trim.pdbs {bio3d}

Filter or Trim a PDBs Object

Description

Trim residues and/or filter out structures from a PDBs object.

Usage

## S3 method for class 'pdbs'
trim(pdbs, row.inds=NULL, col.inds=NULL, ...)

Arguments

pdbs

an object of class pdbs as obtained from function pdbaln or read.fasta.pdb; a xyz matrix containing the cartesian coordinates of C-alpha atoms.

row.inds

a numeric vector of indices pointing to the PDB structures to keep (rows in the pdbs$ali matrix).

col.inds

a numeric vector of indices pointing to the alignment columns to keep (columns in the pdbs$ali matrix).

...

additional arguments passed to and from functions.

Details

Utility function to remove structures, or trim off columns, in a ‘pdbs’ object.

Value

Returns an updated ‘pdbs’ object with the following components:

xyz

numeric matrix of aligned C-alpha coordinates.

resno

character matrix of aligned residue numbers.

b

numeric matrix of aligned B-factor values.

chain

character matrix of aligned chain identifiers.

id

character vector of PDB sequence/structure names.

ali

character matrix of aligned sequences.

call

the matched call.

Author(s)

Lars Skjaerven

References

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

See Also

pdbaln, gap.inspect, read.fasta,read.fasta.pdb, trim.pdb,

Examples

## Not run: 
## Fetch PDB files and split to chain A only PDB files
ids <- c("1a70_A", "1czp_A", "1frd_A", "1fxi_A", "1iue_A", "1pfd_A")
raw.files <- get.pdb(ids, path = "raw_pdbs")
files <- pdbsplit(raw.files, ids, path = "raw_pdbs/split_chain")

## Sequence Alignement, and connectivity check
pdbs <- pdbaln(files)

cons <- inspect.connectivity(pdbs)

## omit files with missing residues
trim.pdbs(pdbs, row.inds=which(cons))

## End(Not run)