bio3d (version 2.1-3)

read.fasta.pdb: Read Aligned Structure Data

Description

Read aligned PDB structures and store their C-alpha atom data, including xyz coordinates, residue numbers, residue type and B-factors.

Usage

read.fasta.pdb(aln, prefix = "", pdbext = "", fix.ali = FALSE,
             ncore = 1, nseg.scale = 1, ...)

Arguments

aln

an alignment data structure obtained with read.fasta.

prefix

prefix to aln$id to locate PDB files.

pdbext

the file name extention of the PDB files.

fix.ali

logical, if TRUE check consistence between $ali and $resno, and correct $ali if they don't match.

ncore

number of CPU cores used to do the calculation. ncore>1 requires package parallel installed.

nseg.scale

split input data into specified number of segments prior to running multiple core calculation. See fit.xyz.

...

other parameters for read.pdb.

Value

• Returns a list of class "pdbs" with the following five components:
• xyz
  numeric matrix of aligned C-alpha coordinates.
• resno
  character matrix of aligned residue numbers.
• b
  numeric matrix of aligned B-factor values.
• chain
  character matrix of aligned chain identifiers.
• id
  character vector of PDB sequence/structure names.
• ali
  character matrix of aligned sequences.
• resid
  character matrix of aligned 3-letter residue names.
• call
  the matched call.

Details

The input aln, produced with read.fasta, must have identifers (i.e. sequence names) that match the PDB file names. For example the sequence corresponding to the structure 1bg2.pdb should have the identifer 1bg2. See examples below. Sequence miss-matches will generate errors. Thus, care should be taken to ensure that the sequences in the alignment match the sequences in their associated PDB files.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

See Also

read.fasta, read.pdb, core.find, fit.xyz, read.all

Examples

# Read sequence alignment
file <- system.file("examples/kif1a.fa",package="bio3d")
aln  <- read.fasta(file)

# Read aligned PDBs
pdbs <- read.fasta.pdb(aln)

# Structure/sequence names/ids
basename( pdbs$id )

# Alignment positions 335 to 339
pdbs$ali[,335:339]
pdbs$resid[,335:339]
pdbs$resno[,335:339]
pdbs$b[,335:339]

# Alignment C-alpha coordinates for these positions
pdbs$xyz[, atom2xyz(335:339)]

# See 'fit.xyz()' function for actual coordinate superposition
#  e.g. fit to first structure
# xyz <- fit.xyz(pdbs$xyz[1,], pdbs)
# xyz[, atom2xyz(335:339)]