Read in a Protein Data Bank file
read.pdb(fileName, createAsS4 = TRUE)character string for location and name of file to be read.
Logical indicating whether to create the new protein object as S4 or not. Defaults to TRUE if not specified. This argument is optional.
A new protein object as either an S3 or S4 object.
In general terms, the new object will be a list of two, a data frame containing the atomic record, and a list of header elements.
A Protein object. List comprised of several sublists and dataframes
header: List of 2, Header Line and Title
header_line: List of 3, Classification, depDate, and idCode
classifiation: Classification of the Protein in the PDB
depDat: Date the PDB was deposited or created
idCode: 4 digit identifier for the PDB. Always unique.
title: The title of the PDB.
structure: Dataframe of 16 variables
record_type:Type of record in this section. Generally ATOM or HETATM
serial_num: The serial number for the position of the atom in the sequence
atom_name: A name to identify the atom in a structure
alt_location_id:
residue_name: 3 character identifier for a residue
chain_id:
residue_seq_num: Number representing where in the sequence a residue is.
insert_residue_code:
x_ortho_coord: X coordinate in <U+00C5>ngstroms on an orthogonal plane
y_ortho_coord: Y coordinate in <U+00C5>ngstroms on an orthogonal plane
z_ortho_coord: Z coordinate in <U+00C5>ngstroms on an orthogonal plane
occupancy:
temp_factor: The amount of overall error in the measurement of an atom.
segment_id:
element_symbol: Periodic symbol representing an atom.
charge: Charge of the given atom. Can be +, -, or none at all
Reads a Protein Data Bank file (PDB) from the given location. The function then parses the file and creates a new object of the Protein class. This object can be either defined as an S3 or S4 object if different capabilities are required.