The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules that serves a global community of researchers, educators, and students. The data contained in the archive include atomic coordinates, crystallographic structure factors and NMR experimental data. Aside from coordinates, each deposition also includes the names of molecules, primary and secondary structure information, sequence database references, where appropriate, and ligand and biological assembly information, details about data collection and structure solution, and bibliographic citations. The pdb file format is a textual file format describing the three-dimensional structures of molecules held in the Protein Data Bank. In this project you are asked to develop a computer software to read and process the data in the pdb file.

Write a GUI program (Using java programmming language) that reads a pdb file (either saved in the personal computer or fetch it from online servers like www.rcsb.org). If the user chooses to download the pdb file directly from online, s/he should be able to provide the ID of the protein and the chain (optional). You have to use object-oriented concepts to implement your program (20 points). Define the following classes and the appropriate methods in each class. 1. Class Protein 2. Class Chain 3. Class AminoAcid 4. Class Atom An instance of class Protein may have one or more instances of class Chain. An instance of class Chain may have one or more instances of class AminoAcid. An instance of class AminoAcid may have one or more instances of class Atom. A read method have to be defined in the class Protein where the user can send the path of the protein, if saved locally, or the ID, if to be fetched from online database, and, optionally, the user can send the ID of the chain to read, otherwise all chains have to be read. Also, define classes Helix and Sheet. Instance of Chain have one or more instances of Helix or Sheet. In addition, your program should be able to find the following: 1. Show the number of atoms in a particular Amino acid in a given chain (by aa sequence number). 2. Show the number of atoms in the side chain for particular aa in a given chain (aa sequence number should be provided). 3. Show the number of amino acids in a given chain. 4. Show the number of helices or sheets in the chain. 5. Return the coordinates of a particular atom (The user should provide aa number and the name of the atom). 6. show the name and number of the amino acid at the beginning or end of a given helix by its number. 7. Find the distance between any two atoms in the chain (the user should provide aa numbers and atom names).

use this link for file format to write a java program : https://www.rcsb.org/pdb/explore/explore.do?structureId=1BMC

this file you need to use as input