write.pqr: Write PQR Format Coordinate File

In bio3d: Biological Structure Analysis

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,
append = FALSE, verbose = FALSE, chainter = FALSE, file = "R.pdb")

Arguments

pdb	a PDB structure object obtained from read.pdb or read.pqr.
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	atomic partial charge values of length equal to length(xyz)/3.
b	atomic radii values of length equal to length(xyz)/3.
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.

Details

PQR file format is basically the same as PDB format except for the fields of o and b. In PDB, these two fields are filled with ‘Occupancy’ and ‘B-factor’ values, respectively, with each field 6-column long. In PQR, they are atomic ‘partial charge’ and ‘radii’ values, respectively, with each field 8-column long.

Only the xyz argument is strictly required. Other arguments assume a default poly-ALA C-alpha structure with a blank chain id, atomic charge values of 0.00 and atomic radii equal to 1.00.

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.

Value

Called for its effect.

Note

Check that: (1) chain is one character long e.g. “A”, and (2) resno and eleno do not exceed “9999”.

Author(s)

Barry Grant with contributions from Joao Martins.

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.pqr, read.pdb, write.pdb, read.dcd, read.fasta.pdb, read.fasta

Examples

# PDB server connection required - testing excluded
try({

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

# Write out in PQR format 
outfile = file.path(tempdir(), "eg.pqr")
write.pqr(pdb=pdb, file = outfile)

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

}, silent=TRUE)
if(inherits(.Last.value, "try-error")) {
   message("Need internet to run the example")
}

bio3d documentation built on Oct. 30, 2024, 1:08 a.m.