Bonds and Angles handle wildcards for bonds and sites. #928
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## main #928 +/- ##
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- Coverage 94.20% 93.93% -0.27%
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Files 67 67
Lines 7591 7668 +77
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+ Hits 7151 7203 +52
- Misses 440 465 +25 ☔ 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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I specified connectivity as a ClassVar, so it's not modifiable across classes, and doesn't get treated the same way as other pydantic variables, which are defined under with pydantic Field.
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So also no alias here.
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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?
gmso/core/forcefield.py
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| 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. |
…gmso into wildcard-apply
…to wildcard-apply
for more information, see https://pre-commit.ci
… and dynamically set bonds based on connection_members when initialized with set_dependent_value_default
…via masking, remove unused functions
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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