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

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

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...

Files in this package

Rknots
Rknots/inst
Rknots/inst/extdata
Rknots/inst/extdata/2K0A.pdb
Rknots/inst/extdata/1AJC_chainA.pdb
Rknots/inst/doc
Rknots/inst/doc/Rknots_vignette.html
Rknots/inst/doc/Rknots_vignette.R
Rknots/inst/doc/Rknots_vignette.Rmd
Rknots/NAMESPACE
Rknots/data
Rknots/data/link.table.rda
Rknots/data/Rolfsen.table.rda
Rknots/R
Rknots/R/edgeIntersections.R Rknots/R/msr.R Rknots/R/class_def.R Rknots/R/findGaps.R Rknots/R/skeinIterator.R Rknots/R/singleIntersection.R Rknots/R/grm.R Rknots/R/fileImport.R Rknots/R/polyConversion.R Rknots/R/intersectionMatrix.R Rknots/R/mva.R Rknots/R/getKnotType.R Rknots/R/methods.R Rknots/R/plotKnotDiagram.R Rknots/R/HOMFLYpolynomial.R Rknots/R/PCAProjection.R Rknots/R/makeExamples.R Rknots/R/auxFunctions.R Rknots/R/plotKnot3D.R Rknots/R/centroidClosure.R Rknots/R/AlexanderBriggs.R Rknots/R/linkingNumber.R Rknots/R/rMatrix.R
Rknots/vignettes
Rknots/vignettes/Rplotvignette4.pdf
Rknots/vignettes/Rplotvignette3.pdf
Rknots/vignettes/Rknots_vignette.Rmd
Rknots/vignettes/Rplotvignette5.png
Rknots/vignettes/Rplotvignette1.pdf
Rknots/vignettes/Rplotvignette2.pdf
Rknots/README.md
Rknots/MD5
Rknots/build
Rknots/build/vignette.rds
Rknots/DESCRIPTION
Rknots/man
Rknots/man/Rknots-package.Rd Rknots/man/polyConversion.Rd Rknots/man/computeInvariant.Rd Rknots/man/Rolfsen.table.Rd Rknots/man/skeinIterator.Rd Rknots/man/msr.Rd Rknots/man/Rknots-internal.Rd Rknots/man/rMatrix.Rd Rknots/man/Knot-class.Rd Rknots/man/PCAProjection.Rd Rknots/man/loadProtein.Rd Rknots/man/HOMFLYpolynomial.Rd Rknots/man/makeExampleKnot.Rd Rknots/man/plot3D.Rd Rknots/man/HOMFLY2mirror.Rd Rknots/man/plotKnot3D.Rd Rknots/man/closeAndProject.Rd Rknots/man/linkingNumber.Rd Rknots/man/centroidClosure.Rd Rknots/man/plotDiagram.Rd Rknots/man/mVA.Rd Rknots/man/getKnotType.Rd Rknots/man/print.Rd Rknots/man/newKnot.Rd Rknots/man/findGaps.Rd Rknots/man/setters.Rd Rknots/man/intersectionMatrix.Rd Rknots/man/plot.Rd Rknots/man/makeExampleProtein.Rd Rknots/man/link.table.Rd Rknots/man/reduceStructure.Rd Rknots/man/accessors.Rd Rknots/man/AlexanderBriggs.Rd

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