Protein-class: Protein Class Definitions

In protein8k: Perform Analysis and Create Visualizations of Proteins

Protein Class Definitions

Description

Protein Class used to Define Protein Objects of S3 and S4 Types. Currently still in development, Integrity checks still need to be added.

Format

Breakdown of a Protein Object's structure:

• 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

protein8k documentation built on Dec. 22, 2025, 1:06 a.m.