bio3d (version 2.1-2)

pdbs2pdb: PDBs to PDB Converter

Description

Convert a list of PDBs from an "pdbs" object to a list of pdb objects.

Usage

pdbs2pdb(pdbs, inds = NULL, rm.gaps = FALSE)

Arguments

pdbs

a list of class "pdbs" containing PDB file data, as obtained from read.fasta.pdb or pdbaln.

inds

a vector of indices that selects the PDB structures to convert.

rm.gaps

logical, if TRUE atoms in gap containing columns are removed in the output pdb objects.

Value

• Returns a list of pdb objects.

Details

This function will generate a list of pdb objects from a "pdbs" class.

See examples for more details/

References

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

See Also

read.pdb, pdbaln, read.fasta.pdb.

Examples

## Fetch PDBs
pdb.ids <- c("1YX5_B", "3NOB", "1P3Q_U")
#outdir <- paste(tempdir(), "/raw_pdbs", sep="")
outdir = "raw_pdbs"
raw.files <- get.pdb(pdb.ids, path = outdir)

## Split PDBs by chain ID and multi-model records
all.files <- pdbsplit(raw.files, pdb.ids, 
                path =paste(outdir, "/split_chain", sep=""))

## Align and fit
pdbs     <- pdbaln(all.files, fit=TRUE)

## Convert back to PDB objects
all.pdbs <- pdbs2pdb(pdbs)

## Access the first PDB object
## all.pdbs[[1]]

## Return PDB objects consisting of only
## atoms in non-gap positions
all.pdbs <- pdbs2pdb(pdbs, rm.gaps=TRUE)