Helper Functions for Translation of Atomic Coordinates
Translation of atomic coordinates along a specific Cartesian or lattice vector.
Tx(...) ## S3 method for class 'coords' Tx(obj, x = 0, mask = TRUE, thickness = NULL, cryst1 = NULL, ...) ## S3 method for class 'pdb' Tx(obj, x = 0, mask = TRUE, thickness = NULL, cryst1 = obj$cryst1, ...) Ty(...) ## S3 method for class 'coords' Ty(obj, y = 0, mask = TRUE, thickness = NULL, cryst1 = NULL, ...) ## S3 method for class 'pdb' Ty(obj, y = 0, mask = TRUE, thickness = NULL, cryst1 = obj$cryst1, ...) Tz(...) ## S3 method for class 'coords' Tz(obj, z = 0, mask = TRUE, thickness = NULL, cryst1 = NULL, ...) ## S3 method for class 'pdb' Tz(obj, z = 0, mask = TRUE, thickness = NULL, cryst1 = obj$cryst1, ...) Ta(...) ## S3 method for class 'coords' Ta(obj, a = 0, mask = TRUE, cryst1 = NULL, ...) ## S3 method for class 'pdb' Ta(obj, a = 0, mask = TRUE, cryst1 = obj$cryst1, ...) Tb(...) ## S3 method for class 'coords' Tb(obj, b = 0, mask = TRUE, cryst1 = NULL, ...) ## S3 method for class 'pdb' Tb(obj, b = 0, mask = TRUE, cryst1 = obj$cryst1, ...) Tc(...) ## S3 method for class 'coords' Tc(obj, c = 0, mask = TRUE, cryst1 = NULL, ...) ## S3 method for class 'pdb' Tc(obj, c = 0, mask = TRUE, cryst1 = obj$cryst1, ...)
obj |
an R object containing atomic coordinates. |
x |
the x-component of the translation vector. |
mask |
a logical vector indicating the set of coordinates to which to apply the translation. |
thickness |
a numeric value indicating the fraction of the thicknees of the selected atom to be added to the translation vector (Usually 0, 0.5 or 1. See details). |
cryst1 |
an object of class ‘cryst1’ use to convert Cartesian into fraction coordinates (or Vis Versa) when need. |
y |
the y-component of the translation vector. |
z |
the z-component of the translation vector. |
a |
the a-component of the translation vector. |
b |
the b-component of the translation vector. |
c |
the c-component of the translation vector. |
... |
further arguments passed to or from other methods. |
These functions are helper functions to perform a translation along a
specific Cartesian or lattice vector. All of them call either the Txyz
or Tabc function.
An object of the same class as x with translated coordinates.
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb",package="Rpdb"))
visualize(x, mode = NULL)
visualize(Ty(x, 10), mode = NULL)
visualize(Ty(x, 10, mask=x$atoms$resid==1), mode = NULL)
visualize(Tb(x, 1 ), mode = NULL)
visualize(Tb(x, 1 , mask=x$atoms$resid==1), mode = NULL)
# Lets build a C70/Pentacene dimer with an inter-molecular distance equal to 3.5
C70 <- read.pdb(system.file("examples/C70.pdb",package="Rpdb"))
Pen <- read.pdb(system.file("examples/Pentacene.pdb",package="Rpdb"))
x <- merge(C70,Pen)
visualize(x, mode = NULL)
viewXY()
visualize(Tz(x, z=3.5, mask=x$atoms$resname=="C70", thickness=0.5), mode = NULL)
viewXY()Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.