rmsd_calc: Least Root Mean Squared Deviation for Molecule Conformations

In wongswk/compass: Conformational manipulations of protein atomic structures and sequences

Description

LRMSD or RMSD calculation between two coordinate sets (3 by n matrices).

Usage

rmsd_calc(pred, truth, n=NULL, m=NULL, atype='all', optimal=FALSE)

Arguments

pred	matrix containing predicted coordinates of atoms in protein conformation.
truth	matrix containing true coordinates of atoms in protein conformation.
n	The Resno to start at for the rmsd calculation.
m	The Resno to end at for the rmsd calculation.
atype	Can be Null, CA, CaCNO, specifies the types of items to consider. Null means consider all atoms.
optimal	TRUE to apply optimal rotations as described in https://cnx.org/contents/HV-RsdwL@23/Molecular-Distance-Measures Otherwise calculates RMSD without rotations

Value

Returns the calculated LRMSD value and the rotation matrix used to achieve optimal rotation.

Examples

predicted <- bio3d::read.pdb("TR928prediction.pdb")
truthful <- bio3d::read.pdb("TR928truth.pdb")
rmsd_calc(predicted, truthful,n=6, m=8, 'all', T)
rmsd_calc(predicted, truthful,n=6, m=8, 'CA', T)
rmsd_calc(predicted, truthful,n=6, m=8, "CaCNO", T)
rmsd_calc(predicted, truthful,n=6, m=8, "CaCNO", F)
rmsd_calc(predicted, truthful, n=8, m=NULL, "all", T)
rmsd_calc(predicted, truthful, n=NULL, m=NULL, 'all', F)
rmsd_calc(predicted, truthful)

wongswk/compass documentation built on Jan. 9, 2022, 8:31 p.m.