idptools-pimms 1.0.1__tar.gz

idptools_pimms-1.0.1/LICENSE

@@ -0,0 +1,57 @@
+
+GNU LESSER GENERAL PUBLIC LICENSE
+Version 3, 29 June 2007
+
+Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+
+Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
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+This version of the GNU Lesser General Public License incorporates the terms and conditions of version 3 of the GNU General Public License, supplemented by the additional permissions listed below.
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idptools_pimms-1.0.1/MANIFEST.in

@@ -0,0 +1,7 @@
+include LICENSE
+include MANIFEST.in
+include pimms/*.pyx
+
+
+graft pimms
+global-exclude *.py[cod] __pycache__ *.so

idptools_pimms-1.0.1/PKG-INFO

@@ -0,0 +1,138 @@
+Metadata-Version: 2.4
+Name: idptools-pimms
+Version: 1.0.1
+Summary: A lattice-based coarse-grained Monte Carlo engine for polymer phase behaviour and biomolecular condensates.
+Author: Ryan Emenecker
+Author-email: Alex Holehouse <alex.holehouse@wustl.edu>
+Maintainer-email: Alex Holehouse <alex.holehouse@wustl.edu>
+License: LGPLv3
+Project-URL: Homepage, https://github.com/holehouse-lab/PIMMS
+Project-URL: Documentation, https://idptools-pimms.readthedocs.io
+Project-URL: Repository, https://github.com/holehouse-lab/PIMMS
+Project-URL: Issues, https://github.com/holehouse-lab/PIMMS/issues
+Project-URL: Changelog, https://github.com/holehouse-lab/PIMMS/blob/master/changelog.md
+Keywords: monte carlo,lattice model,polymer physics,phase separation,biomolecular condensates,coarse-grained simulation
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Cython
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.20
+Requires-Dist: scipy>=1.7
+Requires-Dist: mdtraj>=1.9
+Requires-Dist: python-dateutil>=2.8
+Provides-Extra: docs
+Requires-Dist: sphinx<9,>=7; extra == "docs"
+Requires-Dist: sphinx_rtd_theme>=2.0; extra == "docs"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Dynamic: license-file
+
+<p align="center">
+  <img src="branding/logo.png" alt="PIMMS logo" width="480"/>
+</p>
+
+<h1 align="center">PIMMS: Polymer Interactions in Multi-component MixtureS</h1>
+
+<!-- Badges -->
+<p align="center">
+  <a href="https://idptools-pimms.readthedocs.io/en/latest/?badge=latest"><img src="https://readthedocs.org/projects/idptools-pimms/badge/?version=latest" alt="Documentation Status"/></a>
+  <a href="https://www.gnu.org/licenses/lgpl-3.0"><img src="https://img.shields.io/badge/License-LGPL_v3-blue.svg" alt="License: LGPL v3"/></a>
+  <a href="https://www.python.org/downloads/"><img src="https://img.shields.io/badge/python-3.8%2B-blue.svg" alt="Python 3.8+"/></a>
+  <a href="https://github.com/holehouse-lab/PIMMS/commits/master"><img src="https://img.shields.io/github/last-commit/holehouse-lab/PIMMS" alt="Last commit"/></a>
+  <a href="https://github.com/holehouse-lab/PIMMS/issues"><img src="https://img.shields.io/github/issues/holehouse-lab/PIMMS" alt="Open issues"/></a>
+  <a href="https://github.com/holehouse-lab/PIMMS/pulls"><img src="https://img.shields.io/badge/PRs-welcome-brightgreen.svg" alt="PRs welcome"/></a>
+  <a href="https://github.com/holehouse-lab/PIMMS/stargazers"><img src="https://img.shields.io/github/stars/holehouse-lab/PIMMS?style=social" alt="GitHub stars"/></a>
+</p>
+
+---
+
+**PIMMS** is a lattice-based, coarse-grained Monte Carlo simulation engine for exploring the phase behaviour and conformational properties of polymer systems — single homo- or hetero-polymers, many-chain mixtures, and biomolecular condensates — in both 2D and 3D.
+
+📖 **Full documentation:** https://idptools-pimms.readthedocs.io
+
+## What is PIMMS?
+
+PIMMS discretises space into a square (2D) or cubic (3D) lattice. A polymer is a chain of **beads** on that lattice, with consecutive beads occupying lattice-adjacent sites (in the Chebyshev sense, so chains can fold compactly), and every site holds at most one bead (hard-sphere exclusion). You define a system in a plain-text **keyfile** and the interactions in a **parameter file**, then run it with a single command-line executable:
