Rpdb (version 2.0)

atoms: Create atoms Object

Description

Creates an object of class atoms containing the data related to ATOM and HETATM records of a PDB file.

Usage

atoms(...)
## S3 method for class 'default':
atoms(recname, eleid, elename, alt, resname, chainid,
resid, insert, x1, x2, x3, occ, temp, segid, basis = "xyz", ...)

Arguments

...

arguments passed to methods.

recname

a character vector containing the record name for each element.

eleid

a integer vector containing the element ID for each element.

elename

a character vector containing the element name for each element.

alt

a character vector containing the alternate location indicator for each element.

resname

a character vector containing the residue name for each element.

chainid

a character vector containing the chain ID for each element.

resid

a integer vector containing the residue ID for each element.

insert

a character vector containing the codes for insertion of residue of each element.

x1, x2, x3

a numeric vector containing the first, second and third coordinate for each element.

occ

a numeric vector containing the occupancie for each element.

temp

a numeric vector containing the temperature factor for each element.

segid

a character vector containing the segment ID for each element.

basis

a single element character vector indicating the type of basis vector used to express the atomic coordinates.

Value

• Return a data.frame of class atoms with the following components:
• recname
  a character vector containing the record name for each element.
• eleid
  a integer vector containing the element ID for each element.
• elename
  a character vector containing the element name for each element.
• alt
  a character vector containing the alternate location indicator for each element.
• resname
  a character vector containing the residue name for each element.
• chainid
  a character vector containing the chain ID for each element.
• resid
  a integer vector containing the residue ID for each element.
• insert
  a character vector containing the codes for insertion of residue for each element.
• x1, x2, x3
  a numeric vector containing the first, second and third coordinate for each element.
• occ
  a numeric vector containing the occupencie for each element.
• temp
  a numeric vector containing the temperature factor for each element.
• segid
  a character vector containing the segment ID for each element.
• basis
  a single element character vector indicating the type of basis vector used to express the atomic coordinates.

encoding

UTF-8

Details

atoms is a generic function to create objects of class atoms. The purpose of this class is to store ATOM and HETATM records from PDB files. The default method creates a atoms object from its different components, i.e.: recname, eleid, elename, alt, resname, chainid, resid, insert, x1, x2, x3, occ, temp, segid and basis. All the arguments have to be specified except basis which by default is set to "xyz" (Cartesian coordinates).

See Also

basis, coords, pdb

Examples

x <- 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"))
print(x)
class(x)