read.pdb {protein8k}

read.pdb

Description

Read in a Protein Data Bank file

Usage

read.pdb(fileName, createAsS4 = TRUE)

Arguments

fileName

character string for location and name of file to be read.

createAsS4

Logical indicating whether to create the new protein object as S4 or not. Defaults to TRUE if not specified. This argument is optional.

Format

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

  1. record_type:Type of record in this section. Generally ATOM or HETATM

  2. serial_num: The serial number for the position of the atom in the sequence

  3. atom_name: A name to identify the atom in a structure

  4. alt_location_id:

  5. residue_name: 3 character identifier for a residue

  6. chain_id:

  7. residue_seq_num: Number representing where in the sequence a residue is.

  8. insert_residue_code:

  9. x_ortho_coord: X coordinate in Ångstroms on an orthogonal plane

  10. y_ortho_coord: Y coordinate in Ångstroms on an orthogonal plane

  11. z_ortho_coord: Z coordinate in Ångstroms on an orthogonal plane

  12. occupancy:

  13. temp_factor: The amount of overall error in the measurement of an atom.

  14. segment_id:

  15. element_symbol: Periodic symbol representing an atom.

  16. charge: Charge of the given atom. Can be +, -, or none at all

Details

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.

Value

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.