How can I calculate hydrogen bonds in a specific direction w.r.t. a C-

[user366312]

TL;DR Summary

I need to calculate H-bonds in a specific direction of a C-alpha atom of a protein. And, I need to calculate that from a PDB file.

Can anyone give me a general guideline/direction/idea regarding how to do that?

N.B. I need to write a python program.

I need to calculate H-bonds in a specific direction of a C-alpha atom of a protein. And, I need to calculate that from a PDB file.

Can anyone give me a general guideline/direction/idea regarding how to do that?

N.B. I need to write a python program.

 

[jbsteele]

You can calculate H-bonds from a PDB file using the BioPython library. BioPython provides functions to parse PDB files and access information about the atoms, such as their name, coordinates, and other properties. You can use this information to calculate the distances between atoms, which will give you an indication of whether or not they form an H-bond. For example, you could write a Python program that reads in a PDB file, then iterates over all of the C-alpha atoms. For each C-alpha atom, you could then loop through all of the other atoms in the file and calculate the distance between the two atoms. If the distance is within a certain threshold, you can classify it as a potential H-bond. You can also add additional criteria to your program, such as the angle between the two atoms, to help filter out false positives. Once you have identified all of the potential H-bonds, you can output the results in whatever format you like.