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

Contains functions for the topological analysis of polymers, with a focus on protein structures.

- Author
- Federico Comoglio and Maurizio Rinaldi
- Date of publication
- 2015-12-23 11:24:13
- Maintainer
- Federico Comoglio <federico.comoglio@gmail.com>
- License
- GPL-2
- Version
- 1.3.1

## Man pages

- accessors
- Accessors for the 'points3D' and 'ends' slots of a Knot...
- accessors
- Accessors for the 'points3D' and 'ends' slots of a Knot...
- AlexanderBriggs
- Alexander-Briggs reduction of a polygonal knot or link
- AlexanderBriggs
- Alexander-Briggs reduction of a polygonal knot or link
- centroidClosure
- Structure closure with the centroid method
- centroidClosure
- Structure closure with the centroid method
- closeAndProject
- Close the protein backbone and perform a Principal Component...
- closeAndProject
- Close the protein backbone and perform a Principal Component...
- computeInvariant
- Compute an invariant of 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...
- findGaps
- Find gaps in proteins based on euclidean distance between...
- getKnotType
- Given a polynomial invariant, obtain information on the knot...
- getKnotType
- Given a polynomial invariant, obtain information on the knot...
- HOMFLY2mirror
- Convert the HOMFLY polynomial of a knot into the polynomial...
- HOMFLY2mirror
- Convert the HOMFLY polynomial of a knot into the polynomial...
- HOMFLYpolynomial
- Compute the HOMFLY polynomial of a polygonal link
- HOMFLYpolynomial
- Compute the HOMFLY polynomial of a polygonal link
- intersectionMatrix
- Compute the intersection matrix 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...
- Knot-class
- Class "Knot" - a container for knot and link coordinates and...
- linkingNumber
- Compute the linking number of a polygonal link
- linkingNumber
- Compute the linking number of a polygonal link
- link.table
- Three dimensional coordinates and separators of polygonal...
- link.table
- Three dimensional coordinates and separators of polygonal...
- loadProtein
- Import a pdb file or fetch it from the Protein Data Bank....
- 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
- makeExampleKnot
- Randomly select a knot or a link from the local repository
- makeExampleProtein
- Load the coordinates of a protein structure used in many of...
- makeExampleProtein
- Load the coordinates of a protein structure used in many of...
- msr
- Minimal Structure Reduction
- msr
- Minimal Structure Reduction
- mVA
- Compute the multivariable Alexander polynomial of a polygonal...
- mVA
- Compute the multivariable Alexander polynomial of a polygonal...
- newKnot
- Create a Knot object
- newKnot
- Create a Knot object
- PCAProjection
- Two-dimensional projection by Principal Component Analysis
- 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'
- plot3D
- 3D plot of an object of class 'Knot'
- plotDiagram
- Plot a knot or a link diagram
- plotDiagram
- Plot a knot or a link diagram
- plotKnot3D
- 3D plot of a polygonal link
- plotKnot3D
- 3D plot of a polygonal link
- polyConversion
- Convert the HOMFLY polynomial into the Alexander or Jones...
- polyConversion
- Convert the HOMFLY polynomial into the Alexander or Jones...
- print the content of the slots of a Knot object.
- print the content of the slots of a Knot object.
- reduceStructure
- Structure reduction of an object of class 'Knot'
- reduceStructure
- Structure reduction of an object of class 'Knot'
- Rknots-internal
- Internal Rknots functions
- Rknots-internal
- Internal Rknots functions
- Rknots-package
- Rknots: topological characterization of knotted 3D structures...
- Rknots-package
- Rknots: topological characterization of knotted 3D structures...
- rMatrix
- Rotation matrix along the z axis
- rMatrix
- Rotation matrix along the z axis
- Rolfsen.table
- Knots (up to 10 crossings) three dimensional coordinates,...
- Rolfsen.table
- Knots (up to 10 crossings) three dimensional coordinates,...
- setters
- Setters for the 'points3D' and 'ends' slots of a Knot object.
- setters
- Setters for the 'points3D' and 'ends' slots of a Knot object.
- skeinIterator
- Iterate the skein relation to build a skein tree of a...
- skeinIterator
- Iterate the skein relation to build a skein tree of a...

