molcrafts-molpy 0.2.2__tar.gz

molcrafts_molpy-0.2.2/LICENSE

@@ -0,0 +1,28 @@
+BSD 3-Clause License
+
+Copyright (c) 2024-2025, Roy Kid
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

molcrafts_molpy-0.2.2/MANIFEST.in

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+recursive-include src/molpy/parser *.lark
+recursive-include src/molpy/data *

molcrafts_molpy-0.2.2/PKG-INFO

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+Metadata-Version: 2.4
+Name: molcrafts-molpy
+Version: 0.2.2
+Summary: Modern Python framework for molecular simulation and analysis
+Author-email: Roy Kid <lijichen365@gmail.com>
+Maintainer-email: Roy Kid <lijichen365@gmail.com>
+License: BSD-3-Clause
+Project-URL: Homepage, https://github.com/MolCrafts/molpy
+Project-URL: Documentation, https://molcrafts.github.io/molpy
+Project-URL: Repository, https://github.com/MolCrafts/molpy.git
+Project-URL: Issues, https://github.com/MolCrafts/molpy/issues
+Project-URL: Changelog, https://molcrafts.github.io/molpy/changelog/
+Keywords: molecular-simulation,computational-chemistry,molecular-dynamics,force-fields,scientific-computing
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Typing :: Typed
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=2.0
+Requires-Dist: python-igraph>=1.0.0
+Requires-Dist: lark>=1.3.1
+Requires-Dist: h5py>=3.0.0
+Provides-Extra: dev
+Requires-Dist: pytest>=6.0.0; extra == "dev"
+Requires-Dist: pytest-cov>=3.0.0; extra == "dev"
+Requires-Dist: pytest-mock>=3.10.0; extra == "dev"
+Requires-Dist: pre-commit>=4.0.0; extra == "dev"
+Provides-Extra: doc
+Requires-Dist: mkdocs>=1.4.0; extra == "doc"
+Requires-Dist: mkdocs-material>=9.7.0; extra == "doc"
+Requires-Dist: mkdocstrings[python]>=0.24.0; extra == "doc"
+Requires-Dist: mkdocs-jupyter==0.24.7; extra == "doc"
+Requires-Dist: packmol; extra == "doc"
+Requires-Dist: rdkit; extra == "doc"
+Requires-Dist: matplotlib; extra == "doc"
+Requires-Dist: scienceplots; extra == "doc"
+Provides-Extra: all
+Requires-Dist: molcrafts-molpy[dev,doc]; extra == "all"
+Dynamic: license-file
+
+# 🚀 MolPy — A fast, clean, and composable toolkit for molecular modeling
+
+[![Python](https://img.shields.io/badge/python-3.12+-blue)](https://www.python.org/downloads/)
+[![License](https://img.shields.io/badge/license-BSD--3--Clause-green)](./LICENSE)
+[![Docs](https://img.shields.io/badge/docs-online-blue)](https://molcrafts.github.io/molpy)
+[![CI](https://github.com/MolCrafts/molpy/workflows/CI/badge.svg)](https://github.com/MolCrafts/molpy/actions)
+
+> **⚠️ MolPy is under active development.**
+> The API is evolving rapidly and may change between minor versions.
+
+**MolPy** is a modern, strongly typed, and extensible toolkit for molecular modeling.
+It provides a clean data model, flexible builders, explicit force-field typing, and lightweight analysis — a foundation designed for reproducible workflows and AI-assisted development.
+
+## 🚀 Installation
+
+```bash
+pip install molcrafts-molpy
+```
+
+For development:
+
+```bash
+git clone https://github.com/MolCrafts/molpy.git
+cd molpy
+pip install -e ".[dev]"
+```
+
+---
+
+## ✨ Features
+
+- **Unified Data Model** — `Frame` / `Block` / `Box` for molecular structures
+- **Explicit Topology** — `Atom`, `Bond`, `Angle`, `Dihedral` with typed metadata
+- **Force-Field Typing** — rule-based, engine-agnostic typifiers (OPLS-AA, custom SMARTS/SMIRKS)
+- **Polymer Builders** — automatic polymer assembly from BigSMILES/GBigSMILES/CGSmiles
+  - Linear, branched, and cyclic topologies
+  - Polydisperse systems with Schulz-Zimm, Poisson, Uniform, Flory-Schulz distributions
+  - Reaction-based crosslinking and network formation
+- **Chemistry Parsers** — SMILES, BigSMILES, GBigSMILES, and CGSmiles support
+- **Adapter System** — seamless integration with RDKit, LAMMPS, OpenMM, Packmol
+- **Reaction Framework** — explicit chemical reactions with leaving groups
+- **Lightweight Analysis** — composable compute operators
+- **Robust I/O** — PDB, XYZ, LAMMPS DATA, JSON-based formats
+- **AI-Friendly APIs** — predictable, strongly typed, minimal magic
+
+---
+
+## 📚 Documentation
+
+Full documentation: **[https://molcrafts.github.io/molpy](https://molcrafts.github.io/molpy)**
+
+---
+
+## 🌌 MolCrafts Ecosystem
+
+### **MolVis** — Interactive Molecular Visualization
+
+WebGL-based visualization and editing.
+
+### **MolRS** — High-Performance Rust Backend
+
+Typed array structures, compute kernels, and fast builders (native + WASM).
+
+---
+
+## 🤝 Contributing
+
+```bash
+pip install -e ".[dev]"
+pre-commit install
+pytest -q
+```
+
+We welcome issues and pull requests.
+
+---
+
+## 📄 License
+
+BSD-3-Clause — see [LICENSE](LICENSE).
+
+---
+
+**Built with ❤️ by MolCrafts.**