+
+```bash
+PIMMS -k KEYFILE.kf
+```
+
+The engine samples configurations with **Metropolis Monte Carlo**. Interactions act over three nested length scales (short / long / super-long range) plus solvation and backbone-angle terms, all set in the parameter file, so you can build anything from a single self-avoiding chain to a multi-component condensate. A rich move set — local **crankshaft** moves, whole-chain **reptation (slither)** and cooperative **pull** megamoves, rigid-body **cluster** moves, **virtual-move Monte Carlo (VMMC)**, and **temperature-switch (TSMMC)** excursions — samples efficiently and escapes kinetic traps, under either periodic or hard-wall boundaries.
+
+The hot loops are written in optimised **Cython** that compiles to native C, with an optional multi-threaded **OpenMP** kernel for large systems. Trajectories are written as standard `.pdb` + `.xtc` (via `mdtraj`), and the bundled **`lemonade`** package provides fast, hierarchical post-hoc analysis (conformational properties, cluster/condensate physics, coexistence densities and interfacial tension). See the [documentation](https://idptools-pimms.readthedocs.io) for the full model, keyword reference, and worked examples.
+
+## Who develops PIMMS?
+
+Alex Holehouse developed an initial version of PIMMS during his time in the [Pappu lab](http://pappulab.wustl.edu/), where it was used in a number of publications (most notably in Martin/Holehouse/Peran et al. Science 2020, which used an old Python 2.7 implementation [available on Zenodo](https://zenodo.org/records/3588456)). Since starting [his own lab](http://holehouse.wustl.edu/), the majority of PIMMS has been rewritten, and Dr. Ryan Emenecker has joined as a core developer. PIMMS is developed and maintained exclusively by the [Holehouse lab](http://holehouse.wustl.edu/) at Washington University in St. Louis, with contributions from many lab members of the years. 
+
+## Installation
+
+PIMMS is available on PyPI. Because the performance-critical parts are written in Cython, installing PIMMS compiles native C extensions on your machine, so you need a working **C compiler** (clang on macOS, gcc on Linux) and **Python ≥ 3.8** (3.10+ recommended; our development/test environment is 3.12).
+
+These steps mirror the [installation guide](https://idptools-pimms.readthedocs.io/en/latest/installation.html) in the documentation.
+
+**1. Create a clean environment** (with `conda` or `uv`):
+
+```bash
+# with conda
+conda create -n pimms python=3.12 -y
+conda activate pimms
+
+# ...or with uv
+uv venv --python 3.12
+source .venv/bin/activate
+```
+
+**2. Install the dependencies** (with `uv`, prefix each with `uv pip` instead of `pip`):
+
+```bash
+pip install numpy scipy cython versioningit
+pip install mdtraj
+```
+
+**3. Install PIMMS** from PyPI:
+
+```
+pip install idptools-pimms
+```
+
+**4. Install PIMMS** directly from GitHub:
+
+```bash
+pip install --no-build-isolation git+https://github.com/holehouse-lab/PIMMS.git
+```
+
+...or from a source checkout (recommended if you intend to develop PIMMS):
+
+```bash
+git clone https://github.com/holehouse-lab/PIMMS.git
+cd PIMMS
+pip install -e . --upgrade --force-reinstall     # ...or: uv pip install -e . --no-deps --reinstall
+```
+
+Verify the install with `PIMMS --version` and `PIMMS --info` (which lists every keyfile keyword).
+
+## Referencing PIMMS
+
+A dedicated PIMMS methods paper is in preparation; this section will be updated with its citation once it is available. In the meantime, if PIMMS is useful in your work, please cite the repository:
+
+> Holehouse, A. S. & Emenecker, R. J. *PIMMS: Polymer Interactions in Multi-component MixtureS*. Holehouse Lab, Washington University in St. Louis. https://github.com/holehouse-lab/PIMMS
+
+## License
+
+PIMMS is released under the **GNU Lesser General Public License v3.0 (LGPLv3)**. See [`LICENSE`](LICENSE) for details.

