PDBs to PDB Converter

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.

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=""))


  |======================================================================| 100%


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

Reading PDB files:
raw_pdbs/split_chain/1YX5_B.pdb
raw_pdbs/split_chain/3NOB_A.pdb
raw_pdbs/split_chain/3NOB_B.pdb
raw_pdbs/split_chain/3NOB_C.pdb
raw_pdbs/split_chain/3NOB_D.pdb
raw_pdbs/split_chain/3NOB_E.pdb
raw_pdbs/split_chain/3NOB_F.pdb
raw_pdbs/split_chain/3NOB_G.pdb
raw_pdbs/split_chain/3NOB_H.pdb
raw_pdbs/split_chain/1P3Q_U.pdb
..........

Extracting sequences

pdb/seq: 1   name: raw_pdbs/split_chain/1YX5_B.pdb 
pdb/seq: 2   name: raw_pdbs/split_chain/3NOB_A.pdb 
pdb/seq: 3   name: raw_pdbs/split_chain/3NOB_B.pdb 
pdb/seq: 4   name: raw_pdbs/split_chain/3NOB_C.pdb 
pdb/seq: 5   name: raw_pdbs/split_chain/3NOB_D.pdb 
pdb/seq: 6   name: raw_pdbs/split_chain/3NOB_E.pdb 
pdb/seq: 7   name: raw_pdbs/split_chain/3NOB_F.pdb 
pdb/seq: 8   name: raw_pdbs/split_chain/3NOB_G.pdb 
pdb/seq: 9   name: raw_pdbs/split_chain/3NOB_H.pdb 
pdb/seq: 10   name: raw_pdbs/split_chain/1P3Q_U.pdb 


## 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)

See also

Author