Description Usage Arguments Value Note Author(s) References Examples

For being treated as a mathematical knot, the protein backbone needs to be closed. This function implements the centroid method (also called CENTER), where the protein endpoints (C-terminus and N-terminus) are extended outside the sphere containing the protein backbone in the direction of the centroid of the structure.

1 | ```
centroidClosure(points3D, w = 2)
``` |

`points3D` |
an |

`w` |
given the radius |

an *(N+2)* x 3 matrix of the *x*, *y*, *z* coordinates of a polygonal link.
The first and the last rows contain the coordinates of the extended endpoints.

This is a low-level function.

Federico Comoglio, federico.comoglio@bsse.ethz.ch

Lua RC, Grosberg AY (2006) Statistics of Knots, Geometry of Conformations, and Evolution of Proteins. PLoS Comput Biol 2(5): e45. doi:10.1371/journal.pcbi.0020045

1 2 3 4 5 6 7 8 9 10 | ```
## Not run:
## Import a PDB file from the web
protein <- makeExampleProtein()
closed <- centroidClosure(protein$A)
##Plot the result
plotKnot3D(closed, ends = c(), text = TRUE, showNC = TRUE,
radius = 0.01, lwd = 5)
## End(Not run)
``` |

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