[ENH]: Residue Depth Calculation for Exposed Residues in SERD

[jvsguerra]

Problem

As discussed with @helder-ribeiro, we need a function within SERD that can calculate the depth of residues identified by SERD as exposed. This depth value should be calculated for each residue, providing a comparable metric across different proteins. At a first glance, use centroid of residues for the depth calculation, but we can implement different metrics for residues.

Proposed solution

>>> from pyKVFinder import Molecule
>>> molecule = Molecule(vdw=radii)
>>> molecule.surface("SES", probe=4.0)
>>> depth = dist2surf(residues, surface)  # TODO: Implement dist2surf

dist2surf function:

• surface: Contains all points in contact with the bulk/solvent, represented by coords.
• distance calculation: Compute the minimum distance between coords and atom_coords to determine the depth.

[jvsguerra]

The linked branch atomic-depth adds a run.py to calculate atomic and residue depth. The implementation allows users to calculate residue depth based on the minimum or centroid distance between atoms and the molecular surface.

The following example demonstrates loading a structure and computing atomic and residue depths:

>>> from run import Structure
>>> structure = Structure()
>>> structure.load("examples/1FMO.pdb")
>>> structure.model_surface(type="SES", step=0.6, probe=1.4)
>>> atom_depth = structure.atom_depth()
>>> residue_depth = structure.residue_depth(metric="minimum", keep_only_interface=True, ignore_backbone=True)

To facilitate testing and make calculations accessible via the command line, a CLI was added to run.py:

$ python run.py examples/1FMO.pdb --probe 4.0
     ResidueNumber Chain ResidueName AtomName  AtomicDepth
0               13     E         GLU        N     0.092225
1               13     E         GLU       CA     0.514987
2               13     E         GLU        C     0.658996
3               13     E         GLU        O     1.601955
4               13     E         GLU       CB     0.117721
...            ...   ...         ...      ...          ...
2787           350     E         PHE      CD2     3.179295
2788           350     E         PHE      CE1     2.449123
2789           350     E         PHE      CE2     3.688604
2790           350     E         PHE       CZ     3.434604
2791           350     E         PHE      OXT     2.102817

[2792 rows x 5 columns]
    ResidueNumber Chain  ResidueDepth
0              13     E      0.087646
1              14     E      0.066218
2              15     E      0.070899
3              16     E      0.100228
4              17     E      0.094145
..            ...   ...           ...
333           346     E      0.102317
334           347     E      0.792791
335           348     E      0.084797
336           349     E      0.076201
337           350     E      1.437794

[338 rows x 3 columns]