Index

A

alexander() (in module topoly) ALL (topoly.params.Bridges attribute)

aps() (in module topoly) ATOMS (topoly.params.OutputType attribute)

B

blmho() (in module topoly)

Bridges (class in topoly.params)

C

Ccode (topoly.params.OutputFormat attribute) close_curve() (in module topoly) CLOSED (topoly.params.Closure attribute)

Closure (class in topoly.params) Colors (class in topoly.params) conway() (in module topoly) COVALENT (topoly.params.Bridges attribute)

D

DensitySurface (class in topoly.params) Dictionary (topoly.params.OutputFormat attribute)

DIRECTION (topoly.params.Closure attribute) DONTPLOT (topoly.params.SurfacePlotFormat attribute)

E

EASY (topoly.params.ReduceMethod attribute)

EMcode (topoly.params.OutputType attribute) exportpoly() (in module topoly)

F

find_handcuffs() (in module topoly) find_loops() (in module topoly)

find_matching() (in module topoly) find_spots() (in module topoly) find_thetas() (in module topoly)

G

generate_handcuff() (in module topoly) generate_lasso() (in module topoly) generate_link() (in module topoly) generate_loop() (in module topoly)

generate_theta() (in module topoly) generate_walk() (in module topoly) getpoly() (in module topoly) GLN (topoly.params.Colors attribute) gln() (in module topoly)

H

HIGH (topoly.params.DensitySurface attribute) (topoly.params.PrecisionSurface attribute)

homfly() (in module topoly)

I

IDENT (topoly.params.OutputType attribute)

import_structure() (in module topoly) ION (topoly.params.Bridges attribute)

J

jones() (in module topoly)

JSMOL (topoly.params.SurfacePlotFormat attribute)

K

kauffman_bracket() (in module topoly) kauffman_polynomial() (in module topoly)

KMT (topoly.params.ReduceMethod attribute) KnotProt (topoly.params.OutputFormat attribute) Knots (topoly.params.Colors attribute)

L

lasso_type() (in module topoly)

LOW (topoly.params.DensitySurface attribute) (topoly.params.PrecisionSurface attribute)

M

make_surface() (in module topoly) MASS_CENTER (topoly.params.Closure attribute) Mathematica (topoly.params.OutputType attribute) MATHEMATICA (topoly.params.SurfacePlotFormat attribute)

Matrix (topoly.params.OutputFormat attribute) MEDIUM (topoly.params.DensitySurface attribute) (topoly.params.PrecisionSurface attribute) MMCIF (topoly.params.OutputType attribute)

N

NO (topoly.params.ReduceMethod attribute)

NXYZ (topoly.params.OutputType attribute)

O

ONE_POINT (topoly.params.Closure attribute)

OutputFormat (class in topoly.params) OutputType (class in topoly.params)

P

PDB (topoly.params.OutputType attribute) PDcode (topoly.params.OutputType attribute) PDF (topoly.params.PlotFormat attribute) plot_graph() (in module topoly)

plot_matrix() (in module topoly) PlotFormat (class in topoly.params) PNG (topoly.params.PlotFormat attribute) PrecisionSurface (class in topoly.params) PSF (topoly.params.OutputType attribute)

R

RAYS (topoly.params.Closure attribute) reduce_structure() (in module topoly)

ReduceMethod (class in topoly.params) REIDEMEISTER (topoly.params.ReduceMethod attribute)

S

SSBOND (topoly.params.Bridges attribute) Structure (topoly.params.Colors attribute)

SurfacePlotFormat (class in topoly.params) SVG (topoly.params.PlotFormat attribute)

T

translate_code() (in module topoly)

translate_matrix() (in module topoly) TWO_POINTS (topoly.params.Closure attribute)

V

VMD (topoly.params.SurfacePlotFormat attribute)

W

writhe() (in module topoly)

X

XYZ (topoly.params.OutputType attribute)

xyz2vmd() (in module topoly)

Y

yamada() (in module topoly)