From 8dbc44a4d9e7de599b6d901882a9c8c9bb47838c Mon Sep 17 00:00:00 2001 From: IAlibay Date: Tue, 15 Aug 2023 13:59:41 +0100 Subject: [PATCH] Remove softcore electrostatics entry --- .../protocols/openmm_rfe/_rfe_utils/relative.py | 17 ----------------- .../protocols/openmm_rfe/equil_rfe_methods.py | 3 --- .../protocols/openmm_rfe/equil_rfe_settings.py | 8 -------- openfe/tests/protocols/test_rfe_tokenization.py | 2 +- 4 files changed, 1 insertion(+), 29 deletions(-) diff --git a/openfe/protocols/openmm_rfe/_rfe_utils/relative.py b/openfe/protocols/openmm_rfe/_rfe_utils/relative.py index 2bed42fcd..a9bd4e59e 100644 --- a/openfe/protocols/openmm_rfe/_rfe_utils/relative.py +++ b/openfe/protocols/openmm_rfe/_rfe_utils/relative.py @@ -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): @@ -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, @@ -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") - # TODO: end __init__ here and move everything else to # create_hybrid_system() or equivalent diff --git a/openfe/protocols/openmm_rfe/equil_rfe_methods.py b/openfe/protocols/openmm_rfe/equil_rfe_methods.py index b896dabea..bc6278352 100644 --- a/openfe/protocols/openmm_rfe/equil_rfe_methods.py +++ b/openfe/protocols/openmm_rfe/equil_rfe_methods.py @@ -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, ) diff --git a/openfe/protocols/openmm_rfe/equil_rfe_settings.py b/openfe/protocols/openmm_rfe/equil_rfe_settings.py index 1448b4327..e8e9d2f63 100644 --- a/openfe/protocols/openmm_rfe/equil_rfe_settings.py +++ b/openfe/protocols/openmm_rfe/equil_rfe_settings.py @@ -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) diff --git a/openfe/tests/protocols/test_rfe_tokenization.py b/openfe/tests/protocols/test_rfe_tokenization.py index a0580f91a..86b4ace15 100644 --- a/openfe/tests/protocols/test_rfe_tokenization.py +++ b/openfe/tests/protocols/test_rfe_tokenization.py @@ -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()