[DNM] prelim fixes on ns2b3 misalignment #43
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hmacdope
reviewed
Jul 25, 2024
| return complex | ||
| # first set indexing to an unphysically high number | ||
| original_index = [] | ||
| residue_N = 100000 |
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I would make this number max(residue_numbers + 1) to avoid some kind of cutoff artefact in the extremely unlikely event someone passes in a megaprotein, probably unnecessary but good practice.
| the crystallographer may have come up with. BioPython can do this but there are some | ||
| protections built in against hard re-indexing multi-chain proteins. By first setting | ||
| the indexing super high (starting at 100,000) and then re-indexing starting from 1 we can | ||
| circumvent these protections. For more details see https://github.com/biopython/biopython/pull/4623 |
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We can install from git+ source if you want this functionality in the aforementioned biopython PR. Only issue is we would then be blocked on release upstream until biopython merges and does a release.
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Perhaps its just better to use this hack.
hmacdope
reviewed
Jul 25, 2024
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| def load_pdb(self): | ||
| """ | ||
| Loads an input PDB file | ||
| """ | ||
| complex = PDBParser(QUIET=False).get_structure("COMPLEX", self.path_to_pdb_file) | ||
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| self.check_validity(complex) | ||
| self.reset_complex_sequence(complex) |
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Suggested change
| self.reset_complex_sequence(complex) | |
| complex, _ = self.reset_complex_sequence(complex) |
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closing this, NS2B3 fitness view doesn't have enough ROI as it works on the main asapdiscovery fitness viz workflow. |
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