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

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

Author
Federico Comoglio and Maurizio Rinaldi
Date of publication
2016-10-21 14:09:36
Maintainer
Federico Comoglio <federico.comoglio@gmail.com>
License
GPL-2
Version
1.3.2

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