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User guide updates membrane (#1933)
* Membrane support prototype start * Point to corresponding branch in gufe * Make plain md protocol membrane ready * Dry run for membrane system for debugging * Add box vectors to modeller * Adapt htf to allow for membrane barostat * Fix test * Add test files membrane * Change test to cpu * Prints for debugging * Some more debugginh stuff, remove later * Small fix * Temporarily use branches for openmmtools and openmmforcefield * Small fixes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * support membrane in gather * First pass membrane support for SepTop protocol * Change validation solvent * Move changes in solvent validation to validate_solvent * Some small fixes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add membrane test septop * Change box vector units for handling membrane barostat * Test box vectors SepTop more * First pass at ABFE membrane prototype * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Remove some prints * Revert box changes * Some fixes in SepTop to fix tests * Apply suggestion from @hannahbaumann * Add tests for system creation * FIx test * Add ABFE membrane tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * More tests membrane septop and more dry outputs in septop * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add validation for box vector in ProteinMembraneComponent * Adapt gather for membranes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * small changes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Modify box vectors plain md * Address review comments * Remove unnecessary prints * Subclass membrane test * Small fix * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove unnecessary import * Remove prints * Small fix * Small fix * Larger change to checks for BaseSolventComponent, SolvatedPDBComponent, and adding barostat settings * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Some more changes * Small fix * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * ABFE enforce timestep complex solvent the same * Update test files * Update environment.yaml with new openmmtools and openmmforcefield versions * Remove unnecessary checks for box_vectors which are handled in gufe * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update openfe/protocols/openmm_afe/equil_binding_afe_method.py Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> * Attempt at rewriting validate_solvent * Move get barostat to self * Simplify mapping in test * Add validator for surface_tension and membrane barostat * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add membrane barostat to adaptive settings rfe protocol * Add validation/warning for barostat component mismatch * Fix tests (except CLI) * More merge fixes * Remove unnecessary imports * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add test files * Update tests * Add lipid ff in adaptive settings * remove commented out lines * Update test abfe * Update ABFE results with new settings * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix solvent validation * change env to gufe main * Apply suggestion from @hannahbaumann * Remove files from before src layout change * Update tests * Small fix * mark slow tests * Update env file * Small fix * Update src/openfe/protocols/openmm_afe/equil_binding_afe_method.py Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> * Update src/openfe/protocols/openmm_afe/equil_binding_afe_method.py Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> * Update src/openfe/protocols/openmm_rfe/_rfe_utils/relative.py Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> * Update src/openfe/protocols/openmm_utils/system_validation.py Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> * Address review comments 1 * update doc string * Update src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol.py Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> * Update src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol.py Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> * Update src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol.py Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> * Update src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol.py Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> * Address review comments 2 * Address review comments 3 * fix mypy * Fix system creation tests * Roundtrip box vectors to remove vec3 issues * Roundtrip box vectors to remove vec3 issues * Remove unnecessary imports * Apply suggestion from @hannahbaumann * Test mypy failure * Test mypy failure 2 * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * some fixes * small fixes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update test files * Update SepTop results settings * add more tests for adaptive settings and others * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add news entry * Fix for box vectors hybtop * Make test slow again * Make mypy happy * try to make mypy happy again * Adapt gather RFE membrane component types * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * use reference platform for the membrane energy test * Add ChemicalSystem Component validation to Protocols * Add test for chemicalsystem validation * Apply suggestions from code review Co-authored-by: Josh Horton <joshua.horton@openforcefield.org> * Update with slight variation to @jthorton 's suggestion * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * point gufe back at main * Drop lipid17 from adaptive settings * just a tiny nit change * fix typo * Add extra class to openfecli check * Add total particle checks to abfe protocol tests * remove lipid17 check from adaptive settings * remove lipid17 check from adaptive settings * Add some checks for number of particles & residues * Fix up some tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Minimized protein * Update protein * Revert back to old protein * Apply suggestion from @hannahbaumann * Remove box roundtrip and fix solvent from get_components * Merge conflicts * Update src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol.py Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix merge conflict * Forgot another one * Move box roundtrip to _pre_equilibrate * First go at modifying the user guide for membranes and ABFE and SepTop * some small fixes * Add adaptive_settings to user guide * Add example code loading protein membrane * Add box vector explanation * Some smaller changes * Make adaptive settings subheading * Some more changes * Add warning adaptive settings * Update docs/guide/setup/defining_protocols.rst Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> * Addressing review comments * some more updates * Test out subheadings * Restructure user guide * merge conflicts * Small fix * some small updates * addressing review comments * Small fix * address review comments * small fix * Add news entry * Update docs/guide/setup/chemical_systems_and_thermodynamic_cycles.rst Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com> * Update docs/guide/setup/defining_protocols.rst Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com> * Update docs/guide/setup/chemical_systems_and_thermodynamic_cycles.rst Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com> * Addres review comment * Update docs/guide/setup/chemical_systems_and_thermodynamic_cycles.rst Co-authored-by: Josh Horton <Josh.Horton@newcastle.ac.uk> * Update docs/guide/setup/chemical_systems_and_thermodynamic_cycles.rst Co-authored-by: Josh Horton <Josh.Horton@newcastle.ac.uk> * Address review comment --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com> Co-authored-by: Josh Horton <Josh.Horton@newcastle.ac.uk> Co-authored-by: Josh Horton <joshua.horton@openforcefield.org>
