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

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 or pdbs$id refers to existing PDB files).

ncore

number of CPU cores used to do the calculation.

Details

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

See examples for more details/

Value

Returns a list of pdb objects.

References

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

Author

Lars Skjaerven

See also

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

Examples

if (FALSE) { ## 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) }