Migrate validation to Protocol._validate in HybridTopologyProtocol #1740
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IAlibay
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IAlibay
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| if m.componentA not in alchemical_components["stateA"]: | ||
| raise ValueError( | ||
| f"Mapping componentA {m.componentA} not in alchemical components of stateA" | ||
| ) | ||
| if m.componentB not in alchemical_components["stateB"]: | ||
| raise ValueError( | ||
| f"Mapping componentB {m.componentB} not in alchemical components of stateB" | ||
| ) |
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Could maybe squash the repeated errors into a single loop?
| if m.componentA not in alchemical_components["stateA"]: | |
| raise ValueError( | |
| f"Mapping componentA {m.componentA} not in alchemical components of stateA" | |
| ) | |
| if m.componentB not in alchemical_components["stateB"]: | |
| raise ValueError( | |
| f"Mapping componentB {m.componentB} not in alchemical components of stateB" | |
| ) | |
| for label in ["A", "B"]: | |
| if getattr(m, f"component{label}") not in alchemical_components[f"state{label}"]: | |
| raise ValueError(f"Mapping component{label} {gatattr(m, f'component{label}') not in alchemical components of state{label}") | |
| * If an explicit charge correction is attempted and the | ||
| nonbonded method is not PME. | ||
| * If the absolute charge difference is greater than one | ||
| and an explicit charge correction is attempted. |
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| and an explicit charge correction is attempted. | |
| and an explicit charge correction is attempted. | |
| * If an explicit charge correction is attempted and there is no solvent present. |
| Raises | ||
| ------ | ||
| ValueError | ||
| * If the |
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Aaahh sorry I obviously gave up on the docs some point and never came back - thanks for pointing this out!
| * Mappings which involve element changes in core atoms | ||
| """ | ||
| # if a single mapping is provided, convert to list | ||
| if isinstance(mapping, ComponentMapping): |
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This is done for us in the default_validate method on the base class so we could skip it.
hannahbaumann
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hannahbaumann
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Thanks @IAlibay , love the validate method! Just some small spelling things.
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| if len(clashes) > 0: | ||
| errmsg = ( | ||
| "Found SmallMoleculeComponents are are isomorphic " |
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| "Found SmallMoleculeComponents are are isomorphic " | |
| "Found SmallMoleculeComponents that are isomorphic " |
| return | ||
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| if solvent_component is None: | ||
| errmsg = "Cannot use eplicit charge correction without solvent" |
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| errmsg = "Cannot use eplicit charge correction without solvent" | |
| errmsg = "Cannot use explicit charge correction without solvent" |
| self._validate_endstates(stateA, stateB) | ||
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| # Get alchemical components & validate them + mapping | ||
| # Valildate the mapping |
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| # Valildate the mapping | |
| # Validate the mapping |
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| # Validate charge difference | ||
| # Note: validation depends on the mapping & solvent component checks | ||
| if stateA.contains(SolventComponent): |
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More a note to self, we'll have to see how to best do all these validations with the explicit solvent component.
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I think this is where we will need to make an explicit solvent component be a subclasses of both protein and solvent components
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I think this is where we will need to make an explicit solvent component be a subclasses of both protein and solvent components
Fixes #1739
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