bio3d (version 2.1-1)

read.pqr: Read PQR File

Description

Read a PQR coordinate file.

Usage

read.pqr(file, maxlines = -1, multi = FALSE, rm.insert = FALSE,
         rm.alt = TRUE, verbose = TRUE)

Arguments

file

the name of the PQR file to be read.

maxlines

the maximum number of lines to read before giving up with large files. By default if will read up to the end of input on the connection.

multi

logical, if TRUE multiple ATOM records are read for all models in multi-model files.

rm.insert

logical, if TRUE PDB insert records are ignored.

rm.alt

logical, if TRUE PDB alternate records are ignored.

verbose

print details of the reading process.

Value

• Returns a list of class "pdb" with the following components:
• atom
  a character matrix containing all atomic coordinate ATOM data, with a row per ATOM and a column per record type. See below for details of the record type naming convention (useful for accessing columns).
• het
  a character matrix containing atomic coordinate records for atoms within non-standard HET groups (see atom).
• helix
  start, end and length of H type sse, where start and end are residue numbers resno.
• sheet
  start, end and length of E type sse, where start and end are residue numbers resno.
• seqres
  sequence from SEQRES field.
• xyz
  a numeric vector of ATOM coordinate data.
• calpha
  logical vector with length equal to nrow(atom) with TRUE values indicating a C-alpha elety.

Details

maxlines may require increasing for some large multi-model files. The preferred means of reading such data is via binary DCD format trajectory files (see the read.dcd function).

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

atom.select, write.pdb, read.dcd, read.fasta.pdb, read.fasta

Examples

# Read a PDB file
pdb <- read.pdb( "4q21" )
  
# Print data for the first atom
pdb$atom[1,]
# Look at the first het atom
pdb$het[1,]
# Print some coordinate data
pdb$atom[1:20, c("x","y","z")]

# Print C-alpha coordinates (can also use 'atom.select')
##pdb$xyz[pdb$calpha, c("resid","x","y","z")]

# Print SSE data (for helix and sheet)
pdb$helix
pdb$sheet$start
  
# Print SEQRES data
pdb$seqres

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

# Write out renumbered PDB file
#write.pdb(pdb=pdb,file="eg.pdb")