bio3d (version 2.1-2)

write.pqr: Write PQR Format Coordinate File

Description

Write a PQR file for a given xyz Cartesian coordinate vector or matrix.

Usage

write.pqr(pdb = NULL, xyz = pdb$xyz, resno = NULL, resid = NULL, eleno =
NULL, elety = NULL, chain = NULL, o = NULL, b = NULL, het = FALSE,
append = FALSE, verbose = FALSE, chainter = FALSE, file = "R.pdb")

Arguments

pdb

a PDB structure object obtained from read.pdb.

xyz

Cartesian coordinates as a vector or 3xN matrix.

resno

vector of residue numbers of length equal to length(xyz)/3.

resid

vector of residue types/ids of length equal to length(xyz)/3.

eleno

vector of element/atom numbers of length equal to length(xyz)/3.

elety

vector of element/atom types of length equal to length(xyz)/3.

chain

vector of chain identifiers with length equal to length(xyz)/3.

o

vector of occupancy values of length equal to length(xyz)/3.

b

vector of B-factors of length equal to length(xyz)/3.

het

logical, if TRUE HETATM records from pdb object are written to the output PDB file.

append

logical, if TRUE output is appended to the bottom of an existing file (used primarly for writing multi-model files).

verbose

logical, if TRUE progress details are printed.

chainter

logical, if TRUE a TER line is inserted between chains.

file

the output file name.

Value

• Called for its effect.

Details

Only the xyz argument is strictly required. Other arguments assume a default poly-ALA C-alpha structure with a blank chain id, occupancy values of 1.00 and B-factors equal to 0.00. If the input argument xyz is a matrix then each row is assumed to be a different structure/frame to be written to a multimodel PDB file, with frames separated by END records.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696. For a description of PDB format (version3.3) see: http://www.wwpdb.org/documentation/format33/v3.3.html.

See Also

read.pdb, read.dcd, read.fasta.pdb, read.fasta

Examples

# Read a PDB file
pdb <- read.pdb( "1bg2" )

# Renumber residues
nums <- as.numeric(pdb$atom[,"resno"])
nums <- nums - (nums[1] - 1)

# Write out renumbered PDB file
outfile = file.path(tempdir(), "eg.pdb")
write.pdb(pdb=pdb, resno = nums, file = outfile)

invisible( cat("\nSee the output file:", outfile, sep = "\n") )