bio3d (version 2.4-4)

read.crd: Read Coordinate Data from Amber or Charmm

Description

Read a CHARMM CARD (CRD) or AMBER coordinate file.

Usage

read.crd(file, ...)

Value

See the ‘value’ section for the corresponding functions for more details.

Arguments

file

the name of the coordinate file to be read.

...

additional arguments passed to the methods read.crd.charmm or read.crd.amber.

Author

Barry Grant and Lars Skjaerven

Details

read.crd is a generic function calling the corresponding function determined by the class of the input argument x. Use methods("read.crd") to get all the methods for read.crd generic:

read.crd.charmm will be used for file extension ‘.crd’.

read.crd.amber will be used for file extension ‘.rst’ or ‘.inpcrd’.

See examples for each corresponding function for more details.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

See Also

read.crd.amber, read.crd.charmm, write.crd, read.prmtop, read.pdb, write.pdb, atom.select, read.dcd, read.ncdf

Examples

if (FALSE) {
## Read a PRMTOP file
prmtop <- read.prmtop(system.file("examples/crambin.prmtop", package="bio3d"))
print(prmtop)

## Read a Amber CRD file
crds <- read.crd(system.file("examples/crambin.inpcrd", package="bio3d"))

## Atom selection
ca.inds <- atom.select(prmtop, "calpha")

## Convert to PDB format
pdb <- as.pdb(prmtop, crds, inds=ca.inds)
}