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.

Description

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

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.

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

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

Author

Lars Skjaerven