split.pdb: Divide and Reassemble 'pdb' Objects

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

Divide and Reassemble ‘pdb’ Objects

Description

split divides a ‘pdb’ object by groups of atoms defined by f. unsplit reverses the effect of split.

Usage

## S3 method for class 'pdb'
split(x, f, drop = FALSE, ...)

## S3 method for class 'pdb'
unsplit(value, f, drop = FALSE, ...)

Arguments

x	an object of class ‘pdb’ to be divided into groups.
f	a ‘factor’ in the sense that as.factor(f) defines the grouping, or a list of such factors in which case their interaction is used for the grouping.
drop	logical indicating if levels that do not occur should be dropped (if f is a factor or a list).
...	further potential arguments passed to methods.
value	a list of 'pdb' objects compatible with a splitting of x. Recycling applies if the lengths do not match.

Details

split produce a list of ‘pdb’ objects with the same cryst1, title and remark components as x. Only its atoms component is splitted while its conect component is cleaned to keep only the meaningful connectivity for each ‘pdb’ object of the list returned by the function. unlist produce a ‘pdb’ object with the same cryst1, title and remark components as the first element of value. The atoms and conect components of all the elements of value are combined by row.

Value

The value returned from split is a list of ‘pdb’ objects containing the data for the groups of atoms. The components of the list are named by the levels of f (after converting to a factor, or if already a factor and drop=TRUE, dropping unused levels).
unsplit returns a ‘pdb’ object for which split(x, f) equals value.

See Also

split, unsplit, pdb

Examples

### Split a pdb file by residue IDs and write them into separate files
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))

file.names <- paste0(x$atoms$resname, "_", x$atoms$resid, ".pdb")
file.names <- unique(file.names)
pdb.resid  <- split(x, x$atoms$resid)
length(pdb.resid)
useless <- mapply(write.pdb, pdb.resid, file.names)

# Cleanup
unlink(file.names)

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