Topological Analysis of Knotted Proteins, Biopolymers and 3D Structures

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 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... |

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