merge.coords: Merging Molecular Systems

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

Merging Molecular Systems

Description

Merge two objects containing atomic coordinates

Usage

## S3 method for class 'coords'
merge(x, y, ...)

## S3 method for class 'atoms'
merge(x, y, reindex = TRUE, ...)

## S3 method for class 'pdb'
merge(x, y, reindex = TRUE, ...)

## S3 method for class 'pdb.hetero'
merge(x, y, ...)

## S3 method for class 'pdb.structure'
merge(x, y, ...)

## S3 method for class 'pdb.resolution'
merge(x, y, ...)

Arguments

x, y	objects of class coords to be merged.
...	further arguments passed to or from other methods.
reindex	a single element logical vector indicating if residue and element IDs have to be reindexed after merging.

Details

To merge x and y they must have the same basis attributes (see basis).

For objects of class ‘coords’ and ‘atoms’ the atomic coordinates are directly merged by row.

For objects of class ‘pdb’, the atoms and connect components of the two pdb objects are merged by row and the crystal component of x is used to build the returned object.

For objects of class ‘atoms’ and ‘pdb’ the residue and element IDs of y are shifted to avoid any confusion with those of x. If reindex == TRUE the reindex function is called to reinitialize the indexing of the returned object. The functions of type ‘pdb.hetero’, ‘pdb.structure’ and ‘pdb.resolution’ merge the corresponding pdb fields.

Value

Return an object of the same class as x and y merging x and y. Note: x and y must have the same basis attributes, otherwise an error is returned.

See Also

coords, atoms, pdb, basis, merge, merge.data.frame

Examples

c1 <- coords( 1:3 ,  4:6 ,  7:9 , basis = "xyz")
c2 <- coords(10:12, 13:15, 16:18, basis = "xyz")
merge(c1,c2)


## Merging objects with different basis sets returns an error.
c2 <- coords(9:11, 12:14, 15:17, basis = "abc")
try(merge(c1,c2))


## Prepare a Pentacene/C70 dimer
C70 <- read.pdb(system.file("examples/C70.pdb", package="Rpdb"))
Pen <- read.pdb(system.file("examples/Pentacene.pdb", package="Rpdb"))
x <- merge(Tz(C70, 3.5, thickness=0.5), Pen)
  

Rpdb documentation built on May 12, 2026, 5:06 p.m.