read.pdcBD {bio3d}

Read PQR output from pdcBD File

Description

Read a pdcBD PQR coordinate file.

Usage

read.pdcBD(file, maxlines = 50000, multi = FALSE, rm.insert = FALSE,
         rm.alt = TRUE, verbose = TRUE)

Arguments

file

the name of the pdcBD PQR file to be read.

maxlines

the maximum number of lines to read before giving up with large files. Default is 50,000 lines.

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.

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).

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”.

Note

For both atom and het list components the column names can be used as a convenient means of data access, namely: Atom serial number “eleno” , Atom type “elety”, Alternate location indicator “alt”, Residue name “resid”, Chain identifier “chain”, Residue sequence number “resno”, Code for insertion of residues “insert”, Orthogonal coordinates “x”, Orthogonal coordinates “y”, Orthogonal coordinates “z”, Occupancy “o”, and Temperature factor “b”. See examples for further details.

Author(s)

Barry Grant

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

# PDB server connection required - testing excluded

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