Rknots

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Documentation for package ‘Rknots’ version 1.1

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Rknots-package Rknots: knots detection with R
AlexanderBriggs Alexander-Briggs reduction of a polygonal knot or link
buildLsw Build an L switch configuration
buildLzero Build an L zero configuration
centroidClosure Structure closure with the centroid method
fileImport Import or fetch a PDB file and build the alpha-Carbon trace model
findGaps Find gaps in proteins based on euclidean distance between residues
findKnot Global wrapper function for finding knots in 3D structures
findProteinKnot Global wrapper function for finding knots in proteins via the HOMFLY polynomial
grm Generalized Reidemeister Move
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 one of its mirror image
HOMFLYpolynomial Compute the HOMFLY polynomial of a polygonal link
intersectionMatrix Compute the intersection matrix of a polygonal link
link.table Links three dimensional coordinates and separators
linkingNumber Compute the linking number of a polygonal link
msr Minimal Structure Reduction
mVA Compute the multivariable Alexander polynomial of a polygonal link
PCAProjection Two-dimensional projection by Principal Component Analysis
plotKnot3D 3D plot of a polygonal link
plotKnotDiagram Plot a knot or link diagram
Rknots Rknots: knots detection 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.
singleIntersection Find the intersection of two edges
skeinIterator Iterate the skein relation to build a skein tree of a polygonal link
skeinSign Compute the skein sign of a crossing