Read, Write, Visualize and Manipulate PDB Files
Provides tools to read, write, visualize PDB files, and perform structural manipulations.
This package has been developed for computational chemists wishing to manipulate molecular structures stored in PDB files. PDB files can easily be read, written, visualized and some basic structural manipulations can be achieved with the present package. Convertion of Cartesian coordinates into fractional coordinates. Spliting a molecular structure into fragments. Computation of centers-of-geometry and centers-of-mass. Wrapping molecular structure using periodical boundary conditions. Tranlation, rotation and reflection of atomic coordinates. Calculate atomic bond lengths, angles and dihedrals.
Julien Idé julien.ide.fr@gmail.com
More information on the PDB format can be found here:
http://www.wwpdb.org/documentation/format33/v3.3.html
## Read a PDB file included in the package
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb",package="Rpdb"))
## Visualize the PDB file
visualize(x, mode = NULL)
## From Cartesian to fractional coordinates and vice versa
x <- xyz2abc(x)
basis(x)
natom(x,x$atoms$resid)
range(x)
centres(x)
x <- abc2xyz(x)
basis(x)
natom(x,x$atoms$resid)
range(x)
centres(x)
## Split and unsplit
F <- x$atoms$resid
x <- split(x, F)
x <- unsplit(x, F)
## Subset and merge
x.PCB.only <- subset(x, resname == "PCB")
x.DCB.only <- subset(x, resname == "DCB")
x <- merge(x.PCB.only, x.DCB.only)
## Duplicate and wrap
x <- replicate(x, a.ind = -1:1, b.ind = -1:1, c.ind = -1:1)
x <- wrap(x)
## Write the 'pdb' object 'x' in a temporary file.
write.pdb(x, file = tempfile())Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.