This commit is contained in:
Hannah Baumann
GitHub
@@ -1,3 +1,5 @@
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.. _userguide_abfe_protocol:
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Absolute Binding Protocol
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=========================
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@@ -1,3 +1,5 @@
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.. _userguide_septop_protocol:
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Separated Topologies Protocol
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=============================
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@@ -1,55 +1,201 @@
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.. _userguide_chemicalsystems_and_components:
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Chemical Systems, Components and Thermodynamic Cycles
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Components, Chemical Systems and Thermodynamic Cycles
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=====================================================
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.. _userguide_chemical_systems:
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Chemical Systems
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----------------
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A :class:`.ChemicalSystem` represents the end state of an alchemical transformation,
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which can then be input to a :class:`.Protocol`.
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A :class:`.ChemicalSystem` **does** contain the following information (when present):
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* exact atomic information (including protonation state) of protein, ligands, co-factors, and any crystallographic
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waters
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* atomic positions of all explicitly defined components such as ligands or proteins
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* the abstract definition of the solvation environment, if present
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A :class:`.ChemicalSystem` does **NOT** include the following:
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* forcefield applied to any component, including details on water model or virtual particles
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* thermodynamic conditions (e.g. temperature or pressure)
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This page describes the core building blocks used to define simulation states in openfe:
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:class:`.Component`\s, which describe what is physically present in a system;
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:class:`.ChemicalSystem`\s, which combine components into a complete end state;
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and thermodynamic cycles, which connect end states via alchemical transformations.
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.. _userguide_components:
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Components
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----------
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A :class:`.ChemicalSystem` is composed of many 'component' objects, which together define overall system.
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Components are the composable building blocks that define the chemical
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composition of a simulated system. Splitting a system into components serves three purposes:
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Examples of components include:
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1. Alchemical transformations can be easily understood by comparing the differences in components.
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2. Components can be reused to compose different systems.
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3. :class:`.Protocol`\s can apply component-specific behaviour, e.g. different force fields per component.
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* :class:`.ProteinComponent`: an entire biological assembly, typically the contents of a PDB file.
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* :class:`.SmallMoleculeComponent`: typically ligands and cofactors
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* :class:`.SolventComponent`: solvent conditions
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Splitting the total system into components serves three purposes:
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Component types — overview
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~~~~~~~~~~~~~~~~~~~~~~~~~~
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.. list-table::
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:header-rows: 1
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:widths: 25 30 45
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* - Component
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- Role
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- Key notes
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* - :class:`.ProteinComponent`
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- Biological assembly
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- Typically the contents of a PDB file. May include crystallographic waters and ions (defined as HETATM entries),
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and disulfide bonds (defined via CONECT records).
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* - :class:`.SmallMoleculeComponent`
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- Ligands and cofactors
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- Can optionally contain atomic partial charges. If present, those will be used in the simulation.
