mirror of
https://github.com/OpenFreeEnergy/openfe.git
synced 2026-06-04 14:14:22 +08:00
fix solvent atom index shifting
This commit is contained in:
Josh Horton
@@ -755,6 +755,7 @@ def _scale_angles_and_torsions(htf: HybridTopologyFactory, scale_factor: float =
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softened_hybrid_system = openmm.System()
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# add all the particles
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logger.info("Copying particles and constraints to new hybrid system.")
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print("Copying particles and constraints to new hybrid system.")
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for i in range(htf.hybrid_system.getNumParticles()):
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softened_hybrid_system.addParticle(htf.hybrid_system.getParticleMass(i))
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# add all constraints
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@@ -799,7 +800,9 @@ def _scale_angles_and_torsions(htf: HybridTopologyFactory, scale_factor: float =
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softened_harmonic_angle_force = openmm.HarmonicAngleForce()
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softened_hybrid_system.addForce(softened_harmonic_angle_force)
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logger.info("Processing dummy-core junction angles for softening.")
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print("Processing dummy-core junction angles for softening.")
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logger.info("Adding softened angles to core_angle_force.")
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print("Adding softened angles to core_angle_force.")
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default_hybrid_angle_force = hybrid_forces["standard_angle_force"]
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softened_custom_angle_force = new_hybrid_forces["CustomAngleForce"]
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for i in range(default_hybrid_angle_force.getNumAngles()):
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@@ -812,12 +815,14 @@ def _scale_angles_and_torsions(htf: HybridTopologyFactory, scale_factor: float =
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# add the term to the interpolated custom angle force
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new_k = k * scale_factor
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logger.info(f"Softening angle {angle} at lambda=0: original k = {k}, new k = {new_k}")
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print(f"Softening angle {angle} at lambda=0: original k = {k}, new k = {new_k}")
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softened_custom_angle_force.addAngle(p1, p2, p3, [theta_eq, new_k, theta_eq, k])
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elif 1 <= len(dummy_old_atoms.intersection(angle)) < 3:
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# if we match an old unique atom the angle must be softened at lambda = 1
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# add the term to the interpolated custom angle force
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new_k = k * scale_factor
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logger.info(f"Softening angle {angle} at lambda=1: original k = {k}, new k = {new_k}")
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print(f"Softening angle {angle} at lambda=1: original k = {k}, new k = {new_k}")
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softened_custom_angle_force.addAngle(p1, p2, p3, [theta_eq, k, theta_eq, new_k])
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else:
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# the term does not involve any dummy atoms, so we can just copy it
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@@ -825,7 +830,9 @@ def _scale_angles_and_torsions(htf: HybridTopologyFactory, scale_factor: float =
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# process torsions
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logger.info("Processing dummy-core junction torsions for softening.")
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print("Processing dummy-core junction torsions for softening.")
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logger.info("Adding softened torsions to core_torsion_force.")
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print("Adding softened torsions to core_torsion_force.")
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default_hybrid_torsion_force = hybrid_forces["unique_atom_torsion_force"]
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softened_custom_torsion_force = new_hybrid_forces["CustomTorsionForce"]
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for i in range(default_hybrid_torsion_force.getNumTorsions()):
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@@ -838,6 +845,7 @@ def _scale_angles_and_torsions(htf: HybridTopologyFactory, scale_factor: float =
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# add the term to the interpolated custom torsion force
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new_k = k * scale_factor
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logger.info(f"Softening torsion {torsion} at lambda=0: original k = {k}, new k = {new_k}")
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print(f"Softening torsion {torsion} at lambda=0: original k = {k}, new k = {new_k}")
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softened_custom_torsion_force.addTorsion(p1, p2, p3, p4,
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[periodicity, phase,
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new_k, periodicity,
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@@ -847,6 +855,7 @@ def _scale_angles_and_torsions(htf: HybridTopologyFactory, scale_factor: float =
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# add the term to the interpolated custom torsion force
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new_k = k * scale_factor
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logger.info(f"Softening torsion {torsion} at lambda=1: original k = {k}, new k = {new_k}")
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print(f"Softening torsion {torsion} at lambda=1: original k = {k}, new k = {new_k}")
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softened_custom_torsion_force.addTorsion(p1, p2, p3, p4,
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[periodicity, phase,
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k, periodicity,
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@@ -885,6 +894,10 @@ def _load_ghostly_corrections(ghostly_output_string: str) -> dict:
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def _shift_ghostly_correction_indices(htf: HybridTopologyFactory, corrections: dict) -> dict:
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"""Shift the atom indices in the ghostly corrections to account for the solvent environment in the HTF."""
