Openfe - Alchemical free energy calculations for the masses

Last update: Dec 22, 2022

Related tags

Miscellaneous openfe

Overview

The Open Free Energy library

Alchemical free energy calculations for the masses.

See our website for more information.

License

This library is made available under the MIT open source license.

Important note

This is pre-alpha work, it should not be considered ready for production and API changes are expected at any time without prior warning.

Install

Dependencies can be installed via conda through:

conda env create -f environment.yml

The openfe library can be installed via:

python -m pip install --no-deps .

Authors

The OpenFE development team.

Acknowledgements

OpenFE is an Open Molecular Software Foundation hosted project.

Comments

Add visualization to AtomMapping

Fixes #37

Here is a little snippet to run in a notebook to see the visualization:

from rdkit import Chem
from openfe.setup.lomap_mapper import LomapAtomMapper


mol_1_smi = "c1ccccc1"  # benzene
mol_2_smi = "Oc1ccccc1"  #phenol
mol_1, mol_2 = Chem.MolFromSmiles(mol_1_smi), Chem.MolFromSmiles(mol_2_smi)
mol_1, mol_2 = Chem.AddHs(mol_1), Chem.AddHs(mol_2)
Chem.rdDepictor.Compute2DCoords(mol_1), Chem.rdDepictor.Compute2DCoords(mol_2)

mapper = LomapAtomMapper()
mapping = next(mapper.suggest_mappings(mol_1, mol_2))


mapping.visualize()

I haven't added tests yet since I wasn't sure if this is where we wanted to wire this method in. I also need to wire this into the cli, but we should discuss what we want that to look like as well.

opened by mikemhenry 18

WIP: Perses atom mappers
Here we adress https://github.com/OpenFreeEnergy/tasks/issues/3. Goal is to embed the Perses atom mapping infrastructure like the lomap code.

Todo:

[x] implement perses_mapper

[x] implement perses_scorer

[x] write tests perses_mapper

[x] write tests perses_scorer

[x] pep8

[x] add test for Not implemented error test_perses_scorer

[x] clean up tests with fixtures.

[x] making perses import optional? need to decide on centralized func call or decorators

[x] show results

this is related to: #3 #11 #10
opened by RiesBen 16
use versioneer for the version number
@dwhswenson thoughts on this? The one thing that is nice about using versioneer here is the output is really useful during development, but I will admit I'm not an expert on the plugin cli architecture, so not having an import openfe may be very intentional.

$ openfe --version openfe, version v0.1.post7+gfdc895f

P.S. Really not trying to bike shed hear, so if this PR feels like that is what I'm doing, feel free to close it!
opened by mikemhenry 11
Minor updates to Scorer
This is a small PR where I'm cherry-picking some of the changes that have come up as I've been working on AtomMappers. Main things:

Added setup/errors.py, which currently just contains a string template for errors when using abstract methods.

Make score and annotation functions in Scorer private. This will allow arbitrary functions to be used as scorers (useful if an AtomMapper wants to provide a scoring function as an instance method).

Move the fixtures for atommappings into conftest.py; use one of them instead of the nonsense placeholder for the scoring tests.
opened by dwhswenson 10
Molecular box auto padding

There should probably be a way (i.e. classmethod) to auto generate a box size for a given protein (or largest thing), this description is good for how this should behave:

https://github.com/choderalab/perses/issues/949#issuecomment-1057581435
priority:low

opened by richardjgowers 9
Class renames
To try thinking bigger and be more future proof, label everything currently designed for ligands as for LigandX. i.e.

Molecule -> LigandMolecule

AtomMapper -> LigandAtomMapper

AtomMapping -> LigandAtomMapping

In particular, our Molecule representation will likely not suit a protein molecule (so isn't a generic Molecule, but something we use for a specific use case).

The AtomMapping container works for small molecules, but for larger molecules (i.e. protein mutation) you'd want something smarter at expressing the change.
opened by richardjgowers 9
CLI for AtomMapping
Includes and builds on #49, should only be merged after that one.

This adds some reusable parameters (--mol and --mapper), as well as a command that outputs the mol1_to_mol2 mapping dict.

The current usage is only intended to be a starting point, which we can improve later. It looks something like this:

$ openfe atommapping --mol "Cc1ccccc1" --mol "CC1CCCCC1" --mapper LomapAtomMapper {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6}

Things that aren't ideal there:

Takes SMILES strings (and only SMILES for now). That can easily be extended. Currently this is also using an ugly workaround to avoid issue in openfreeenergy/lomap#4.

There's no way to provide options to mapper. ~I'm not sure that there's an easy way to do that, either.~ [EDIT: I came up with an approach that I think will work, but the question whether it's worth it is still on the table.] Perhaps it would make more sense to load from a serialized network and to find the edge(s?) associated with the two molecules -- in this sense, you'd use it to look at the mapping after it has been generated (but before simulating), instead of generating it before. @richardjgowers, you would have better sense on whether that approach would fit with what was requested.