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* - :class:`.SolventComponent`
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- Abstract solvent definition
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- Defines solvent conditions and ion concentration. Does **not** include coordinates or box vectors. Solvent is added by the protocol at runtime.
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* - :class:`.SolvatedPDBComponent`
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- Explicitly solvated system
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- Includes atomic coordinates and box vectors. Solvent is already present,
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the protocol does not add any further solvation.
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* - :class:`.ProteinMembraneComponent`
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- Protein-membrane complex
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- Subclass of :class:`.SolvatedPDBComponent`. Includes protein, membrane, solvent,
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and box vectors. Replaces :class:`.ProteinComponent` in membrane systems.
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.. _userguide_solvation_models:
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Abstract vs explicit solvation
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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These two approaches are **mutually exclusive**:
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* **Abstract solvation** — use a :class:`.SolventComponent`. The protocol adds solvent
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during system preparation.
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* **Explicit solvation** — use a :class:`.SolvatedPDBComponent` or
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:class:`.ProteinMembraneComponent`. Solvent molecule coordinates (waters and ions) are explicitly defined in the inputs.
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Either define the solvent abstractly, or provide a fully solvated system — do not mix
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both for the same leg of a transformation.
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.. note::
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Some protocols, such as :class:`.SepTopProtocol` and :class:`.AbsoluteBindingProtocol`,
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use a single :class:`.ChemicalSystem` to represent both the complex and solvent legs.
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In this case, a :class:`.ChemicalSystem` may contain both a :class:`.SolventComponent`
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and a :class:`.ProteinMembraneComponent`. However, these apply to *different* legs: the
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:class:`.SolventComponent` is used only for the solvent leg, and the
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:class:`.ProteinMembraneComponent` (which is already explicitly solvated) is used only
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for the complex leg. The mutual exclusivity rule still holds per leg.
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Box vectors for explicitly solvated systems
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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The components :class:`.SolvatedPDBComponent` and :class:`.ProteinMembraneComponent`
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require periodic box vectors. These can be provided in three ways:
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1. **CRYST record in the PDB file** — OpenMM reads box vectors automatically. No additional arguments are needed::
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membrane_protein = openfe.ProteinMembraneComponent.from_pdb_file('./protein_membrane.pdb')
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2. **Manual specification** — box vectors can be provided explicitly as numpy arrays with OpenFF units in OpenMM format via the ``box_vectors`` argument::
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import numpy as np
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import openff.units as offunit
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box_vectors = np.array([
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[6.9587, 0.0, 0.0],
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[0.0, 5.9164, 0.0],
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[0.0, 0.0, 9.2692]
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]) * offunit.nanometer
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membrane_protein = openfe.ProteinMembraneComponent.from_pdb_file(
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'./protein_membrane.pdb', box_vectors=box_vectors
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)
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3. **Inference from atomic coordinates** — box vectors can be estimated from the atomic
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positions by passing ``infer_box_vectors=True``::
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membrane_protein = openfe.ProteinMembraneComponent.from_pdb_file(
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'./protein_membrane.pdb', infer_box_vectors=True
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)
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.. warning::
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Inferring box vectors from atomic positions can be inaccurate if the PDB originates
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from a previous simulation where atoms may be distributed across periodic images.
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.. _userguide_chemical_systems:
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ChemicalSystem
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--------------
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A :class:`.ChemicalSystem` is composed of components that together describe a model of the system to be simulated.
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simulated system. It represents the **end state** of an alchemical transformation
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and is the primary input a :class:`.Protocol` consumes to define a simulation state.
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**What a ChemicalSystem defines**
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* Exact atomic information (including protonation state) of protein, ligands,
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cofactors, and any crystallographic waters.
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* Atomic positions of all explicitly defined components such as ligands or proteins.
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* The abstract or explicit definition of the solvent environment (SolventComponent).
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**What a ChemicalSystem does NOT define**, and are instead handled by the Protocol:
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Any simulation parameters including:
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* Forcefield applied to any component, including water model or virtual particles.
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* Thermodynamic conditions (e.g. temperature or pressure).
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* These are handled by the :class:`.Protocol`.