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core_atoms = htf._atom_classes["core_atoms"]
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unique_old_atoms = htf._atom_classes["unique_old_atoms"]
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# get the maximum index of the core and unique old atoms all stateB atoms are after this
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max_state_a_atom = max(core_atoms.union(unique_old_atoms))
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# we need the shift the indices of the atoms in the corrections to account for the solvent system
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# this involves shifting the unique new atoms to be after the last water atom
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@@ -892,7 +905,11 @@ def _shift_ghostly_correction_indices(htf: HybridTopologyFactory, corrections: d
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if len(htf._atom_classes["environment_atoms"]) > 0:
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print("shifting ghostly correction atom indices to account for solvent environment.")
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last_water_atom = max(htf._atom_classes["environment_atoms"])
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print("last water atom", last_water_atom)
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last_core_atom = max(htf._atom_classes["core_atoms"])
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print("last core atom", last_core_atom)
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print("old unique atoms", htf._atom_classes["unique_old_atoms"])
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print("new unique atoms", htf._atom_classes["unique_new_atoms"])
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shifted_corrections = {}
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for lambda_key in corrections.keys():
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for correction_type in corrections[lambda_key].keys():
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@@ -900,10 +917,10 @@ def _shift_ghostly_correction_indices(htf: HybridTopologyFactory, corrections: d
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shifted_list = []
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for angle in corrections[lambda_key][correction_type]:
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shifted_angle = tuple(
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atom_idx + (last_water_atom - last_core_atom)
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atom_idx + (last_water_atom - max_state_a_atom)
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# only shift if not a core atom and greater than last core atom
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# else this is a unique old atom and should not be shifted
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if atom_idx not in core_atoms and atom_idx > last_core_atom else atom_idx
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if atom_idx not in core_atoms and atom_idx > max_state_a_atom else atom_idx
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for atom_idx in angle
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)
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shifted_list.append(shifted_angle)
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@@ -912,8 +929,8 @@ def _shift_ghostly_correction_indices(htf: HybridTopologyFactory, corrections: d
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new_dict = {}
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for angle, params in corrections[lambda_key][correction_type].items():
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shifted_angle = tuple(
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atom_idx + (last_water_atom - last_core_atom)
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if atom_idx not in core_atoms and atom_idx > last_core_atom else atom_idx
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atom_idx + (last_water_atom - max_state_a_atom)
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if atom_idx not in core_atoms and atom_idx > max_state_a_atom else atom_idx
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for atom_idx in angle
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)
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new_dict[shifted_angle] = params
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@@ -974,6 +991,7 @@ def _apply_ghostly_corrections(htf: HybridTopologyFactory, corrections: dict) ->
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p1, p2, p3, theta_eq, k = old_hybrid_angle_force.getAngleParameters(i)
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# check if we have one ghost atom for this angle
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angle = (p1, p2, p3)
