Add SASA collection to xtb and minor fixes. #179
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lukasturcani
approved these changes
Jul 20, 2024
| @@ -152,6 +156,7 @@ def _properties_dict(self) -> dict[str, str]: | |||
| "total_free_energy": " | TOTAL FREE ENERGY ", | |||
| "ionisation_potential": "delta SCC IP (eV)", | |||
| "electron_affinity": "delta SCC EA (eV)", | |||
| "total_sasa": "total SASA /", | |||
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why the "/" at the end ?
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That is part of the string matching. Just the format of the output file.
| Line of output file to extract property from. | ||
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| """ | ||
| nums = re.compile(r"[+-]?\d+(?:\.\d+)?(?:[eE][+-]?\d+)?") |
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a comment which describes what kinds of things this is meant to match could be nice
| @@ -87,6 +87,11 @@ class XTBEnergy: | |||
| should be ``True``, however this may raise issues on | |||
| clusters. | |||
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| write_sasa_info: | |||
| If ``True``, the detailed info input will request gbsa=True and | |||
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gbsa=True should be inside of double backticks
| string = f"$gbsa\n gbsagrid={self._solvent_grid}" | ||
| string = f"$gbsa\n gbsagrid={self._solvent_grid}\n" | ||
| if self._write_sasa_info: | ||
| string += "$write\n gbsa=true\n" |
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+= on a string is a bit of an anti pattern because repeated use of it has very bad performance. While that doesnt apply here because it only happens once, consider
sasa_info = "$write\n gbsa=true\n" if self._write_sasa_info else ""
string = f"$gbsa\n gbsagrid={self._solvent_grid}\n{sasa_info}"There was a problem hiding this comment.
I did not realise this, updated!
src/stko/_internal/optimizers/xtb.py
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| @@ -124,6 +124,11 @@ class XTB(Optimizer): | |||
| encountered, this should be ``True``, however this may | |||
| raise issues on clusters. | |||
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| write_sasa_info: | |||
| If ``True``, the detailed info input will request gbsa=True and | |||
src/stko/_internal/optimizers/xtb.py
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| string = f"$gbsa\n gbsagrid={self._solvent_grid}" | ||
| string = f"$gbsa\n gbsagrid={self._solvent_grid}\n" | ||
| if self._write_sasa_info: | ||
| string += "$write\n gbsa=true\n" |
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Related Issues: #173 #154
Requested Reviewers: @lukasturcani
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parents=Truein allpathlib.Path.mkdirstatements