mVA: Compute the multivariable Alexander polynomial of a polygonal...
In Rknots: Topological Analysis of Knotted Proteins, Biopolymers and 3D Structures

Description Usage Arguments Details Value Note Author(s) References See Also Examples

Computes the multivariable Alexander polynomial (MVA) of a polygonal link.

1	mVA(points3D, ends, normalized = FALSE, return.A = FALSE)

`points3D`	an N x 3 matrix of the x, y, z coordinates of a polygonal link
`ends`	a vector of positive integers defining the separators of the polygonal link
`normalized`	logical, if FALSE (default) the multivariable non normalized MVA is returned, the normalized MVA otherwise
`return.A`	logical, if TRUE the Alexander matrix is returned in a format that can be parsed to sympy

The polynomial computation relies on rSymPy. Please notice that the first time sympy is invoked is expected to be much slower than subsequent ones.

the multivariable Alexander polynomial

This is a low-level function. If you wish to make computations faster, reduce the structure first with AlexanderBriggs or msr.

Maurizio Rinaldi, maurizio.rinaldi@pharm.unipmn.it

Alexander J. W. (1928) Topological invariants of knots and links. Trans. Amer. Math. Soc. 30: 275-306.

Conway J. H. (1970) An enumeration of knots and links, and some of their algebraic properties. Computational Problems in Abstract Algebra (Proc. Conf.,Oxford, 1967), Pergamon, Oxford: 329-358.

Murakami J. (1993) A state model for the multivariable Alexander polynomial. Pacific J. Math. 157, no. 1: 109-135.

Archibald J. (2008) The weight system of the multivariable Alexander polynomial. Acta Math. Vietnamica. 33: 459-470.

Archibald J. (2010) The Multivariable Alexander Polynomial on Tangles. PhD Thesis, Department of Mathematics University of Toronto

Torres G. (1953) On the Alexander polynomial Ann. Math. 57: 57-89.

Comoglio F. and Rinaldi M. (2011) A Topological Framework for the Computation of the HOMFLY Polynomial and Its Application to Proteins, PLoS ONE 6(4): e18693, doi:10.1371/journal.pone.0018693 ArXiv:1104.3405

msr, AlexanderBriggs

## Not run: 
link <- makeExampleKnot(k = FALSE)
mVA(points3D = link$points3D, ends = link$ends)
mVA(points3D = link$points3D, ends = link$ends, normalized = TRUE)
mVA(points3D = link$points3D, ends = link$ends, normalized = TRUE, return.A = TRUE)

## End(Not run)