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Remove softcore electrostatics entry #521

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Aug 24, 2023
Merged

Remove softcore electrostatics entry #521

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17 changes: 0 additions & 17 deletions openfe/protocols/openmm_rfe/_rfe_utils/relative.py
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Original file line number Diff line number Diff line change
Expand Up @@ -86,9 +86,6 @@ def __init__(self,
softcore_alpha=0.5,
softcore_LJ_v2=True,
softcore_LJ_v2_alpha=0.85,
softcore_electrostatics=True,
softcore_electrostatics_alpha=0.3,
softcore_sigma_Q=1.0,
interpolate_old_and_new_14s=False,
flatten_torsions=False,
**kwargs):
Expand Down Expand Up @@ -125,12 +122,6 @@ def __init__(self,
Implement the softcore LJ as defined by Gapsys et al. JCTC 2012.
softcore_LJ_v2_alpha : float, default 0.85
Softcore alpha parameter for LJ v2
softcore_electrostatics : bool, default True
Use softcore electrostatics as defined by Gapsys et al. JCTC 2021.
softcore_electrostatics_alpha : float, default 0.3
Softcore alpha parameter for softcore electrostatics.
softcore_sigma_Q : float, default 1.0
Softcore sigma parameter for softcore electrostatics.
interpolate_old_and_new_14s : bool, default False
Whether to turn off interactions for new exceptions (not just
1,4s) at lambda = 0 and old exceptions at lambda = 1; if False,
Expand Down Expand Up @@ -172,14 +163,6 @@ def __init__(self,
self._check_bounds(softcore_LJ_v2_alpha, "softcore_LJ_v2_alpha")
self._softcore_LJ_v2_alpha = softcore_LJ_v2_alpha

self._softcore_electrostatics = softcore_electrostatics
if self._softcore_electrostatics:
self._softcore_electrostatics_alpha = softcore_electrostatics_alpha
self._check_bounds(softcore_electrostatics_alpha,
"softcore_electrostatics_alpha")
self._softcore_sigma_Q = softcore_sigma_Q
self._check_bounds(softcore_sigma_Q, "softcore_sigma_Q")
Comment on lines -177 to -181
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so these attributes were never used?

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As far as I can tell, I did some digging and there's no way to modulate the nonbondedforce either.


# TODO: end __init__ here and move everything else to
# create_hybrid_system() or equivalent

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3 changes: 0 additions & 3 deletions openfe/protocols/openmm_rfe/equil_rfe_methods.py
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Expand Up @@ -489,9 +489,6 @@ def run(self, *, dry=False, verbose=True,
softcore_alpha=alchem_settings.softcore_alpha,
softcore_LJ_v2=alchem_settings.softcore_LJ_v2,
softcore_LJ_v2_alpha=alchem_settings.softcore_alpha,
softcore_electrostatics=alchem_settings.softcore_electrostatics,
softcore_electrostatics_alpha=alchem_settings.softcore_electrostatics_alpha,
softcore_sigma_Q=alchem_settings.softcore_sigma_Q,
interpolate_old_and_new_14s=alchem_settings.interpolate_old_and_new_14s,
flatten_torsions=alchem_settings.flatten_torsions,
)
Expand Down
8 changes: 0 additions & 8 deletions openfe/protocols/openmm_rfe/equil_rfe_settings.py
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Expand Up @@ -56,16 +56,8 @@ class AlchemicalSettings(SettingsBaseModel):
Whether to use the LJ softcore function as defined by
Gapsys et al. JCTC 2012 Default True.
"""
softcore_electrostatics = True
"""Whether to use softcore electrostatics. Default True."""
softcore_alpha = 0.85
"""Softcore alpha parameter. Default 0.85"""
softcore_electrostatics_alpha = 0.3
"""Softcore alpha parameter for electrostatics. Default 0.3"""
softcore_sigma_Q = 1.0
"""
Softcore sigma parameter for softcore electrostatics. Default 1.0.
"""
interpolate_old_and_new_14s = False
"""
Whether to turn off interactions for new exceptions (not just 1,4s)
Expand Down
2 changes: 1 addition & 1 deletion openfe/tests/protocols/test_rfe_tokenization.py
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Expand Up @@ -39,7 +39,7 @@ def instance(self):

class TestRelativeHybridTopologyProtocol(GufeTokenizableTestsMixin):
cls = openmm_rfe.RelativeHybridTopologyProtocol
key = "RelativeHybridTopologyProtocol-ba8bae8ffc0f48e0839312daa7e74e98"
key = "RelativeHybridTopologyProtocol-8fe3eb4c318673db7d57c1bffca602df"
repr = f"<{key}>"

@pytest.fixture()
Expand Down
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