idptools_pimms-1.0.1/README.md

@@ -0,0 +1,95 @@
+<p align="center">
+  <img src="branding/logo.png" alt="PIMMS logo" width="480"/>
+</p>
+
+<h1 align="center">PIMMS: Polymer Interactions in Multi-component MixtureS</h1>
+
+<!-- Badges -->
+<p align="center">
+  <a href="https://idptools-pimms.readthedocs.io/en/latest/?badge=latest"><img src="https://readthedocs.org/projects/idptools-pimms/badge/?version=latest" alt="Documentation Status"/></a>
+  <a href="https://www.gnu.org/licenses/lgpl-3.0"><img src="https://img.shields.io/badge/License-LGPL_v3-blue.svg" alt="License: LGPL v3"/></a>
+  <a href="https://www.python.org/downloads/"><img src="https://img.shields.io/badge/python-3.8%2B-blue.svg" alt="Python 3.8+"/></a>
+  <a href="https://github.com/holehouse-lab/PIMMS/commits/master"><img src="https://img.shields.io/github/last-commit/holehouse-lab/PIMMS" alt="Last commit"/></a>
+  <a href="https://github.com/holehouse-lab/PIMMS/issues"><img src="https://img.shields.io/github/issues/holehouse-lab/PIMMS" alt="Open issues"/></a>
+  <a href="https://github.com/holehouse-lab/PIMMS/pulls"><img src="https://img.shields.io/badge/PRs-welcome-brightgreen.svg" alt="PRs welcome"/></a>
+  <a href="https://github.com/holehouse-lab/PIMMS/stargazers"><img src="https://img.shields.io/github/stars/holehouse-lab/PIMMS?style=social" alt="GitHub stars"/></a>
+</p>
+
+---
+
+**PIMMS** is a lattice-based, coarse-grained Monte Carlo simulation engine for exploring the phase behaviour and conformational properties of polymer systems — single homo- or hetero-polymers, many-chain mixtures, and biomolecular condensates — in both 2D and 3D.
+
+📖 **Full documentation:** https://idptools-pimms.readthedocs.io
+
+## What is PIMMS?
+
+PIMMS discretises space into a square (2D) or cubic (3D) lattice. A polymer is a chain of **beads** on that lattice, with consecutive beads occupying lattice-adjacent sites (in the Chebyshev sense, so chains can fold compactly), and every site holds at most one bead (hard-sphere exclusion). You define a system in a plain-text **keyfile** and the interactions in a **parameter file**, then run it with a single command-line executable:
+
+```bash
+PIMMS -k KEYFILE.kf
+```
+
+The engine samples configurations with **Metropolis Monte Carlo**. Interactions act over three nested length scales (short / long / super-long range) plus solvation and backbone-angle terms, all set in the parameter file, so you can build anything from a single self-avoiding chain to a multi-component condensate. A rich move set — local **crankshaft** moves, whole-chain **reptation (slither)** and cooperative **pull** megamoves, rigid-body **cluster** moves, **virtual-move Monte Carlo (VMMC)**, and **temperature-switch (TSMMC)** excursions — samples efficiently and escapes kinetic traps, under either periodic or hard-wall boundaries.
+
+The hot loops are written in optimised **Cython** that compiles to native C, with an optional multi-threaded **OpenMP** kernel for large systems. Trajectories are written as standard `.pdb` + `.xtc` (via `mdtraj`), and the bundled **`lemonade`** package provides fast, hierarchical post-hoc analysis (conformational properties, cluster/condensate physics, coexistence densities and interfacial tension). See the [documentation](https://idptools-pimms.readthedocs.io) for the full model, keyword reference, and worked examples.
+
+## Who develops PIMMS?
+
+Alex Holehouse developed an initial version of PIMMS during his time in the [Pappu lab](http://pappulab.wustl.edu/), where it was used in a number of publications (most notably in Martin/Holehouse/Peran et al. Science 2020, which used an old Python 2.7 implementation [available on Zenodo](https://zenodo.org/records/3588456)). Since starting [his own lab](http://holehouse.wustl.edu/), the majority of PIMMS has been rewritten, and Dr. Ryan Emenecker has joined as a core developer. PIMMS is developed and maintained exclusively by the [Holehouse lab](http://holehouse.wustl.edu/) at Washington University in St. Louis, with contributions from many lab members of the years. 
+
+## Installation
+
+PIMMS is available on PyPI. Because the performance-critical parts are written in Cython, installing PIMMS compiles native C extensions on your machine, so you need a working **C compiler** (clang on macOS, gcc on Linux) and **Python ≥ 3.8** (3.10+ recommended; our development/test environment is 3.12).
+
+These steps mirror the [installation guide](https://idptools-pimms.readthedocs.io/en/latest/installation.html) in the documentation.
+
+**1. Create a clean environment** (with `conda` or `uv`):
+
+```bash
+# with conda
+conda create -n pimms python=3.12 -y
+conda activate pimms
+
+# ...or with uv
+uv venv --python 3.12
+source .venv/bin/activate
+```
+
+**2. Install the dependencies** (with `uv`, prefix each with `uv pip` instead of `pip`):
+
+```bash
+pip install numpy scipy cython versioningit
+pip install mdtraj
+```
+
+**3. Install PIMMS** from PyPI:
+
+```
+pip install idptools-pimms
+```
+
+**4. Install PIMMS** directly from GitHub:
+
+```bash
+pip install --no-build-isolation git+https://github.com/holehouse-lab/PIMMS.git
+```
+
+...or from a source checkout (recommended if you intend to develop PIMMS):
+
+```bash
+git clone https://github.com/holehouse-lab/PIMMS.git
+cd PIMMS
+pip install -e . --upgrade --force-reinstall     # ...or: uv pip install -e . --no-deps --reinstall
+```
+
+Verify the install with `PIMMS --version` and `PIMMS --info` (which lists every keyfile keyword).
+
+## Referencing PIMMS
+
+A dedicated PIMMS methods paper is in preparation; this section will be updated with its citation once it is available. In the meantime, if PIMMS is useful in your work, please cite the repository:
+
+> Holehouse, A. S. & Emenecker, R. J. *PIMMS: Polymer Interactions in Multi-component MixtureS*. Holehouse Lab, Washington University in St. Louis. https://github.com/holehouse-lab/PIMMS
+
+## License
+
+PIMMS is released under the **GNU Lesser General Public License v3.0 (LGPLv3)**. See [`LICENSE`](LICENSE) for details.

