| 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. |