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Release 0.1.0 (#57)
Minor doc fixes and infrastructure for citation. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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‎CITATION.cff

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# This CITATION.cff file was generated with cffinit.
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# Visit https://bit.ly/cffinit to generate yours today!
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cff-version: 1.2.0
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title: FEflow
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message: >-
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If you use this software, please cite it using the
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metadata from this file.
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type: software
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authors:
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- given-names: Iván
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family-names: Pulido Sánchez
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orcid: 'https://orcid.org/0000-0002-7178-8136'
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- given-names: Irfan
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family-names: Alibay
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orcid: 'https://orcid.org/0000-0001-5787-9130'
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- given-names: David
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family-names: Dotson
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orcid: 'https://orcid.org/0000-0001-5879-2942'
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- given-names: Richard
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family-names: Gowers
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orcid: 'https://orcid.org/0000-0002-3241-1846'
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- given-names: Hannah
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family-names: Baumann
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orcid: 'https://orcid.org/0000-0002-1736-7744'
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- given-names: Michael M.
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family-names: Henry
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orcid: 'https://orcid.org/0000-0002-3870-9993'
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repository-code: 'https://github.com/choderalab/feflow'
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version: '0.1'
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date-released: '2024-07-29'

‎README.md

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Copyright (c) 2023, ChoderaLab
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#### Acknowledgements
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### Acknowledgements
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[Choderalab -- Perses](https://github.com/choderalab/perses)
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[Open Free energy Consortium](https://openfree.energy/)
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Project based on the
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[Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.1.
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### References
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[1] Van Der Walt, S., Colbert, S.C. & Varoquaux, G., 2011. The NumPy array: a structure for efficient numerical computation. Computing in Science & Engineering, 13(2), pp.22–30.
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[2] Identifying and Overcoming the Sampling Challenges in Relative Binding Free Energy Calculations of a Model Protein:Protein Complex
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Ivy Zhang, Dominic A. Rufa, Iván Pulido, Michael M. Henry, Laura E. Rosen, Kevin Hauser, Sukrit Singh, and John D. Chodera
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Journal of Chemical Theory and Computation 2023 19 (15), 4863-4882
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DOI: 10.1021/acs.jctc.3c00333
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[3] Chodera, J. et al., 2023. choderalab/openmmtools: 0.23.1.
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[4] Eastman, P. et al., 2017. OpenMM 7: Rapid development of high performance algorithms for molecular dynamics R. Gentleman, ed.. PLOS Computational Biology, 13(7), p.1005659.
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‎docs/CHANGELOG.rst

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=================
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feflow Change Log
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=================
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.. current developments
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v0.1
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====================
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First release. Base implementation of Nonequilibrium cycling protocol.
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‎docs/api.rst

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API Documentation
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=================
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.. module:: feflow
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:no-index:
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.. autosummary::
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:toctree: autosummary
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:toctree: autosummary
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:recursive:
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feflow.canvas
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feflow.protocols
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feflow.settings
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feflow.utils

‎docs/conf.py

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project = "feflow"
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copyright = (
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"2023, Iván Pulido. Project structure based on the "
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"2023, ChoderaLab. Project structure based on the "
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"Computational Molecular Science Python Cookiecutter version 1.1"
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)
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author = "Iván Pulido"
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author = "ChoderaLab"
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# The short X.Y version
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version = ""

‎feflow/__init__.py

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from importlib.metadata import version
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__version__ = version("openfe")
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__version__ = version("feflow")

‎feflow/protocols/nonequilibrium_cycling.py

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from ..utils.data import serialize, deserialize
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# Specific instance of logger for this module
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# logger = logging.getLogger(__name__)
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logger = logging.getLogger(__name__)
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class SetupUnit(ProtocolUnit):
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"""
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Initial unit of the protocol. Sets up a Nonequilibrium cycling simulation given the chemical
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systems, mapping and settings.
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"""
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@staticmethod
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def _check_states_compatibility(state_a, state_b):
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"""
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class CycleUnit(ProtocolUnit):
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"""
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Monolithic unit for simulation. It runs a single NEQ cycle simulation from chemical systems
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and stores the work computed in numpy-formatted files, to be analyzed by a result unit.
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Monolithic unit for the cycle part of the simulation.
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It runs a number of NEq cycles from the outputs of a setup unit and stores the work computed in
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numpy-formatted files, to be analyzed by a result unit.
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"""
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@staticmethod

‎feflow/settings/nonequilibrium_cycling.py

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"""
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Settings objects for the different protocols using gufe objects.
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This module implements the objects that will be needed to run relative binding free
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energy calculations using perses.
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"""
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from typing import Optional

‎news/TEMPLATE.rst

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**Added:**
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* <news item>
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**Changed:**
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**Deprecated:**
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**Removed:**
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**Security:**
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‎rever.xsh

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$PROJECT = $GITHUB_REPO = 'feflow'
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$GITHUB_ORG = 'choderalab'
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$ACTIVITIES = ['changelog']
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$CHANGELOG_FILENAME = 'docs/CHANGELOG.rst'
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$CHANGELOG_TEMPLATE = 'TEMPLATE.rst'

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