Helper Functions for reflection of Atomic Coordinates
Reflection of atomic coordinates with respect to a specific Cartesian plan or a plan defined by two lattice vectors.
Mxy(...) ## S3 method for class 'coords' Mxy(x, mask = TRUE, cryst1 = NULL, ...) ## S3 method for class 'pdb' Mxy(x, mask = TRUE, cryst1 = x$cryst1, ...) Myz(...) ## S3 method for class 'coords' Myz(x, mask = TRUE, cryst1 = NULL, ...) ## S3 method for class 'pdb' Myz(x, mask = TRUE, cryst1 = x$cryst1, ...) Mzx(...) ## S3 method for class 'coords' Mzx(x, mask = TRUE, cryst1 = NULL, ...) ## S3 method for class 'pdb' Mzx(x, mask = TRUE, cryst1 = x$cryst1, ...) Mab(...) ## S3 method for class 'coords' Mab(x, cryst1, mask = TRUE, ...) ## S3 method for class 'pdb' Mab(x, cryst1 = x$cryst1, mask = TRUE, ...) Mbc(...) ## S3 method for class 'coords' Mbc(x, cryst1, mask = TRUE, ...) ## S3 method for class 'pdb' Mbc(x, cryst1 = x$cryst1, mask = TRUE, ...) Mca(...) ## S3 method for class 'coords' Mca(x, cryst1, mask = TRUE, ...) ## S3 method for class 'pdb' Mca(x, cryst1 = x$cryst1, mask = TRUE, ...)
x |
an R object containing atomic coordinates. |
mask |
a logical vector indicating the set of coordinates to which to apply the reflection. |
cryst1 |
an object of class ‘cryst1’ use to convert fractional into Cartesian coordinates when need. |
... |
further arguments passed to or from other methods. |
These functions are helper functions to perform a reflection with respect to
a specific Cartesian plan or a plan defined by two lattice vectors. All of
them call the mirror function.
An object of the same class as x with reflected coordinates.
# First lets read a pdb file
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb",package="Rpdb"))
visualize(x,mode = NULL)
# Mirror operation with respect to the ab-plan
visualize(Mab(x), mode = NULL)
# Mirror operation with respect to the ab-plan for residue 1
visualize(Mab(x, mask=x$atoms$resid==1), mode = NULL)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.