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 an idea regarding how to do that?
N.B. I need to write a python program.
If I understand correctly what you need - and it wouldn't hurt if you elaborated a bit - this is somewhat similar to half-sphere exposure (HSE), which calculates protein residue's solvent accessibility on the opposite sides of a C-alpha atom. There is a paper about it:
https://pubmed.ncbi.nlm.nih.gov/15688434/
And there is a BioPython code to calculate it:
https://biopython.org/docs/dev/api/Bio.PDB.HSExposure.html
This may give you some idea how to approach the problem, but it requires a thorough understanding of protein structure
the keyword in my question was "hydrogen bond". your supplied links do not say anything about hydrogen bonds.
I can read you keywords. I can also read this part:
Can anyone give me a general direction/idea regarding how to do that?
I said clearly that the links are about solvent accessibility, which is to say that I tried to give you a general idea. You can try that, or stock up with popcorn and soda and wait for someone to give you a complete solution.
I am sorry but your answer is not helpful. You are trying to explain a cat using a dog.
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