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.. _userguide_system_composition:
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System composition examples
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---------------------------
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The components that make up each :class:`.ChemicalSystem` depend on the protocol and
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the nature of the system. The table below summarises the composition for each combination.
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.. note::
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Protocol-specific behaviour:
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For :class:`.SepTopProtocol` and :class:`.AbsoluteBindingProtocol`, a single
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:class:`.ChemicalSystem` represents both legs of the thermodynamic cycle. The protocol
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determines internally what is the complex leg and what is the solvent leg.
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This differs from the :class:`.RelativeHybridTopologyProtocol`, where each leg (e.g. complex and solvent) is defined by
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separate :class:`.ChemicalSystem`\s. This behaviour is expected to change in future versions.
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.. list-table::
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:header-rows: 1
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:widths: 20 40 40
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* - System
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- :ref:`RBFE <userguide_relative_hybrid_topology_protocol>` (:class:`.RelativeHybridTopologyProtocol`)
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- :ref:`SepTop <userguide_septop_protocol>` / :ref:`ABFE <userguide_abfe_protocol>` (:class:`.SepTopProtocol`, :class:`.AbsoluteBindingProtocol`)
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* - **Standard protein–ligand**
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- | **Complex leg:**
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| :class:`.ProteinComponent` + :class:`.SmallMoleculeComponent`\s + :class:`.SolventComponent`
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|
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| **Solvent leg:**
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| :class:`.SmallMoleculeComponent`\s + :class:`.SolventComponent`
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- | **Single ChemicalSystem (both legs):**
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| :class:`.ProteinComponent` + :class:`.SmallMoleculeComponent`\s + :class:`.SolventComponent`
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* - **Membrane system**
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- | **Complex leg:**
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| :class:`.ProteinMembraneComponent` + :class:`.SmallMoleculeComponent`\s
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| *(no* :class:`.SolventComponent` *— already explicitly solvated)*
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|
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| **Solvent leg:**
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| :class:`.SmallMoleculeComponent`\s + :class:`.SolventComponent`
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- | **Single ChemicalSystem (both legs):**
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| :class:`.ProteinMembraneComponent` + :class:`.SmallMoleculeComponent`\s + :class:`.SolventComponent`
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| *(protocol applies* :class:`.SolventComponent` *only in the solvent leg)*
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1. alchemical transformations can be easily understood by comparing the differences in components.
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2. components can be reused to compose different systems.
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3. :class:`.Protocol`\s can have component-specific behavior. E.g. different force fields for each component.
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Thermodynamic Cycles
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--------------------
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We can now describe a thermodynamic cycle as a set of :class:`.ChemicalSystem`\s.
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The exact end states to construct are detailed in the :ref:`pages for each specific Protocol <userguide_protocols>`.
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A thermodynamic cycle can be described as a set of :class:`.ChemicalSystem`\s (nodes) connected by
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alchemical transformations (edges). The :class:`.Protocol` defines how the
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:class:`.ChemicalSystem`\s map onto the cycle and how they are used in practice.
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The same :class:`.ChemicalSystem` can be reused across multiple thermodynamic states
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depending on the protocol. For details of which end states to construct, consult the
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:ref:`pages for each specific Protocol <userguide_protocols>`.
