pdb {Rpdb} | R Documentation |
Create an Object of Class ‘pdb’
Description
Creates an object of class 'pdb'.
Usage
pdb(...)
## Default S3 method:
pdb(atoms, cryst1 = NULL, conect = NULL, remark = NULL, title = NULL, ...)
is.pdb(x)
Arguments
... |
further arguments passed to or from other methods. |
atoms |
a data.frame of class |
cryst1 |
a list of class |
conect |
a data.frame of class |
remark |
a character vector containing some REMARK records to be added to the |
title |
a character vector containing some TITLE records to be added to the |
x |
an R object to be tested |
Details
This function is the generic function to create objects of class
‘pdb’. The purpose of this class is to store the data of molecular
systems contained in PDB files. The default method of the pdb
function
creates an object of class ‘pdb’ from its different components, i.e.:
title
, remark
, cryst1
, atoms
and conect
.
At least an object of class ‘atoms’ has to be specified.
is.pdb
tests if x is an object of class ‘pdb’, i.e. if x has a
“class” attribute equal to pdb
.
Value
pdb
returns a list of class ‘pdb’ with the following components:
title |
a character vector containing the TITLE records found in a PDB file. |
remark |
a character vector containing the REMARK records found in a PDB file. |
cryst1 |
a list of class ‘cryst1’ containing the first CRYST1 record found in a PDB file. All others are ignored. |
atoms |
a data.frame of class ‘atoms’ containing the ATOM and HETATM records found in a PDB file. |
conect |
a data.frame of class ‘conect’ containing the CONECT records found in a PDB file. |
is.pdb
returns TRUE if x is an object of class ‘pdb’ and FALSE otherwise.
See Also
atoms
, coords
, cryst1
, conect
and read.pdb
Examples
title <- "This is just an example"
remark <- NULL
cryst1 <- cryst1(c(10,10,10))
atoms <- atoms(recname = c("ATOM","ATOM"), eleid = 1:2, elename = c("H","H"), alt = "",
resname = c("H2","H2"), chainid = "", resid = c(1,1), insert = "",
x1 = c(0,0), x2 = c(0,0), x3 = c(0,1), occ = c(0.0,0.0), temp = c(1.0,1.0),
segid = c("H2","H2"))
conect <- conect(eleid.1 = c(1), eleid.2 = c(2))
x <- pdb(atoms = atoms, cryst1 = cryst1, conect = conect, remark = remark, title = title)
is.pdb(x)