CalcAlignOverlap: Calculate Alignment Overlap

In vanddraabe: Identification and Statistical Analysis of Conserved Waters Near Proteins

Description

Calculate the amount of alignment overlap between two protein structures using C-alpha atoms.

Usage

CalcAlignOverlap(ref.num.atoms, ref.ca, ref.idc, soi.PDB, CA.dist)

Arguments

ref.num.atoms	Number of atoms in the reference structure
ref.ca	PDB formatted data.frame containing only C-alpha atoms
ref.idc	The indices of the reference structure atoms; from 1 to the number of atoms in the reference structure
soi.PDB	The structure of interest (SoI) being compared to the reference structure. This is the full PDB structure read into R using the bio3d::read.pdb2() function
CA.dist	The minimum distance between C-alpha atoms for the two C-alpha atoms to be considered aligned; default: 1.25

Details

Using the C-alpha atoms of two aligned proteins, the amount of atomic overlap is determined. This function is within the AlignOverlap function.

This is a non-public function and is NOT available for general use. Please contact the author if you believe this function should be available for general use.

Value

This function returns:

• ratio.intersection: fraction of SOI overlapping with the reference structure

• soi.chain: Chain letter designations for the aligned SOI

• soi.chain.overlap: Unique chain letter designations for the aligned SOI These values are then used within the AlignOverlap() function to determine if the structures are adequately aligned.

Author(s)

Emilio Xavier Esposito [e-mail]

See Also

Other "Alignment Overlap": AlignOverlap

vanddraabe documentation built on June 8, 2019, 1:03 a.m.