Write PQR Format Coordinate File

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

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.

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.

Author

Barry Grant with contributions from Joao Martins.

Note

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

See also

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

Examples

# \donttest{
# PDB server connection required - testing excluded

# Read a PDB file
pdb <- read.pdb( "1bg2" )
#>   Note: Accessing on-line PDB file
#> Warning: /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp4WslmZ/1bg2.pdb  exists. Skipping download

# 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") )
#> 
#> See the output file:
#> /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp4WslmZ/eg.pqr

# }