write.pqr {bio3d} | R Documentation |
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, het = FALSE, append = FALSE, verbose = FALSE, chainter = FALSE, file = "R.pdb")
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. |
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.
Called for its effect.
Check that:
(1) chain
is one character long e.g. “A”, and
(2) resno
and eleno
do not exceed “9999”.
Barry Grant with contributions from Joao Martins.
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
For a description of PDB format (version2.2) see:
http://www.rcsb.org/pdb/file_formats/pdb/.
read.pdb
, read.dcd
,
read.fasta.pdb
, read.fasta
# Read a PDB file pdb <- read.pdb(system.file("examples/d1bg2__.ent", package="bio3d")) # Renumber residues nums <- as.numeric(pdb$atom[,"resno"]) nums <- nums - (nums[1] - 1) # Write out renumbered PDB file write.pdb(pdb=pdb, resno = nums, file="eg.pdb")