idptools_pimms-1.0.1/idptools_pimms.egg-info/PKG-INFO

@@ -0,0 +1,138 @@
+Metadata-Version: 2.4
+Name: idptools-pimms
+Version: 1.0.1
+Summary: A lattice-based coarse-grained Monte Carlo engine for polymer phase behaviour and biomolecular condensates.
+Author: Ryan Emenecker
+Author-email: Alex Holehouse <alex.holehouse@wustl.edu>
+Maintainer-email: Alex Holehouse <alex.holehouse@wustl.edu>
+License: LGPLv3
+Project-URL: Homepage, https://github.com/holehouse-lab/PIMMS
+Project-URL: Documentation, https://idptools-pimms.readthedocs.io
+Project-URL: Repository, https://github.com/holehouse-lab/PIMMS
+Project-URL: Issues, https://github.com/holehouse-lab/PIMMS/issues
+Project-URL: Changelog, https://github.com/holehouse-lab/PIMMS/blob/master/changelog.md
+Keywords: monte carlo,lattice model,polymer physics,phase separation,biomolecular condensates,coarse-grained simulation
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Cython
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.20
+Requires-Dist: scipy>=1.7
+Requires-Dist: mdtraj>=1.9
+Requires-Dist: python-dateutil>=2.8
+Provides-Extra: docs
+Requires-Dist: sphinx<9,>=7; extra == "docs"
+Requires-Dist: sphinx_rtd_theme>=2.0; extra == "docs"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Dynamic: license-file
+
+<p align="center">
+  <img src="branding/logo.png" alt="PIMMS logo" width="480"/>
+</p>
+
+<h1 align="center">PIMMS: Polymer Interactions in Multi-component MixtureS</h1>
+
+<!-- Badges -->
+<p align="center">
+  <a href="https://idptools-pimms.readthedocs.io/en/latest/?badge=latest"><img src="https://readthedocs.org/projects/idptools-pimms/badge/?version=latest" alt="Documentation Status"/></a>
+  <a href="https://www.gnu.org/licenses/lgpl-3.0"><img src="https://img.shields.io/badge/License-LGPL_v3-blue.svg" alt="License: LGPL v3"/></a>
+  <a href="https://www.python.org/downloads/"><img src="https://img.shields.io/badge/python-3.8%2B-blue.svg" alt="Python 3.8+"/></a>
+  <a href="https://github.com/holehouse-lab/PIMMS/commits/master"><img src="https://img.shields.io/github/last-commit/holehouse-lab/PIMMS" alt="Last commit"/></a>
+  <a href="https://github.com/holehouse-lab/PIMMS/issues"><img src="https://img.shields.io/github/issues/holehouse-lab/PIMMS" alt="Open issues"/></a>
+  <a href="https://github.com/holehouse-lab/PIMMS/pulls"><img src="https://img.shields.io/badge/PRs-welcome-brightgreen.svg" alt="PRs welcome"/></a>
+  <a href="https://github.com/holehouse-lab/PIMMS/stargazers"><img src="https://img.shields.io/github/stars/holehouse-lab/PIMMS?style=social" alt="GitHub stars"/></a>
+</p>
+
+---
+
+**PIMMS** is a lattice-based, coarse-grained Monte Carlo simulation engine for exploring the phase behaviour and conformational properties of polymer systems — single homo- or hetero-polymers, many-chain mixtures, and biomolecular condensates — in both 2D and 3D.
+
+📖 **Full documentation:** https://idptools-pimms.readthedocs.io
+
+## What is PIMMS?
+
+PIMMS discretises space into a square (2D) or cubic (3D) lattice. A polymer is a chain of **beads** on that lattice, with consecutive beads occupying lattice-adjacent sites (in the Chebyshev sense, so chains can fold compactly), and every site holds at most one bead (hard-sphere exclusion). You define a system in a plain-text **keyfile** and the interactions in a **parameter file**, then run it with a single command-line executable:
+
+```bash
+PIMMS -k KEYFILE.kf
+```
+
