinemol.model) process() (in module cinemol.fitting) PubChemAtomRadius (class in cinemol.style)

R

RadialGradient (class in cinemol.style)

rotate() (Point3D method)

S

same_side_of_plane() (in module cinemol.geometry) Scene (class in cinemol.model) Shape2D (class in cinemol.svg) sign() (in module cinemol.geometry) Solid (class in cinemol.style) Sphere (class in cinemol.geometry)

sphere_intersects_with_cylinder() (in module cinemol.geometry) sphere_intersects_with_sphere() (in module cinemol.geometry) Style (class in cinemol.api) subtract() (Vector3D method) subtract_point() (Point2D method) Svg (class in cinemol.svg)

T

to_angstrom() (AtomRadiusScheme method) (PubChemAtomRadius method) to_hex() (Color method) to_svg() (Circle2D method) (Fill method) (Line2D method) (Polygon2D method) (Shape2D method) (Svg method) (ViewBox method)

translate() (Point3D method)

V

Vector3D (class in cinemol.geometry)

ViewBox (class in cinemol.svg)

W

Wire (class in cinemol.style)