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**Rknots**: Topological Analysis of Knotted Proteins, Biopolymers and 3D Structures**Rknots-internal**: Internal Rknots functions

# Internal Rknots functions

### Description

Internal Rknots functions

### Details

These are not meant to be called by the user (by the way, many of them are low-level functions).

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- 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...