Functions
	helicity sel ?tol?

	helicity_3 sel ?tol? ?debug?

	atomselectRefine sel txt

	veccenter l

	vecangle d1 d2

	transinertia sel

	boundingBoxCenter sel

	minDist s1 s2

Detailed Description

Function Documentation

◆ atomselectRefine()

atomselectRefine			sel txt

Refine an atom selection: return a new atomselection consisting of the atoms in the old one, as long as they ALSO match the selection text txt

◆ boundingBoxCenter()

boundingBoxCenter			sel

Return the center of the bounding box for the selection $sel.

◆ helicity()

helicity			sel ?tol?

Count the fraction of residues that have phi/psi in the canonical alpha region of the Ramachandran plot (φ,ψ)=(-57,-47). Pass a selection of CA only. The ''tolerance'' argument sets the allowed slack (default 40 degrees). The result is normalized to 1.0 for a fully alpha-helical segment.

◆ helicity_3()

helicity_3			sel ?tol? ?debug?

Count helicities as in: Kelley J Mol Biol. 2009 May 22; 388(5):919–927. At least 3 residues within the canonical Ramachandran alpha region are required to count one. Pass a selection of CA only. The result is normalized to 1.0 for a fully alpha-helical segment.

◆ minDist()

minDist			s1 s2

Compute the minimum distance between atoms in selections s1 and s2

◆ transinertia()

transinertia			sel

Return the matrix which reorients the principal axes of inertia with x, y, z. The largest inertia axis will be aligned along z.

◆ vecangle()

vecangle			d1 d2

Returns the angle between two vectors

◆ veccenter()

veccenter			l

Return a zero-centered version of the input list

Functions