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print(angle)
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if 1<= len(dummy_old_atoms.intersection(angle)) < 3 or 1<= len(dummy_new_atoms.intersection(angle)) < 3:
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angle_reversed = (p3, p2, p1)
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# set up containers for the end state values
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92
openfe/tests/data/htf/ejm_46.sdf
Normal file
92
openfe/tests/data/htf/ejm_46.sdf
Normal file
@@ -0,0 +1,92 @@
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ejm_46
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RDKit 3D
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36 38 0 0 0 0 0 0 0 0999 V2000
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||||
-3.2903 22.5712 -29.5240 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-3.9192 21.7173 -28.5965 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-3.2025 21.1503 -27.5518 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-5.2582 25.0245 -31.6039 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-4.1053 23.0704 -30.6507 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-5.9452 24.4099 -32.6722 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-6.7996 25.1874 -33.4514 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.9269 22.8784 -29.3601 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.8593 21.4510 -27.4045 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.2252 22.3093 -28.3025 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-5.6128 21.4071 -28.7312 Cl 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-4.4756 22.2608 -31.5073 O 0 0 0 0 0 0 0 0 0 0 0 0
|
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-4.4499 24.3695 -30.6718 N 0 0 0 0 0 0 0 0 0 0 0 0
|
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-6.9355 26.4911 -33.2090 N 0 0 0 0 0 0 0 0 0 0 0 0
|
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-6.3008 27.1207 -32.2194 C 0 0 0 0 0 0 0 0 0 0 0 0
|
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-5.4625 26.3854 -31.3778 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-6.4935 28.5024 -32.0877 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-5.7410 29.3927 -31.4053 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-4.7130 29.1087 -30.7881 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-6.2261 30.8526 -31.4064 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-5.9465 31.6762 -30.1512 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-5.1392 31.9250 -31.3944 C 0 0 0 0 0 0 0 0 0 0 0 0
|
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-1.0986 23.9892 -30.4092 Cl 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-3.6932 20.4911 -26.8557 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-5.8817 23.3629 -32.9126 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-7.3630 24.7668 -34.2730 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.2990 21.0136 -26.5902 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.1903 22.5719 -28.1610 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-4.0744 24.9351 -29.9290 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-4.9676 26.8422 -30.5384 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-7.3482 28.8436 -32.5018 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-7.1314 31.0429 -31.9814 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-5.4329 31.2354 -29.2953 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-6.6880 32.4155 -29.8451 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-5.3071 32.8596 -31.9267 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-4.0875 31.6318 -31.4083 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1 2 2 0
|
||||
1 5 1 0
|
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1 8 1 0
|
||||
2 3 1 0
|
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2 11 1 0
|
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3 9 2 0
|
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3 24 1 0
|
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4 6 2 0
|
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4 13 1 0
|
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4 16 1 0
|
||||
5 12 2 0
|
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5 13 1 0
|
||||
6 7 1 0
|
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6 25 1 0
|
||||
7 14 2 0
|
||||
7 26 1 0
|
||||
8 10 2 0
|
||||
8 23 1 0
|
||||
9 10 1 0
|
||||
9 27 1 0
|
||||
10 28 1 0
|
||||
13 29 1 0
|
||||
14 15 1 0
|
||||
15 16 2 0
|
||||
15 17 1 0
|
||||
16 30 1 0
|
||||
17 18 1 0
|
||||
17 31 1 0
|
||||
18 19 2 0
|
||||
18 20 1 0
|
||||
20 21 1 0
|
||||
20 22 1 0
|
||||
20 32 1 0
|
||||
21 22 1 0
|
||||
21 33 1 0
|
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21 34 1 0
|
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22 35 1 0
|
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22 36 1 0
|
