Add input module #137
Add input module #137
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laumalo
commented
Apr 9, 2021
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laumalo
commented
- Tag issue being addressed
- Add tests
- Update docstrings/documentation, if applicable
- Update changelog
- All tests successfully pass
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This pull request introduces 1 alert when merging 37f1cbb into de108f4 - view on LGTM.com new alerts:
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It is a very nice feature. Thanks @laumalo! After minor changes I think we are good to go:)
| It defines the chain of the molecule to parameterize from the input PDB file. | ||
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| - Flag: ``--chain`` | ||
| - Default: ``None`` |
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Since the default is None we should explain here the behaviour of the algorithm when this parameter is not initialized. What will happen when no chain is supplied? Then do we need to supply a PDB with a single chain?
peleffy/tests/test_utils.py
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| @@ -618,5 +620,147 @@ def test_parse_charges_from_mae(self): | |||
| _ = parse_charges_from_mae(PATH_PDB_BHP, parameters) | |||
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| class TestPDB(object): | |||
peleffy/utils/input.py
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| from peleffy.utils import Logger | ||
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| class PDB(object): |
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Class name might be too ambiguous (I know it was me the one who suggested it). I would change it for PDBFile, for instance (or any other that you might think of).
| Examples | ||
| -------- | ||
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| Load all the hetero molecules from a PDB |
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This is so cool! Thanks @laumalo
peleffy/utils/input.py
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| # Check if there is more than one hetero molecule in the same chain | ||
| residues_ids = set([line[22:26].strip() for line in self.pdb_content | ||
| if line.startswith('HETATM') and line[21:22] == chain |
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Be careful with code styling. These lines are not correctly aligned.
peleffy/utils/input.py
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| # Select which atoms compose this hetero molecule | ||
| atom_ids = [line[6:11].strip() for line in self.pdb_content | ||
| if line.startswith('HETATM') |
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Same happens here. Lines are not aligned
