In Biopython-PDB, please teach me about all atoms distance
Hello, Nice people.
I want to get all atoms distance in a PDB file by biopython
especially,
all atoms in all protein residue - all atoms in all water(HOH)
And, I want to take <2.5A
But, I don't know these methods
Please teach me.
p=PDBParser() s=p.get_structure('ID','file')
next.....?
need all atoms in all residue
need all atoms in all HOH
1 answer
In order to get all atoms in a residue, you can either:
use the unfold_entities function inside of the Selection module in Bio.PDB. If you want all of the atoms in a residue, this means that you use the target level "A" and the entity list is the the name of your residue.
or
Use the .get_list() instance method on your residue.
Hope this helps !
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