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M END
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> <atom.dprop.PartialCharge> (1)
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-0.14360000000000001 0.052400000000000009 -0.129 0.12659999999999999 0.69169999999999998 -0.30330000000000001 0.44419999999999998 0.052400000000000009 -0.095999999999999988 -0.129
|
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-0.059899999999999995 -0.55010000000000003 -0.46010000000000001 -0.73599999999999999 0.55020000000000002 -0.32029999999999997 -0.5474 0.70009999999999994 -0.59309999999999996
|
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-0.22969999999999999 -0.10389999999999999 -0.10389999999999999 -0.059899999999999995 0.157 0.183 0.025100000000000011 0.14799999999999999 0.157 0.33050000000000002 0.17799999999999999
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0.33350000000000002 0.09870000000000001 0.084200000000000011 0.084200000000000011 0.084200000000000011 0.084200000000000011
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> <ofe-name> (1)
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ejm_46
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> <r_exp_dg> (1)
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-11.31
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$$$$
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92
openfe/tests/data/htf/jmc_27.sdf
Normal file
92
openfe/tests/data/htf/jmc_27.sdf
Normal file
@@ -0,0 +1,92 @@
|
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jmc_27
|
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RDKit 3D
|
||||
|
||||
36 38 0 0 0 0 0 0 0 0999 V2000
|
||||
-3.2903 22.5712 -29.5240 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-3.9192 21.7173 -28.5965 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-3.2025 21.1503 -27.5518 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-5.2582 25.0245 -31.6039 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-4.1053 23.0704 -30.6507 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-5.9452 24.4099 -32.6722 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-6.7996 25.1874 -33.4514 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.9269 22.8784 -29.3601 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.8593 21.4510 -27.4045 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.2252 22.3093 -28.3025 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-5.6128 21.4071 -28.7312 Cl 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-4.4756 22.2608 -31.5073 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-4.4499 24.3695 -30.6718 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-6.9355 26.4911 -33.2090 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-6.3008 27.1207 -32.2194 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-5.4625 26.3854 -31.3778 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-6.5061 28.4999 -32.0789 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-5.7409 29.4041 -31.4257 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-4.6551 29.1451 -30.9087 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-6.3480 30.8113 -31.2740 C 0 0 1 0 0 0 0 0 0 0 0 0
|
||||
-5.9277 31.5796 -30.0153 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-5.4977 32.0811 -31.3560 C 0 0 1 0 0 0 0 0 0 0 0 0
|
||||
-1.0986 23.9892 -30.4092 Cl 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-3.6931 20.4910 -26.8557 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-5.8816 23.3628 -32.9125 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-7.3629 24.7669 -34.2730 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.2990 21.0136 -26.5902 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.1903 22.5719 -28.1611 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-4.0740 24.9351 -29.9293 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-4.9684 26.8537 -30.5430 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-7.4039 28.8141 -32.4185 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-7.3665 30.8855 -31.6383 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-5.1588 31.1817 -29.3505 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-6.6706 32.1636 -29.4737 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-5.9673 33.0048 -31.6947 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-3.7666 32.1420 -31.7726 Cl 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1 2 2 0
|
||||
1 5 1 0
|
||||
1 8 1 0
|
||||
2 3 1 0
|
||||
2 11 1 0
|
||||
3 9 2 0
|
||||
3 24 1 0
|
||||
4 6 2 0
|
||||
4 13 1 0
|
||||
4 16 1 0
|
||||
5 12 2 0
|
||||
5 13 1 0
|
||||
6 7 1 0
|
||||
6 25 1 0
|
||||
7 14 2 0
|
||||
7 26 1 0
|
||||
8 10 2 0
|
||||
8 23 1 0
|
||||
9 10 1 0
|
||||
9 27 1 0
|
||||
10 28 1 0
|
||||
13 29 1 0
|
||||
14 15 1 0
|
||||
15 16 2 0
|
||||
15 17 1 0
|
||||
16 30 1 0
|
||||
17 18 1 0
|
||||
17 31 1 0
|
||||
18 19 2 0
|
||||
18 20 1 0
|
||||
20 21 1 0
|
||||
20 22 1 0
|
||||
20 32 1 6
|
