# Rknots

## Documentation for package ‘Rknots’ version 1.1

- DESCRIPTION file.

## Help Pages

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