Rpdb (version 2.0)

reindex: Reinitialize Object Indexing

Description

Reinitialize the indexing of an object.

Usage

reindex(...)
## S3 method for class 'atoms':
reindex(x, eleid = TRUE, resid = TRUE, \dots)
## S3 method for class 'pdb':
reindex(x, eleid = TRUE, resid = TRUE, \dots)

Arguments

...

further arguments passed to or from other methods

x

an R object

eleid

a single element logical vector indicating if elements IDs have to reindexed

resid

a single element logical vector indicating if residues IDs have to reindexed

Value

• Return an object of the same class as x with updated indexes.

Details

reindex is a generic function to reinitialize the indexing of an object or its components. The methods for objects of class atoms reinitialize the residue and element IDs starting from 1 and avoiding gaps in the indexes. For objects of class pdb their atoms and conect components are reindexed consistently.

See Also

pdb, atoms, subset.atoms, subset.pdb

Examples

x <- read.pdb(system.file("examples/PCBM_ODCB.pdb",package="Rpdb"))
x <- subset(x, x$atoms$eleid %in% sample(x$atoms$eleid, 10))
print(x)
x <- reindex(x)
print(x)