Difference Vector
Define a difference vector between two conformational states.
difference.vector(xyz, xyz.inds=NULL, normalize=FALSE)
xyz |
numeric matrix of Cartesian coordinates with a row per structure. |
xyz.inds |
a vector of indices that selects the elements of columns upon which the calculation should be based. |
normalize |
logical, if TRUE the difference vector is normalized. |
Squared overlap (or dot product) is used to measure the similiarity between a displacement vector (e.g. a difference vector between two conformational states) and mode vectors obtained from principal component or normal modes analysis.
Returns a numeric vector of the structural difference (normalized if desired).
Lars Skjaerven
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
attach(kinesin)
# Ignore gap containing positions
gaps.pos <- gap.inspect(pdbs$xyz)
#-- Do PCA
pc.xray <- pca.xyz(pdbs$xyz[, gaps.pos$f.inds])
# Define a difference vector between two structural states
diff.inds <- c(grep("d1v8ka", pdbs$id),
grep("d1goja", pdbs$id))
## Calculate the difference vector
dv <- difference.vector( pdbs$xyz[diff.inds,], gaps.pos$f.inds )
# Calculate the squared overlap between the PCs and the difference vector
o <- overlap(pc.xray, dv)
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