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. |