bio3d: clean.pdb – R documentation

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clean.pdb

Inspect And Clean Up A PDB Object

Description

Inspect alternative coordinates, chain breaks, bad residue numbering, non-standard/unknow amino acids, etc. Return a 'clean' pdb object with fixed residue numbering and optionally relabeled chain IDs, corrected amino acid names, removed water, ligand, or hydrogen atoms. All changes are recorded in a log in the returned object.

Usage

clean.pdb(pdb, consecutive = TRUE, force.renumber = FALSE,
  fix.chain = FALSE, fix.aa = FALSE, rm.wat = FALSE, rm.lig = FALSE,
  rm.h = FALSE, verbose = FALSE)

Arguments

`pdb`	an object of class `pdb` as obtained from function `read.pdb`.
`consecutive`	logical, if TRUE renumbering will result in consecutive residue numbers spanning all chains. Otherwise new residue numbers will begin at 1 for each chain.
`force.renumber`	logical, if TRUE atom and residue records are renumbered even if no 'insert' code is found in the `pdb` object.
`fix.chain`	logical, if TRUE chains are relabeled based on chain breaks detected.
`fix.aa`	logical, if TRUE non-standard amino acid names are converted into equivalent standard names.
`rm.wat`	logical, if TRUE water atoms are removed.
`rm.lig`	logical, if TRUE ligand atoms are removed.
`rm.h`	logical, if TRUE hydrogen atoms are removed.
`verbose`	logical, if TRUE details of the conversion process are printed.

Details

call for its effects.

Value

a 'pdb' object with an additional $log component storing all the processing messages.

Author(s)

Xin-Qiu Yao & Barry Grant

Examples

# PDB server connection required - testing excluded

   pdb <- read.pdb("1a7l")
   clean.pdb(pdb)

bio3d

Biological Structure Analysis

v2.4-2

GPL (>= 2)

Authors

Barry Grant [aut, cre], Xin-Qiu Yao [aut], Lars Skjaerven [aut], Julien Ide [aut]

Initial release