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As an example, we can construct the classic relative binding free energy cycle by defining four components: two ligands,
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a protein, and a solvent:
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Hybrid topology RBFE example
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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As an example, the relative binding free energy cycle requires four
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:class:`.ChemicalSystem`\s — one for each node in the cycle:
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.. figure:: ../protocols/img/rbfe_thermocycle.png
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:scale: 40%
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@@ -75,12 +221,27 @@ a protein, and a solvent:
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ligand_B_complex = openfe.ChemicalSystem(components={'ligand': ligand_B, 'protein': protein, 'solvent': solvent})
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# ligand_A + solvent
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ligand_A_solvent = openfe.ChemicalSystem(components={'ligand': ligand_A, 'solvent': solvent})
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# ligand_A + solvent
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# ligand_B + solvent
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ligand_B_solvent = openfe.ChemicalSystem(components={'ligand': ligand_B, 'solvent': solvent})
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Explicitly solvated variant
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~~~~~~~~~~~~~~~~~~~~~~~~~~~
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When using a :class:`.SolvatedPDBComponent` or :class:`.ProteinMembraneComponent`, replace :class:`.ProteinComponent`
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and :class:`.SolventComponent` for the complex leg. No separate :class:`.SolventComponent`
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is required:
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::
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# explicitly solvated protein-membrane complex (box vectors read from CRYST1 record)
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protein_membrane = openfe.ProteinMembraneComponent.from_pdb_file('./protein_membrane.pdb')
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# ligand_A + explicitly solvated protein-membrane — no SolventComponent needed
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ligand_A_complex = openfe.ChemicalSystem(components={'ligand': ligand_A, 'protein_membrane': protein_membrane})
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See Also
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--------
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* To see how to construct a :class:`.ChemicalSystem` \s from your files, see :ref:`the cookbook entry on loading molecules <Loading Molecules>`
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* For details of what thermodynamic cycles to construct, consult the :ref:`pages for each specific Protocol <userguide_protocols>`
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* To see how to construct a :class:`.ChemicalSystem` from your files, see :ref:`the cookbook entry on loading molecules <Loading Molecules>`
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* For details of which thermodynamic cycles to construct, consult the :ref:`pages for each specific Protocol <userguide_protocols>`
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@@ -10,6 +10,8 @@ there are multiple available ``Protocol``\s to choose from.
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For example, included in the ``openfe`` package are the following:
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* :class:`.RelativeHybridTopologyProtocol`
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* :class:`.AbsoluteBindingProtocol`
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* :class:`.SepTopProtocol`
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* :class:`.AbsoluteSolvationProtocol`
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* :class:`.PlainMDProtocol`
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@@ -47,6 +49,40 @@ For example, to customise the production run length of the RFE Protocol::
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protocol = openmm_rfe.RelativeHybridTopologyProtocol(settings)
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Adaptive Settings
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~~~~~~~~~~~~~~~~~
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.. warning::
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The ``_adaptive_settings()`` method is experimental and subject to change.
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In addition to the ``.default_settings()`` method, some protocols
|
||||
provide an ``_adaptive_settings`` method. This method generates recommended settings
|
||||
based on properties of the input :class:`.ChemicalSystem`\s and, where required, the :class:`.AtomMapping`.
|
||||
|
||||
For example::
|
||||
|
||||
from openfe.protocols import openmm_rfe
|
||||
|
||||
settings = openmm_rfe.RelativeHybridTopologyProtocol._adaptive_settings(
|
||||
stateA=stateA,
|
||||
stateB=stateB,
|
||||
mapping=mapping,
|
||||
)
|
||||
|
||||
protocol = openmm_rfe.RelativeHybridTopologyProtocol(settings)
|
||||
|
||||
The adaptive settings may modify parameters based on properties of the input systems.
|
||||
For example (:class:`.RelativeHybridTopologyProtocol`):
|
||||
|
||||
* Transformations involving a change in net charge use a larger number of lambda windows and longer production simulations.
|
||||
* If both states contain a :class:`.ProteinComponent`, the solvation padding is set to 1 nm.
|
||||
|
||||
Optionally, you can pass a preexisting settings object to the ``_adaptive_settings`` method via the ``initial_settings`` argument. If provided, an adapted copy of these settings will be returned instead
|
||||
of using the default settings.
|
||||
|
||||
In systems containing membrane-protein complexes (i.e. using a
|
||||
:class:`.ProteinMembraneComponent`), adaptive settings select a membrane-appropriate barostat, the ``MonteCarloMembraneBarostat``.
|
||||
|
||||
Creating Transformations from Protocols
|
||||
-----------------------------------------
|
||||
|
||||
23
news/user_guide_membranes.rst
Normal file
23
news/user_guide_membranes.rst
Normal file
@@ -0,0 +1,23 @@
|
||||
**Added:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Changed:**
|
||||
|
||||
* Updated the chemical systems user guide and the defining protocols user guide to reflect recent protocol updates, including adding membrane support.
|
||||
|
||||
**Deprecated:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Removed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Fixed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Security:**
|
||||
|
||||
* <news item>
|
||||
Reference in New Issue
Block a user