ptm (version 0.2.2)

res.dist: Compute Distances Between Residues

Description

Computes the euclidean distance between two given residues

Usage

res.dist(pdb,  rA, chainA, rB, chainB, backbone = FALSE, hatoms = FALSE)

Arguments

pdb

is either a PDB id, or the path to a pdb file.

rA

an integer indicating the position of the first residue.

chainA

a character indicating the chain to which belong the first residue.

rB

an integer indicating the position of the second residue.

chainB

a character indicating the chain to which belong the second residue.

backbone

logical, when TRUE it means that we include those atoms belonging to the main chain (CA, N, O and C) beside all the side chain atoms.

hatoms

logical, if TRUE we include all the hydrogen atoms in the computation as long as the PDB provides their coordinates.

Value

This function returns a list of three elements, where each of these elements is, in turn, a list of three elements providing information regarding minimal, maximal and averaged distances.

See Also

pairwise.dist(), dist2closest(), ball()

Examples

# NOT RUN {
res.dist('1q8k', 51, 'A', 55, 'A', backbone = TRUE, hatoms = TRUE)
# }