Convert Restraints to CV-Based #1059
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All tests pass locally
andrrizzi
approved these changes
Aug 2, 2018
Yank/tests/test_restraints.py
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| @@ -290,7 +290,8 @@ def test_partial_parametrization(): | |||
| particles, _ = force.getBondParameters(0) | |||
| assert particles == tuple(restraint.restrained_receptor_atoms + restraint.restrained_ligand_atoms) | |||
| # RMSD restraint. | |||
| elif OpenMM73.dev_validate and isinstance(force, openmm.CustomCVForce): | |||
| elif OpenMM73.dev_validate and isinstance(force, openmm.CustomCVForce) and \ | |||
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If remember correctly, the OpenMM73.dev_validate we added some time ago is unnecessary now since the CV force is openmm>=7.2 and we've pinned it in the conda recipe, correct?
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RMSD Force is still a 7.3 thing, but I need to fix that to be more generic
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Ah! I see, I forgot about the RMSD restraint.
Yank/restraints.py
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| self.restrained_ligand_atoms[0], | ||
| self.restrained_ligand_atoms[1], | ||
| []) | ||
| force_components.append(['TorsionB', torsion_b_force]) |
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I think you forgot to change TorsionB to boresch_torsion_b.
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Ah, I did, that might explain the NaN's
Yank/restraints.py
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| self.restrained_ligand_atoms[1], | ||
| self.restrained_ligand_atoms[2], | ||
| []) | ||
| force_components.append(['TorsionC', torsion_c_force]) |
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This PR converts ALL of the restraints to
CustomCVForceobjects.This feature now requires OpenMMTools 0.16.0, which is still in development, but the local tests pass. The OpenMMTools PR/branch which I am using is here:
choderalab/openmmtools#363
This changes many things so could use a review. Many of the changes here are reflections of the linked OpenMMTools issues