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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

29

Version

1.3.1

License

GPL-2

Maintainer

Federico Comoglio

Last Published

December 23rd, 2015

Functions in Rknots (1.3.1)

intersectionMatrix

Compute the intersection matrix of a polygonal link
centroidClosure

Structure closure with the centroid method
makeExampleProtein

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

Compute the HOMFLY polynomial of a polygonal link
makeExampleKnot

Randomly select a knot or a link from the local repository
link.table

Three dimensional coordinates and separators of polygonal links.
plot3D

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

Alexander-Briggs reduction of a polygonal knot or link
HOMFLY2mirror

Convert the HOMFLY polynomial of a knot into the polynomial of its mirror image
mVA

Compute the multivariable Alexander polynomial of a polygonal link
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.
plotDiagram

Plot a knot or a link diagram
Rknots-package

Rknots: topological characterization of knotted 3D structures with R
Knot-class

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

Compute the linking number of a polygonal link
Rknots-internal

Internal Rknots functions
print-methods

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

Create a Knot object
HOMFLY2Jones

Convert the HOMFLY polynomial into the Alexander or Jones polynomials
getCoordinates-methods

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

Two-dimensional projection by Principal Component Analysis
plotKnot3D

3D plot of a polygonal link
closeAndProject

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

Minimal Structure Reduction
getKnotType

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

Rotation matrix along the $z$ axis
Rolfsen.table

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

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

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

Structure reduction of an object of class 'Knot'
plot-methods

Plot the diagram of a Knot object.
skeinIterator

Iterate the skein relation to build a skein tree of a polygonal link
setCoordinates<--methods

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