Difference Vector

Usage

difference.vector(xyz, xyz.inds=NULL, normalize=FALSE)

Arguments

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.

Description

Define a difference vector between two conformational states.

Details

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.

Value

Returns a numeric vector of the structural difference (normalized if desired).

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

Examples

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)

detach(kinesin)

See also

overlap

Author

Lars Skjaerven