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

Author | Federico Comoglio and Maurizio Rinaldi |

Date of publication | 2016-10-21 14:09:36 |

Maintainer | Federico Comoglio <federico.comoglio@gmail.com> |

License | GPL-2 |

Version | 1.3.2 |

**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...

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
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