Rpdb (version 2.2)

subset.pdb: Subsetting ‘atoms’ and ‘pdb’ Objects

Description

Return subsets of ‘atoms’ or ‘pdb’ objects which meet conditions.

Usage

"subset"(x, subset, drop = FALSE, reindex.all = TRUE, ...)
"subset"(x, subset, drop = FALSE, reindex.all = TRUE, ...)

Arguments

x

object to be subsetted.

subset

logical expression indicating elements or rows to keep: missing values are taken as false.

drop

passed on to [ indexing operator.

reindex.all

a single element logical vector indicating if residues and elements IDs have to be reindexed after subsetting.

...

further arguments to be passed to or from other methods.

Value

Return a subsetted object of the same class as x.

Details

For a ‘atoms’ object the method is similar to the data.frame method (see subset) but allow to directly reindex the elements and residues IDs. For a ‘pdb’ object subsetting is apply on the atoms and conect components of the object in a consistent way. First the atoms component is subsetted and then the conect component is filtered to keep only the conectivity for the subset.

See Also

subset, pdb, atoms, reindex

Examples

x <- read.pdb(system.file("examples/PCBM_ODCB.pdb",package="Rpdb"))
y <- subset(x, x$atoms$eleid %in% sample(x$atoms$eleid, 10))
is(y)
y <- subset(x$atoms, x$atoms$eleid %in% sample(x$atoms$eleid, 10))
is(y)
x <- coords(x)
y <- subset(x, x < 0)
is(y)