Description

CENG 465
Assignment #3
Programming Assignment on Protein Structures

Finding the diameter of a protein structure

In this assignment, your goal is to write a program (in a language of your choice) which will process any given protein structure provided as a PDB file and find the diameter of the protein structure as the longest distance between any two alpha Carbon atoms in its backbone.

http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM

The format uses fixed column (i.e., character) positions for different information provided in a single ATOM record (i.e., on a single line).

Example outputs

Report the amino acid pair in the order that they appear in the PDB file: the first one that appears in the PDB as the first amino acid in the information line, for example, like “Between <first aa> and <second aa>”. Use three digits after the decimal point when reporting the diameter.

Input:
7dwb.pdb
Example run on commmand line:
$hw3 7dwb.pdb
Diameter = 137.409 Angstroms
Between A:SER(265) and F:ASP(387)

Input:
2wfi.pdb
Example run on commmand line:
$hw3 2wfi.pdb
Diameter = 41.852 Angstroms
Between A:GLN(6) and A:ALA(161)

Test cases

Run your program on the 10 protein structures provided in the following link:

http://www.ceng.metu.edu.tr/~tcan/ceng465_s2021/hw3_proteins.zip

and report the outputs of your program in a single TXT file in the following format:

#<test case number>
<pdb file name>
<output of test case>
#<test case number>
<pdb file name> <output of test case>
…..
…..

Please follow this format strictly and do not forget to report theinformation on amino acid pairs in the order that they appear in the PDB files. Your output txt for the two examples given above should look like:

Content of output.txt:

#1
7dwb.pdb
Diameter = 137.409 Angstroms
Between A:SER(265) and F:ASP(387)
#2
2wfi.pdb
Diameter = 41.852 Angstroms
Between A:GLN(6) and A:ALA(161)

It is guaranteed that the pair of amino acids that define the diameter is unique in each of the test cases.

Submission