Bonds and Angles handle wildcards for bonds and sites. #928
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| return f"<{self.__class__.__name__} {self.name}, id: {id(self)}> " | ||
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| def get_connection_identifiers(self): | ||
| from gmso.core.bond import Bond |
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Cyclic import Note
| def _get_virtual_type( | ||
| self, atom_types, return_match_order=False, exact_match=False | ||
| ): |
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Code scanning / CodeQL
Explicit returns mixed with implicit (fall through) returns Note
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #928 +/- ##
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- Coverage 94.17% 93.89% -0.29%
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Files 67 67
Lines 7536 7646 +110
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+ Hits 7097 7179 +82
- Misses 439 467 +28 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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| __members_creator__: ClassVar[Callable] = Atom.model_validate | ||
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| connectivity: ClassVar[Tuple[Tuple[int]]] = ((0, 1), (1, 2)) |
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We should add a description here.
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Also, do we need an alias?
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| @bonds.setter | ||
| def bonds(self, bonds): | ||
| """Return the bonds that makeup this Improper. |
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I think these doc strings aren't correct for this setter method?
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| @model_validator(mode="before") | ||
| @classmethod | ||
| def set_dependent_value_default(cls, data): |
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I think a concise doc string for this method would be helpful.
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| __members_creator__: ClassVar[Callable] = Atom.model_validate | ||
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| connectivity: ClassVar[Tuple[Tuple[int]]] = ((0, 1),) |
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Same as in angle.py. Do we need a description and alias here?
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| @property | ||
| def bonds(self): | ||
| """Return the bond_order symbol of this bond.""" |
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Update the doc string to say that it returns a tuple of gmso.core.Bond instances that make up this angle.
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| @bonds.setter | ||
| def bonds(self, bonds): | ||
| """Return the bonds that makeup this Improper. |
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Update doc strings here.
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| @model_validator(mode="before") | ||
| @classmethod | ||
| def set_dependent_value_default(cls, data): |
There was a problem hiding this comment.
I think a concise doc string for this method would be helpful.
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| @model_validator(mode="before") | ||
| @classmethod | ||
| def set_dependent_value_default(cls, data): |
There was a problem hiding this comment.
I think a concise doc string for this method would be helpful.
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| @bonds.setter | ||
| def bonds(self, new_bonds): | ||
| """Return the bonds that makeup this Improper. |
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Update the doc strings here.
| return virtual_type_graph | ||
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| def create_pattern(combination): |
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A quick doc string here would be helpful.
| raise MissingPotentialError(msg) | ||
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| def _get_angle_type(self, atom_types, return_match_order=False, warn=False): | ||
| for i in range(1, 3): |
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TODO: This masking schema won't work, should try masking outside in, i.e. -opls_135- should be masked before opls_135--.
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This PR will not work until mosdef-hub/foyer#640 is completed. |
2 participants
PR Summary:
This PR should allow for matching of forcefield connection parameters for Bonds and Angles. This was already usable with Dihedrals, the functionality has just been extended to dihedrals using the "*" syntax.
Additionally, the ability to match connections by the bond_order of the internal bonds of the connection is also included, using the "~" syntax to designate wildcard bonds, and the SMILES tokens for single, double, triple, and aromatic bonds.
PR Checklist