- 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.