Filter or Trim a PDBs Object
Trim residues and/or filter out structures from a PDBs object.
## S3 method for class 'pdbs' trim(pdbs, row.inds=NULL, col.inds=NULL, ...)
pdbs |
an object of class |
row.inds |
a numeric vector of indices pointing to the PDB
structures to keep (rows in the |
col.inds |
a numeric vector of indices pointing to the
alignment columns to keep (columns in the |
... |
additional arguments passed to and from functions. |
Utility function to remove structures, or trim off columns, in a ‘pdbs’ object.
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. |
Lars Skjaerven
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
## 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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.