Topological Analysis of Knotted Proteins, Biopolymers and 3D Structures


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Documentation for package ‘Rknots’ version 1.3.2

Help Pages

Rknots-package Rknots: topological characterization of knotted 3D structures with R
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 Analysis (requires an object of class 'Knot')
computeInvariant Compute an invariant of an object of class 'Knot'
findGaps Find gaps in proteins based on euclidean distance between residues of the backbone
getCoordinates Accessors for the 'points3D' and 'ends' slots of a Knot object.
getCoordinates-method Accessors for the 'points3D' and 'ends' slots of a Knot object.
getCoordinates-methods Accessors for the 'points3D' and 'ends' slots of a Knot object.
getEnds Accessors for the 'points3D' and 'ends' slots of a Knot object.
getEnds-method Accessors for the 'points3D' and 'ends' slots of a Knot object.
getEnds-methods Accessors for the 'points3D' and 'ends' slots of a Knot object.
getKnotType Given a polynomial invariant, obtain information on the knot type
HOMFLY2Alexander Convert the HOMFLY polynomial into the Alexander or Jones polynomials
HOMFLY2Jones Convert the HOMFLY polynomial into the Alexander or Jones polynomials
HOMFLY2mirror Convert the HOMFLY polynomial of a knot into the polynomial of its mirror image
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 ends
link.table Three dimensional coordinates and separators of polygonal links.
linkingNumber Compute the linking number 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.
makeExampleKnot Randomly select a knot or a link from the local repository
makeExampleProtein Load the coordinates of a protein structure used in many of the package help pages
msr Minimal Structure Reduction
mVA Compute the multivariable Alexander polynomial of a polygonal link
newKnot Create a Knot object
PCAProjection Two-dimensional projection by Principal Component Analysis
plot-method 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
print-method print the content of the slots of a Knot object.
reduceStructure Structure reduction of an object of class 'Knot'
Rknots Rknots: topological characterization of knotted 3D structures with R
rMatrix Rotation matrix along the z axis
Rolfsen.table Knots (up to 10 crossings) three dimensional coordinates, enumerated accordingly to Rolfsen.
Rolfsen.table.ms Knots (up to 10 crossings) three dimensional coordinates, enumerated accordingly to Rolfsen.
setCoordinates Setters for the 'points3D' and 'ends' slots of a Knot object.
setCoordinates<- Setters for the 'points3D' and 'ends' slots of a Knot object.
setCoordinates<--method Setters for the 'points3D' and 'ends' slots of a Knot object.
setCoordinates<--methods Setters for the 'points3D' and 'ends' slots of a Knot object.
setEnds Setters for the 'points3D' and 'ends' slots of a Knot object.
setEnds<- Setters for the 'points3D' and 'ends' slots of a Knot object.
setEnds<--method Setters for the 'points3D' and 'ends' slots of a Knot object.
setEnds<--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
[ Accessors for the 'points3D' and 'ends' slots of a Knot object.
[-method Accessors for the 'points3D' and 'ends' slots of a Knot object.
[-methods Accessors for the 'points3D' and 'ends' slots of a Knot object.
[<- Setters for the 'points3D' and 'ends' slots of a Knot object.
[<--method Setters for the 'points3D' and 'ends' slots of a Knot object.
[<--methods Setters for the 'points3D' and 'ends' slots of a Knot object.