||||
21 22 1 0
|
||||
21 33 1 0
|
||||
21 34 1 0
|
||||
22 35 1 6
|
||||
22 36 1 0
|
||||
M END
|
||||
> <atom.dprop.PartialCharge> (1)
|
||||
-0.14357222222222224 0.052427777777777768 -0.12897222222222224 0.12662777777777776 0.69172777777777772 -0.30227222222222222 0.44422777777777778 0.052427777777777768 -0.095972222222222237
|
||||
-0.12897222222222224 -0.06037222222222223 -0.5500722222222223 -0.46107222222222222 -0.73097222222222225 0.54822777777777776 -0.31927222222222218 -0.53937222222222225 0.70012777777777768
|
||||
-0.58207222222222221 -0.21167222222222223 -0.092372222222222231 -0.02427222222222223 -0.06037222222222223 0.15702777777777777 0.18302777777777776 0.026127777777777771 0.14802777777777776
|
||||
0.15702777777777777 0.33052777777777781 0.17702777777777776 0.33852777777777782 0.11472777777777776 0.095727777777777759 0.095727777777777759 0.10972777777777777 -0.11737222222222224
|
||||
|
||||
> <ofe-name> (1)
|
||||
jmc_27
|
||||
|
||||
> <r_exp_dg> (1)
|
||||
-11.279999999999999
|
||||
|
||||
$$$$
|
||||
@@ -440,4 +440,76 @@ def chloroethane_to_ethane_mapping_ghostly(chloroethane_to_ethane_mapping, chlor
|
||||
componentA=chloro_ghostly,
|
||||
componentB=chloroethane_to_ethane_mapping.componentB,
|
||||
componentA_to_componentB=chloroethane_to_ethane_mapping.componentA_to_componentB
|
||||
)
|
||||
)
|
||||
|
||||
@pytest.fixture(scope="module")
|
||||
def tyk2_ghostly_modifications():
|
||||
return {
|
||||
"lambda_0": {
|
||||
"removed_angles": [],
|
||||
"removed_dihedrals": [
|
||||
"33,20,21,36",
|
||||
"19,20,21,36",
|
||||
"17,19,21,36",
|
||||
"31,19,21,36",
|
||||
"20,19,21,36",
|
||||
"32,20,21,36"
|
||||
],
|
||||
"stiffened_angles": [],
|
||||
"softened_angles": {
|
||||
"19,21,36": {
|
||||
"k": 5.0,
|
||||
"theta0": 2.222322474687164
|
||||
},
|
||||
"34,21,36": {
|
||||
"k": 5.0,
|
||||
"theta0": 2.000809911756968
|
||||
},
|
||||
"20,21,36": {
|
||||
"k": 5.0,
|
||||
"theta0": 1.6181044310934367
|
||||
}
|
||||
}
|
||||
},
|
||||
"lambda_1": {
|
||||
"removed_angles": [],
|
||||
"removed_dihedrals": [
|
||||
"33,20,21,35",
|
||||
"19,20,21,35",
|
||||
"17,19,21,35",
|
||||
"31,19,21,35",
|
||||
"20,19,21,35",
|
||||
"32,20,21,35"
|
||||
],
|
||||
"stiffened_angles": [],
|
||||
"softened_angles": {
|
||||
"19,21,35": {
|
||||
"k": 5.0,
|
||||
"theta0": 2.2915349600475916
|
||||
},
|
||||
"34,21,35": {
|
||||
"k": 5.0,
|
||||
"theta0": 1.6334317078992815
|
||||
},
|
||||
"20,21,35": {
|
||||
"k": 5.0,
|
||||
"theta0": 2.395734337620435
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@pytest.fixture(scope="module")
|
||||
def tyk2_ghostly_mapping(tyk2_ghostly_modifications):
|
||||
"""Return a mapping from tyk2 ligand ejm_31 to ejm_32 with ghosted corrections stored on componentA."""
|
||||
with resources.as_file(resources.files("openfe.tests.data.htf")) as f:
|
||||
jmc_27 = openfe.SmallMoleculeComponent.from_sdf_file(f / "jmc_27.sdf")
|
||||
ejm_46 = openfe.SmallMoleculeComponent.from_sdf_file(f / "ejm_46.sdf")
|
||||
from kartograf import KartografAtomMapper
|
||||
|
||||
# we need to use the exact mappings we use in the hybrid topology so only map Hs to Hs
|
||||
mapper = KartografAtomMapper(map_hydrogens_on_hydrogens_only=True)
|
||||
|
||||
tyk2_ghostly = jmc_27.copy_with_replacements(**{"molprops": {"ghostly_corrections": json.dumps(tyk2_ghostly_modifications)}})
|
||||
return next(mapper.suggest_mappings(tyk2_ghostly, ejm_46))
|
||||
@@ -797,6 +797,32 @@ def test_apply_ghostly_corrections_torsions_chloro(chloroethane_to_ethane_mappin
|
||||
assert k == ethane_torsion.k[term_index].m_as(unit.kilojoule_per_mole) * omm_unit.kilojoule_per_mole
|
||||
|
||||
|
||||
def test_tyk2_ghostly_corrections(tyk2_ghostly_mapping, solv_settings, tmpdir, vac_settings):
|
||||
"""Test that the Tyk2 ligand transformation with ghostly corrections runs without error and applies corrections."""
|
||||
|
||||
state_a_dict = {"ligand": tyk2_ghostly_mapping.componentA}
|
||||
state_b_dict = {"ligand": tyk2_ghostly_mapping.componentB}
|
||||
# settings = vac_settings
|
||||
settings = solv_settings
|
||||
state_a_dict["solvent"] = openfe.SolventComponent()
|
||||
state_b_dict["solvent"] = openfe.SolventComponent()
|
||||
|
||||
|
||||
protocol = openmm_rfe.RelativeHybridTopologyProtocol(settings=settings)
|
||||
|
||||
# create DAG from protocol and take first (and only) work unit from within
|
||||
dag = protocol.create(
|
||||
stateA=openfe.ChemicalSystem(state_a_dict),
|
||||
stateB=openfe.ChemicalSystem(state_b_dict),
|
||||
mapping=tyk2_ghostly_mapping,
|
||||
)
|
||||
dag_unit = list(dag.protocol_units)[0]
|
||||
|
||||
with tmpdir.as_cwd():
|
||||
sampler = dag_unit.run(dry=True)["debug"]["sampler"]
|
||||
htf = sampler._hybrid_factory
|
||||
|
||||
|
||||
def test_dry_run_gaff_vacuum(
|
||||
benzene_vacuum_system, toluene_vacuum_system, benzene_to_toluene_mapping, vac_settings, tmpdir
|
||||
):
|
||||
|
||||
Reference in New Issue
Block a user