| accessors | Accessors for the 'points3D' and 'ends' slots of a Knot... |
| 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... |
| computeInvariant | Compute an invariant of an object of class 'Knot' |
| findGaps | Find gaps in proteins based on euclidean distance between... |
| getKnotType | Given a polynomial invariant, obtain information on the knot... |
| HOMFLY2mirror | Convert the HOMFLY polynomial of a knot into the polynomial... |
| 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... |
| linkingNumber | Compute the linking number of a polygonal link |
| link.table | Three dimensional coordinates and separators of polygonal... |
| loadProtein | Import a pdb file or fetch it from the Protein Data Bank.... |
| makeExampleKnot | Randomly select a knot or a link from the local repository |
| makeExampleProtein | Load the coordinates of a protein structure used in many of... |
| msr | Minimal Structure Reduction |
| mVA | Compute the multivariable Alexander polynomial of a polygonal... |
| newKnot | Create a Knot object |
| PCAProjection | Two-dimensional projection by Principal Component Analysis |
| plot | 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 |
| polyConversion | Convert the HOMFLY polynomial into the Alexander or Jones... |
| print | print the content of the slots of a Knot object. |
| reduceStructure | Structure reduction of an object of class 'Knot' |
| Rknots-internal | Internal Rknots functions |
| Rknots-package | Rknots: topological characterization of knotted 3D structures... |
| rMatrix | Rotation matrix along the z axis |
| Rolfsen.table | Knots (up to 10 crossings) three dimensional coordinates,... |
| setters | Setters for the 'points3D' and 'ends' slots of a Knot object. |
| skeinIterator | Iterate the skein relation to build a skein tree of a... |
