AlexanderBriggs         Alexander-Briggs reduction of a polygonal knot
                        or link
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
Knot-class              Class "Knot" - a container for knot and link
                        coordinates and ends
PCAProjection           Two-dimensional projection by Principal
                        Component Analysis
Rknots-package          Rknots: topological characterization of knotted
                        3D structures with R
Rolfsen.table           Knots (up to 10 crossings) three dimensional
                        coordinates, enumerated accordingly to Rolfsen.
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-methods
                        Accessors for the 'points3D' and 'ends' slots
                        of a Knot object.
getKnotType             Given a polynomial invariant, obtain
                        information on the knot type
intersectionMatrix      Compute the intersection matrix of a polygonal
                        link
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.
mVA                     Compute the multivariable Alexander polynomial
                        of a polygonal link
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
newKnot                 Create a Knot object
plot,Knot-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,Knot-method       print the content of the slots of a Knot
                        object.
rMatrix                 Rotation matrix along the z axis
reduceStructure         Structure reduction of an object of class
                        'Knot'
setCoordinates<--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
