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Rknots

##Topological analysis of knotted biological polymers (e.g. proteins, DNA) with R

The Rknots package contains functions for the topological analysis of knots and links with a particular focus on biological polymers like proteins.

For more details, see http://federicocomoglio.github.io/Rknots/

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Version

Install

install.packages('Rknots')

Monthly Downloads

28

Version

1.3.2

License

GPL-2

Maintainer

Federico Comoglio

Last Published

October 21st, 2016

Functions in Rknots (1.3.2)

HOMFLYpolynomial

Compute the HOMFLY polynomial of a polygonal link
getKnotType

Given a polynomial invariant, obtain information on the knot type
AlexanderBriggs

Alexander-Briggs reduction of a polygonal knot or link
Knot-class

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

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

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

Structure closure with the centroid method
getCoordinates-methods

Accessors for the 'points3D' and 'ends' slots of a Knot object.
computeInvariant

Compute an invariant of an object of class 'Knot'
link.table

Three dimensional coordinates and separators of polygonal links.
PCAProjection

Two-dimensional projection by Principal Component Analysis
plotKnot3D

3D plot of a polygonal link
plot3D

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

Create a Knot object
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.
plot-methods

Plot the diagram of a Knot object.
makeExampleKnot

Randomly select a knot or a link from the local repository
print-methods

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

Load the coordinates of a protein structure used in many of the package help pages
mVA

Compute the multivariable Alexander polynomial of a polygonal link
setCoordinates<--methods

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

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

Structure reduction of an object of class 'Knot'
Rknots-package

Rknots: topological characterization of knotted 3D structures with R
Rolfsen.table

Knots (up to 10 crossings) three dimensional coordinates, enumerated accordingly to Rolfsen.
Rknots-internal

Internal Rknots functions