+The engine samples configurations with **Metropolis Monte Carlo**. Interactions act over three nested length scales (short / long / super-long range) plus solvation and backbone-angle terms, all set in the parameter file, so you can build anything from a single self-avoiding chain to a multi-component condensate. A rich move set — local **crankshaft** moves, whole-chain **reptation (slither)** and cooperative **pull** megamoves, rigid-body **cluster** moves, **virtual-move Monte Carlo (VMMC)**, and **temperature-switch (TSMMC)** excursions — samples efficiently and escapes kinetic traps, under either periodic or hard-wall boundaries.
+
+The hot loops are written in optimised **Cython** that compiles to native C, with an optional multi-threaded **OpenMP** kernel for large systems. Trajectories are written as standard `.pdb` + `.xtc` (via `mdtraj`), and the bundled **`lemonade`** package provides fast, hierarchical post-hoc analysis (conformational properties, cluster/condensate physics, coexistence densities and interfacial tension). See the [documentation](https://idptools-pimms.readthedocs.io) for the full model, keyword reference, and worked examples.
+
+## Who develops PIMMS?
+
+Alex Holehouse developed an initial version of PIMMS during his time in the [Pappu lab](http://pappulab.wustl.edu/), where it was used in a number of publications (most notably in Martin/Holehouse/Peran et al. Science 2020, which used an old Python 2.7 implementation [available on Zenodo](https://zenodo.org/records/3588456)). Since starting [his own lab](http://holehouse.wustl.edu/), the majority of PIMMS has been rewritten, and Dr. Ryan Emenecker has joined as a core developer. PIMMS is developed and maintained exclusively by the [Holehouse lab](http://holehouse.wustl.edu/) at Washington University in St. Louis, with contributions from many lab members of the years. 
+
+## Installation
+
+PIMMS is available on PyPI. Because the performance-critical parts are written in Cython, installing PIMMS compiles native C extensions on your machine, so you need a working **C compiler** (clang on macOS, gcc on Linux) and **Python ≥ 3.8** (3.10+ recommended; our development/test environment is 3.12).
+
+These steps mirror the [installation guide](https://idptools-pimms.readthedocs.io/en/latest/installation.html) in the documentation.
+
+**1. Create a clean environment** (with `conda` or `uv`):
+
+```bash
+# with conda
+conda create -n pimms python=3.12 -y
+conda activate pimms
+
+# ...or with uv
+uv venv --python 3.12
+source .venv/bin/activate
+```
+
+**2. Install the dependencies** (with `uv`, prefix each with `uv pip` instead of `pip`):
+
+```bash
+pip install numpy scipy cython versioningit
+pip install mdtraj
+```
+
+**3. Install PIMMS** from PyPI:
+
+```
+pip install idptools-pimms
+```
+
+**4. Install PIMMS** directly from GitHub:
+
+```bash
+pip install --no-build-isolation git+https://github.com/holehouse-lab/PIMMS.git
+```
+
+...or from a source checkout (recommended if you intend to develop PIMMS):
+
+```bash
+git clone https://github.com/holehouse-lab/PIMMS.git
+cd PIMMS
+pip install -e . --upgrade --force-reinstall     # ...or: uv pip install -e . --no-deps --reinstall
+```
+
+Verify the install with `PIMMS --version` and `PIMMS --info` (which lists every keyfile keyword).
+
+## Referencing PIMMS
+
+A dedicated PIMMS methods paper is in preparation; this section will be updated with its citation once it is available. In the meantime, if PIMMS is useful in your work, please cite the repository:
+
+> Holehouse, A. S. & Emenecker, R. J. *PIMMS: Polymer Interactions in Multi-component MixtureS*. Holehouse Lab, Washington University in St. Louis. https://github.com/holehouse-lab/PIMMS
+
+## License
+
+PIMMS is released under the **GNU Lesser General Public License v3.0 (LGPLv3)**. See [`LICENSE`](LICENSE) for details.