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Rknots (version 1.3.0)

Topological Analysis of Knotted Proteins, Biopolymers and 3D Structures

Description

The Rknots package contains functions for the topological analysis of polymers, with a focus on protein structures.

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Version

Install

install.packages('Rknots')

Monthly Downloads

28

Version

1.3.0

License

GPL-2

Maintainer

Federico Comoglio

Last Published

December 22nd, 2015

Functions in Rknots (1.3.0)

Rknots-internal

Internal Rknots functions
linkingNumber

Compute the linking number of a polygonal link
findGaps

Find gaps in proteins based on euclidean distance between residues of the backbone
getKnotType

Given a polynomial invariant, obtain information on the knot type
getCoordinates-methods

Accessors for the 'points3D' and 'ends' slots of a Knot object.
plot-methods

Plot the diagram of a Knot object.
plot3D

3D plot of an object of class 'Knot'
reduceStructure

Structure reduction of an object of class 'Knot'
setCoordinates<--methods

Setters for the 'points3D' and 'ends' slots of a Knot object.
newKnot

Create a Knot object
plotDiagram

Plot a knot or a link diagram
HOMFLY2Jones

Convert the HOMFLY polynomial into the Alexander or Jones polynomials
PCAProjection

Two-dimensional projection by Principal Component Analysis
intersectionMatrix

Compute the intersection matrix of a polygonal link
Rolfsen.table

Knots (up to 10 crossings) three dimensional coordinates, enumerated accordingly to Rolfsen.
HOMFLY2mirror

Convert the HOMFLY polynomial of a knot into the polynomial of its mirror image
print-methods

print the content of the slots of a Knot object.
mVA

Compute the multivariable Alexander polynomial of a polygonal link
HOMFLYpolynomial

Compute the HOMFLY polynomial of a polygonal link
computeInvariant

Compute an invariant of an object of class 'Knot'
makeExampleKnot

Randomly select a knot or a link from the local repository
centroidClosure

Structure closure with the centroid method
closeAndProject

Close the protein backbone and perform a Principal Component Analysis (requires an object of class 'Knot')
msr

Minimal Structure Reduction
skeinIterator

Iterate the skein relation to build a skein tree of a polygonal link
rMatrix

Rotation matrix along the $z$ axis
AlexanderBriggs

Alexander-Briggs reduction of a polygonal knot or link
plotKnot3D

3D plot of a polygonal link
Knot-class

Class "Knot" -- a container for knot and link coordinates and ends
makeExampleProtein

Load the coordinates of a protein structure used in many of the package help pages
link.table

Three dimensional coordinates and separators of polygonal links.
Rknots-package

Rknots: topological characterization of knotted 3D structures with R
loadProtein

Import a pdb file or fetch it from the Protein Data Bank. Check for structural gaps. Build and return a backbone trace for each polypeptide chain.