Calculate the amount of alignment overlap between two protein structures using C-alpha atoms.
CalcAlignOverlap(ref.num.atoms, ref.ca, ref.idc, soi.PDB, CA.dist)Number of atoms in the reference structure
PDB formatted data.frame containing only C-alpha atoms
The indices of the reference structure atoms; from 1 to the
number of atoms in the reference structure
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
The minimum distance between C-alpha atoms for the two C-alpha atoms to be considered aligned; default: 1.25
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.
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.
Other "Alignment Overlap": AlignOverlap