Rpdb (version 2.2)

merge.coords: Merging Molecular Systems

Description

Merge two objects contaning atomic coordinates

Usage

"merge"(x, y, ...)
"merge"(x, y, reindex = TRUE, ...)
"merge"(x, y, reindex = TRUE, ...)

Arguments

x, y

objects of class 'coords' to be merged.

reindex

a single element logical vector indicating if residue and element IDs have to be reindexed after merging.

...

further arguments passed to or from other methods.

Value

Return a n object of the same class as x and y merging x and y. If x and y have different basis attributes an error is returned.

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 conect components of the two pdb objects are merged by row and the cryst1 components 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.

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)

## Not run: 
# ## Merging objects with different basis sets return an error.
# c2 <- coords(9:11, 12:14, 15:17, basis = "abc")
# merge(c1,c2)
# ## End(Not run)

## 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)