# Topological Analysis of Knotted Proteins, Biopolymers and 3D Structures

## Documentation for package ‘Rknots’ version 1.3.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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.