A few corners are still WIP, but the main ideas are here.

[x] MOL parameter

[x] MAPPER parameter

[x] atommapping command

[x] Tests for everything

[x] Docstrings for everything
opened by dwhswenson 9

Add Versioneer

Fixes issue #23

We need to decide how we want to tag releases https://github.com/python-versioneer/python-versioneer/blob/master/INSTALL.md so we can set tag_prefix correctly.

tag_prefix:

a string, like 'PROJECTNAME-', which appears at the start of all VCS tags. If your tags look like 'myproject-1.2.0', then you should use tag_prefix='myproject-'. If you use unprefixed tags like '1.2.0', this should be an empty string, using either tag_prefix= or tag_prefix=''.

opened by mikemhenry 9

Barebones setup
Please add as desired / tick off as sorted out

We need:

[x] basic setup.py / setup.cfg / pyproject.toml

[x] basic directory structure

[x] license (thanks @richardjgowers !)

[x] README.md

[x] environment.yaml?

[x] dummy workflow in .github folder? (just an action that tests nothing should be fine?)

[x] pep8speaks?

[x] coverage / codecov

[x] linters? (linting will be kept local for now)

[ ] CONTRIBUTING
opened by IAlibay 9
[WIP] quickrun should error if a unit errors
Errors, but saves the details error in the output file (and probably dumps it to stdout as well, though it'll be part of a mess).

[x] raise error at the end if we get any error

[ ] test case with a erroring unit
opened by dwhswenson 7
quickrun CLI command
Takes a ProtocolDAG saved as JSON, runs the DAG, and returns results.

A few things before this is ready to merge:

[x] Decide whether the input is a serialized ProtocolDAG or a serialized Transformation. These are essentially equivalent, but there's some discussion to be had on what it means from user experience.

[x] Decide on how to ensure serializability of results. In particular, we need to decide how to handle Path objects, and whether any non-JSON-serializables other than Paths are allowed return values.

implemented in OpenFreeEnergy/gufe#68

[x] Add a test

[ ] ~Merge openfreeenergy/gufe#62~ This isn't actually needed here, but will be needed in the future.

[x] Merge PR that adds GufeTokenizable support to atom mappings (included in #142, but might split that part off of that PR)

Resolves #172.
opened by dwhswenson 7
Dump system PDB or XML by default

Something I've realise, we don't have a good way to post process coordinates at the moment since we don't have a "topology" equivalent we dump out by default to then pass out to MDA or MDTraj.

opened by IAlibay 1
RBFE protocol: add cpu fallback for minimizing

I'm not convinced this is the best approach (actually I think it's kinda broken).

I think ideally we should attempt to do the GPU minimizing, then if the energy is still positive rewind to before we attempted to minimize and default to the CPU. Is this possible?

Ideally we should migrate this out to openmmtools, just adding this here for an initial test/discussion.

Pinging @mikemhenry and @dwhswenson

opened by IAlibay 1
Clarify RBFE online analysis log and make sure it's available for users

We got a request for monitoring simulations, this is already generated as part of the MultistateSampler online analysis, but we should make sure that those log files are a) documented, b) actually recovered at the end of simulations (and not just left in temp directories).

opened by IAlibay 0
Move mapper/mapping (LigandAtomMapping and LigandAtomMapper) implementations to gufe?

Recent conversations raised that these implementations may be useful to more than one project.

How best should these classes be shared? Should they be moved to gufe?

opened by IAlibay 5

Releases(v0.5)

v0.5(Dec 16, 2022)
Mainly bug fixes concerning constraint mapping in the RBFE Protocol

What's Changed

TST: fix stray directories being made during testing by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/220

Dry run now returns sampler via debug dictionary entry by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/217

MAINT: Fixed up implicit none errors from mypy by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/226

Bug hunt fixes by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/225

Add --log option to CLI by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/218

Xml regression tests by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/231

MAINT: remove old offtk from test matrix by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/236

bump pin on gufe by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/235

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v0.4...v0.5
Source code(tar.gz)
Source code(zip)
v0.4(Nov 1, 2022)
What's Changed

Fix the number of production steps being used by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/141

change Lomap atom mapper to default to threed=True by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/143

Mapping distance by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/145

added check for element changes in openmm rbfe protocol by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/146

Visualization align mapped mols to eachother by @RiesBen in https://github.com/OpenFreeEnergy/openfe/pull/148

WIP: Perses atom mappers by @RiesBen in https://github.com/OpenFreeEnergy/openfe/pull/147

Add lower pin for lomap2 in environment yaml file by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/157

Fixes the openmm rbfe protocol by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/159

