R: Filter or Trim a PDBs Object

trim.pdbs {bio3d} | R Documentation

## 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)

[Package bio3d version 2.4-0 Index]