bio3d (version 2.3-4)

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, all.atom=FALSE, ncore=NULL)

Arguments

pdbs

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

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.

all.atom

logical, if TRUE all atom data are converted (the ‘pdbs’ object must be obtained from read.all).

ncore

number of CPU cores used to do the calculation.

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

# NOT RUN {
## 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)

# }