## Files in this package

Rknots |

Rknots/inst |

Rknots/inst/extdata |

Rknots/inst/extdata/2K0A.pdb |

Rknots/inst/extdata/1AJC_chainA.pdb |

Rknots/inst/doc |

Rknots/inst/doc/Rknots_vignette.html |

Rknots/inst/doc/Rknots_vignette.R |

Rknots/inst/doc/Rknots_vignette.Rmd |

Rknots/NAMESPACE |

Rknots/data |

Rknots/data/link.table.rda |

Rknots/data/Rolfsen.table.rda |

Rknots/R |

Rknots/R/edgeIntersections.R |

Rknots/R/msr.R |

Rknots/R/class_def.R |

Rknots/R/findGaps.R |

Rknots/R/skeinIterator.R |

Rknots/R/singleIntersection.R |

Rknots/R/grm.R |

Rknots/R/fileImport.R |

Rknots/R/polyConversion.R |

Rknots/R/intersectionMatrix.R |

Rknots/R/mva.R |

Rknots/R/getKnotType.R |

Rknots/R/methods.R |

Rknots/R/plotKnotDiagram.R |

Rknots/R/HOMFLYpolynomial.R |

Rknots/R/PCAProjection.R |

Rknots/R/makeExamples.R |

Rknots/R/auxFunctions.R |

Rknots/R/plotKnot3D.R |

Rknots/R/centroidClosure.R |

Rknots/R/AlexanderBriggs.R |

Rknots/R/linkingNumber.R |

Rknots/R/rMatrix.R |

Rknots/vignettes |

Rknots/vignettes/Rplotvignette4.pdf |

Rknots/vignettes/Rplotvignette3.pdf |

Rknots/vignettes/Rknots_vignette.Rmd |

Rknots/vignettes/Rplotvignette5.png |

Rknots/vignettes/Rplotvignette1.pdf |

Rknots/vignettes/Rplotvignette2.pdf |

Rknots/README.md |

Rknots/MD5 |

Rknots/build |

Rknots/build/vignette.rds |

Rknots/DESCRIPTION |

Rknots/man |

Rknots/man/Rknots-package.Rd |

Rknots/man/polyConversion.Rd |

Rknots/man/computeInvariant.Rd |

Rknots/man/Rolfsen.table.Rd |

Rknots/man/skeinIterator.Rd |

Rknots/man/msr.Rd |

Rknots/man/Rknots-internal.Rd |

Rknots/man/rMatrix.Rd |

Rknots/man/Knot-class.Rd |

Rknots/man/PCAProjection.Rd |

Rknots/man/loadProtein.Rd |

Rknots/man/HOMFLYpolynomial.Rd |

Rknots/man/makeExampleKnot.Rd |

Rknots/man/plot3D.Rd |

Rknots/man/HOMFLY2mirror.Rd |

Rknots/man/plotKnot3D.Rd |

Rknots/man/closeAndProject.Rd |

Rknots/man/linkingNumber.Rd |

Rknots/man/centroidClosure.Rd |

Rknots/man/plotDiagram.Rd |

Rknots/man/mVA.Rd |

Rknots/man/getKnotType.Rd |

Rknots/man/print.Rd |

Rknots/man/newKnot.Rd |

Rknots/man/findGaps.Rd |

Rknots/man/setters.Rd |

Rknots/man/intersectionMatrix.Rd |

Rknots/man/plot.Rd |

Rknots/man/makeExampleProtein.Rd |

Rknots/man/link.table.Rd |

Rknots/man/reduceStructure.Rd |

Rknots/man/accessors.Rd |

Rknots/man/AlexanderBriggs.Rd |