reindex: Reinitialize Object Indexing

In Rpdb: Read, Write, Visualize and Manipulate PDB Files

Reinitialize Object Indexing

Description

Reinitialize the indexing of an object.

Usage

reindex(...)

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

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

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.

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.

Value

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

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)

Rpdb documentation built on Sept. 28, 2023, 5:07 p.m.