[ WIP ] Membrane support prototype #635
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| redox_potential: VoltsQuantity | None = Field( | ||
| None, description="Simulation redox potential in millivolts (mV). Compatible units will be converted to mV." | ||
| ) | ||
| membrane: bool = Field( |
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Maybe has_membrane instead
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This flag does feel redundant if we will always have a specific ProteinMembraneComponent that should signifiy to the protocol that we have a membrane system, from what I can tell this is just used to infer what type of barostat to use when making the system generator in the OpenFE protocol. Maybe this should be handled internally there rather than leaving it to the user to change here as well?
Are there anyother membrane specific settings we want the user to be able to controll?
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Example where gziping the PDB would make this diff hard
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| def __init__(self, rdkit: Mol, name: str = "", periodic_box_vectors=None): | ||
| super().__init__(rdkit=rdkit, name=name) | ||
| self._periodic_box_vectors = periodic_box_vectors |
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Guesser for box vectors? Allow manual passing of box vectors?
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- Take Cryst record from PDB 2. Take box from user 3. Guess box vector based on distances (
infer_box_vector = True?).
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Added this, but user supplied box will need validators, I'm not sure if this is actually a good idea since users would likely specify the box in many different ways.
| "Sm": 2, | ||
| "SM": 3, | ||
| "Sn": 2, | ||
| "SOD": 1, |
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Put these non-amber ions into different dict. Or maybe we shouldn't support those names?
| None, description="Simulation redox potential in millivolts (mV). Compatible units will be converted to mV." | ||
| ) | ||
| membrane: bool = Field( | ||
| False, description="Whether to simulate a membrane system and use a MonteCarloMembraneBarostat." |
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Or isinstance component check for barostat?
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…nto membrane_prototype
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No API break detected ✅ |
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