Rknots: Topological Analysis of Knotted Proteins, Biopolymers and 3D Structures

Contains functions for the topological analysis of polymers, with a focus on protein structures.

Install the latest version of this package by entering the following in R:
install.packages("Rknots")
AuthorFederico Comoglio and Maurizio Rinaldi
Date of publication2016-10-21 14:09:36
MaintainerFederico Comoglio <federico.comoglio@gmail.com>
LicenseGPL-2
Version1.3.2

View on CRAN

Man pages

accessors: Accessors for the 'points3D' and 'ends' slots of a Knot...

AlexanderBriggs: Alexander-Briggs reduction of a polygonal knot or link

centroidClosure: Structure closure with the centroid method

closeAndProject: Close the protein backbone and perform a Principal Component...

computeInvariant: Compute an invariant of an object of class 'Knot'

findGaps: Find gaps in proteins based on euclidean distance between...

getKnotType: Given a polynomial invariant, obtain information on the knot...

HOMFLY2mirror: Convert the HOMFLY polynomial of a knot into the polynomial...

HOMFLYpolynomial: Compute the HOMFLY polynomial of a polygonal link

intersectionMatrix: Compute the intersection matrix of a polygonal link

Knot-class: Class "Knot" - a container for knot and link coordinates and...

linkingNumber: Compute the linking number of a polygonal link

link.table: Three dimensional coordinates and separators of polygonal...

loadProtein: Import a pdb file or fetch it from the Protein Data Bank....

makeExampleKnot: Randomly select a knot or a link from the local repository

makeExampleProtein: Load the coordinates of a protein structure used in many of...

msr: Minimal Structure Reduction

mVA: Compute the multivariable Alexander polynomial of a polygonal...

newKnot: Create a Knot object

PCAProjection: Two-dimensional projection by Principal Component Analysis

plot: Plot the diagram of a Knot object.

plot3D: 3D plot of an object of class 'Knot'

plotDiagram: Plot a knot or a link diagram

plotKnot3D: 3D plot of a polygonal link

polyConversion: Convert the HOMFLY polynomial into the Alexander or Jones...

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

reduceStructure: Structure reduction of an object of class 'Knot'

Rknots-internal: Internal Rknots functions

Rknots-package: Rknots: topological characterization of knotted 3D structures...

rMatrix: Rotation matrix along the z axis

Rolfsen.table: Knots (up to 10 crossings) three dimensional coordinates,...

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

skeinIterator: Iterate the skein relation to build a skein tree of a...

Functions

[ Man page
[<- Man page
AlexanderBriggs Man page
auxiliaryAlexander Man page
auxiliaryPoints Man page
bin2N Man page
buildQuadrilateral Man page
buildRis Man page
buildRis2 Man page
buildTriangles Man page
centroidClosure Man page
checkTriangles Man page
checkVertex Man page
closeAndProject Man page
computeFactors Man page
computeInvariant Man page
contribute Man page
correspondence Man page
cp Man page
cpr Man page
cross Man page
cross_product Man page
cyclicP Man page
defineCut Man page
distancePS Man page
distancepstart Man page
edgeIntersections Man page
edgeIntersectionsK Man page
endComponentCorrection Man page
endsAndTriple Man page
escapeDir Man page
escapePath Man page
fillToN Man page
findComplement Man page
findComponent Man page
findGaps Man page
findNextE Man page
get2D Man page
getCoordinates Man page
getCoordinates,Knot-method Man page
getCoordinates-methods Man page
getEnds Man page
getEnds,Knot-method Man page
getEnds-methods Man page
getKnotType Man page
HOMFLY2Alexander Man page
HOMFLY2Jones Man page
HOMFLY2mirror Man page
HOMFLYpolynomial Man page
interiorTriangle Man page
intersectionMatrix Man page
isWholeNumber Man page
Knot-class Man page
[<-,Knot-method Man page
[,Knot-method Man page
lexOrder Man page
linkingNumber Man page
link.table Man page
listVertices Man page
loadProtein Man page
localize Man page
makeExampleKnot Man page
makeExampleProtein Man page
[<--methods Man page
[-methods Man page
move3D Man page
msr Man page
msrFast Man page
mVA Man page
newKnot Man page
norM Man page
orientedSign Man page
parseToR Man page
parseToSympy Man page
PCAProjection Man page
plot3D Man page
plotComponent Man page
plotDiagram Man page
plotKnot3D Man page
plot,Knot-method Man page
print,Knot-method Man page
reduceStructure Man page
residualIndices Man page
Rknots Man page
Rknots-package Man page
rMatrix Man page
Rolfsen.table Man page
Rolfsen.table.ms Man page
rotateQuadrilateral Man page
rotFactor Man page
segmentSet Man page
setCoordinates Man page
setCoordinates<- Man page
setCoordinates<-,Knot-method Man page
setCoordinates<--methods Man page
setEnds Man page
setEnds<- Man page
setEnds<-,Knot-method Man page
setEnds<--methods Man page
singleIntersectionS Man page
skeinIterator Man page
splitUndercrossing Man page
triangleIntersection Man page
vertexPresentation Man page
xClean Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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