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add an operating function to find the surrounding atoms around a residue #223
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Pull Request Test Coverage Report for Build 722769742
💛 - Coveralls |
rgayatri
reviewed
Apr 1, 2021
deeprank/operate/pdb.py
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| residue_position = numpy.array([residue_x, residue_y, residue_z]) | ||
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| if get_squared_distance(atom_position, residue_position) < squared_max_interatomic_distance: |
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You might say we are: all atoms that pdb2sql reads from the pdb file are listed and compared to all atoms in the mutant residue. Does this answer your question?
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Yes, ok. I thought we would only look at C-alpha.
So the code looks at all atoms within 8.5 angstrom distance of every other atom?
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You'd have to insert the 8.5 angstrom as the argument "max_interatomic_distance". I put this in the comments.
added 5 commits
April 1, 2021 13:40
rgayatri
reviewed
Apr 6, 2021
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The function "get_residue_contact_atom_pairs" is intended to be used in the efro project, to get the atoms that surround a residue within a given distance.