Fix rms tolerance check by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/161

154 add test for persesmapper not finding a mapping by @RiesBen in https://github.com/OpenFreeEnergy/openfe/pull/158

Add vacuum support for relative ligand transform by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/160

Fix tests by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/163

remove py 3.8 from CI by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/162

Remove universal bdist_wheel in setup.cfg by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/165

Fix to json by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/168

Add sams and independent samplers to equil RBFE protocol by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/125

Using gufe protocols by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/142

Make dry run return true, add basepath by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/186

Fix results_cls attribute name by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/188

Fix result_cls again by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/189

fix gathering of protocol results by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/191

Make unit close reporter at end of simulation by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/190

some mock based tests by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/193

quickrun CLI command by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/171

pin dependencies for release by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/194

Optional codecov failures by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/196

Atom mapping tests by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/198

add logo badge by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/197

Expose loaders in CLI by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/200

[DOCS] Add quickrun command docs by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/202

Are we there yet? The py310 edition by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/185

squashed a bug in mapping repr by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/207

[DOCS] Fixing RTD by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/204

fix gufe API usage in _create; move setup/methods -> protocols/ by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/211

[DOCS] Add dumping_transformation by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/210

[Docs] Installation info by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/212

[WIP] quickrun should error if a unit errors by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/209

Finish quickrun error handling by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/215

Pin to 0.4 gufe series for release by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/216

New Contributors

@RiesBen made their first contribution in https://github.com/OpenFreeEnergy/openfe/pull/148

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v0.3...v0.4
Source code(tar.gz)
Source code(zip)
v0.2.1(Apr 7, 2022)
Install Instructions

Online Installer

To play with the latest notebook, use this command to install the latest version of our packages:

conda env create openfe/openfe-notebooks Then run:

conda activate openfe-notebooks git clone https://github.com/OpenFreeEnergy/ExampleNotebooks.git openfe-example-notebooks cd openfe-example-notebooks git checkout april-2022 jupyter notebook openmm-rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb

Offline Installer

Download the relevant installer for your operating system and preferred python version. We have attached the version of the example notebook that works with the latest release of openfe.

If you used our single file installer from the last release, download new-deps.tar.gz. Then activate the old environment before extracting and installing the packages with pip:

# Be sure the old environment is activated! mkdir new-deps && tar xzvf new-deps.tar.gz -C new-deps pip install new-deps/*

Bug Fixes

Hotfix of results
Source code(tar.gz)
Source code(zip)
ExampleNotebooks-april-2022.tar.gz(1.18 MB)
new-deps.tar.gz(931.46 KB)
openfe-v0.2.1-py38-Linux-x86_64.sh(1377.49 MB)
openfe-v0.2.1-py38-MacOSX-x86_64.sh(511.41 MB)
openfe-v0.2.1-py39-Linux-x86_64.sh(1401.89 MB)
openfe-v0.2.1-py39-MacOSX-x86_64.sh(513.19 MB)
v0.1(Mar 28, 2022)
What's Changed

Initial skeleton by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/21

Add some changes requested in PR #21 by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/22

Fix setup.cfg to include packages by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/25

Add base Scorer by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/26

atommapping implementation by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/28

Prevent CodeCov from running on forks, cron jobs by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/27

Convert to normal package; add utils; move errors to utils/errors by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/32

AtomMapper base classes by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/30

Remove Scorers by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/33

Molecule class by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/39

[WIP] Network container class by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/40

Add a simple coveragerc to ignore tests in reporting by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/44

Tests for Network object by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/43

Add Versioneer by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/45

WIP: Lomap atommapper by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/31

suggested Network & Molecule changes by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/46

update AtomMapping type annotations by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/48

Set up basic mypy CI by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/50

omit _version.py from coverage by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/53

Proposed API change on AtomMapper by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/56

CLI Skeleton by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/49

network planning functions started by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/41

CLI for AtomMapping by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/57

added stubs for Molecule conversions by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/58

Molecule serialization/deserialization by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/63

Network Serialization by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/64

Docsdocsdocs by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/66

Skip running OE license check on PR by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/71

Add serialization test data script by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/69

Add support to get molecule name from _Name prop by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/68

Add support for CLI --mol to load SDF by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/67

Add visualization to AtomMapping by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/60

[WIP] Combine visualization with CLI by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/72

Full Changelog: https://github.com/OpenFreeEnergy/openfe/commits/v0.1
Source code(tar.gz)
Source code(zip)
ExampleNotebooks.tar.gz(1.23 MB)
macOS-latest_py3.8.sh.zip(504.57 MB)
macOS-latest_py3.9.sh.zip(505.42 MB)
ubuntu-latest_py3.8.sh.zip(1370.76 MB)
ubuntu-latest_py3.9.sh.zip(1396.11 MB)

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