bio3d (version 2.3-0)

convert.pdb: Renumber and Convert Between Various PDB formats

Description

Renumber and convert between CHARMM, Amber, Gromacs and Brookhaven PDB formats.

Usage

convert.pdb(pdb, type=c("original", "pdb", "charmm", "amber", "gromacs"), renumber = FALSE, first.resno = 1, first.eleno = 1, consecutive=TRUE, rm.h = TRUE, rm.wat = FALSE, verbose=TRUE)

Arguments

pdb

a structure object of class "pdb", obtained from read.pdb.

type

output format, one of ‘original’, ‘pdb’, ‘charmm’, ‘amber’, or ‘gromacs’. The default option of ‘original’ results in no conversion.

renumber

logical, if TRUE atom and residue records are renumbered using ‘first.resno’ and ‘first.eleno’.

first.resno

first residue number to be used if ‘renumber’ is TRUE.

first.eleno

first element number to be used if ‘renumber’ is TRUE.

consecutive

logical, if TRUE renumbering will result in consecutive residue numbers spanning all chains. Otherwise new residue numbers will begin at ‘first.resno’ for each chain.

rm.h

logical, if TRUE hydrogen atoms are removed.

rm.wat

logical, if TRUE water atoms are removed.

verbose

logical, if TRUE details of the conversion process are printed.

Value

Returns a list of class "pdb", with the following components:

Details

Convert atom names and residue names, renumber atom and residue records, strip water and hydrogen atoms from pdb objects.

Format type can be one of “ori”, “pdb”, “charmm”, “amber” or “gromacs”.

References

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

For a description of PDB format (version3.3) see: http://www.wwpdb.org/documentation/format33/v3.3.html.

See Also

atom.select, write.pdb, read.dcd, read.fasta.pdb, read.fasta

Examples

## Not run: 
# 
# # Read a PDB file
# pdb <- read.pdb("4q21")
# pdb
# head( pdb$atom[pdb$calpha,"resno"] )
# 
# # Convert to CHARMM format
# new <- convert.pdb(pdb, type="amber", renumber=TRUE, first.resno=22 )
# head( new$atom[new$calpha,"resno"] )
# 
# # Write a PDB file
# #write.pdb(new, file="tmp4amber.pdb")
# 
# ## End(Not run)