molcrafts_molpy-0.2.2/README.md

@@ -0,0 +1,84 @@
+# 🚀 MolPy — A fast, clean, and composable toolkit for molecular modeling
+
+[![Python](https://img.shields.io/badge/python-3.12+-blue)](https://www.python.org/downloads/)
+[![License](https://img.shields.io/badge/license-BSD--3--Clause-green)](./LICENSE)
+[![Docs](https://img.shields.io/badge/docs-online-blue)](https://molcrafts.github.io/molpy)
+[![CI](https://github.com/MolCrafts/molpy/workflows/CI/badge.svg)](https://github.com/MolCrafts/molpy/actions)
+
+> **⚠️ MolPy is under active development.**
+> The API is evolving rapidly and may change between minor versions.
+
+**MolPy** is a modern, strongly typed, and extensible toolkit for molecular modeling.
+It provides a clean data model, flexible builders, explicit force-field typing, and lightweight analysis — a foundation designed for reproducible workflows and AI-assisted development.
+
+## 🚀 Installation
+
+```bash
+pip install molcrafts-molpy
+```
+
+For development:
+
+```bash
+git clone https://github.com/MolCrafts/molpy.git
+cd molpy
+pip install -e ".[dev]"
+```
+
+---
+
+## ✨ Features
+
+- **Unified Data Model** — `Frame` / `Block` / `Box` for molecular structures
+- **Explicit Topology** — `Atom`, `Bond`, `Angle`, `Dihedral` with typed metadata
+- **Force-Field Typing** — rule-based, engine-agnostic typifiers (OPLS-AA, custom SMARTS/SMIRKS)
+- **Polymer Builders** — automatic polymer assembly from BigSMILES/GBigSMILES/CGSmiles
+  - Linear, branched, and cyclic topologies
+  - Polydisperse systems with Schulz-Zimm, Poisson, Uniform, Flory-Schulz distributions
+  - Reaction-based crosslinking and network formation
+- **Chemistry Parsers** — SMILES, BigSMILES, GBigSMILES, and CGSmiles support
+- **Adapter System** — seamless integration with RDKit, LAMMPS, OpenMM, Packmol
+- **Reaction Framework** — explicit chemical reactions with leaving groups
+- **Lightweight Analysis** — composable compute operators
+- **Robust I/O** — PDB, XYZ, LAMMPS DATA, JSON-based formats
+- **AI-Friendly APIs** — predictable, strongly typed, minimal magic
+
+---
+
+## 📚 Documentation
+
+Full documentation: **[https://molcrafts.github.io/molpy](https://molcrafts.github.io/molpy)**
+
+---
+
+## 🌌 MolCrafts Ecosystem
+
+### **MolVis** — Interactive Molecular Visualization
+
+WebGL-based visualization and editing.
+
+### **MolRS** — High-Performance Rust Backend
+
+Typed array structures, compute kernels, and fast builders (native + WASM).
+
+---
+
+## 🤝 Contributing
+
+```bash
+pip install -e ".[dev]"
+pre-commit install
+pytest -q
+```
+
+We welcome issues and pull requests.
+
+---
+
+## 📄 License
+
+BSD-3-Clause — see [LICENSE](LICENSE).
+
+---
+
+**Built with ❤️ by MolCrafts.**

molcrafts_molpy-0.2.2/pyproject.toml

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+[project]
+name = "molcrafts-molpy"
+dynamic = ["version"]
+description = "Modern Python framework for molecular simulation and analysis"
+readme = "README.md"
+requires-python = ">=3.12"
+license = {text = "BSD-3-Clause"}
+
+authors = [
+    { name = "Roy Kid", email = "lijichen365@gmail.com" }
+]
+
+maintainers = [
+    { name = "Roy Kid", email = "lijichen365@gmail.com" }
+]
+
+keywords = [
+    "molecular-simulation",
+    "computational-chemistry",
+    "molecular-dynamics",
+    "force-fields",
+    "scientific-computing"
+]
+
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Chemistry",
+    "Topic :: Scientific/Engineering :: Physics",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+    "Typing :: Typed",
+]
+
+dependencies = [
+    "numpy>=2.0",
+    "python-igraph>=1.0.0",
+    "lark>=1.3.1",
+    "h5py>=3.0.0"
+]
+
+[tool.setuptools.dynamic]
+version = { attr = "molpy.version.version" }
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=6.0.0",
+    "pytest-cov>=3.0.0",
+    "pytest-mock>=3.10.0",
+    "pre-commit>=4.0.0"
+]
+doc = [
+    "mkdocs>=1.4.0",
+    "mkdocs-material>=9.7.0",
+    "mkdocstrings[python]>=0.24.0",
+    "mkdocs-jupyter==0.24.7",
+    "packmol",
+    "rdkit",
+    "matplotlib",
+    "scienceplots",
+]
+all = [
+    "molcrafts-molpy[dev,doc]"
+]
+
+[project.urls]
+Homepage = "https://github.com/MolCrafts/molpy"
+Documentation = "https://molcrafts.github.io/molpy"
+Repository = "https://github.com/MolCrafts/molpy.git"
+Issues = "https://github.com/MolCrafts/molpy/issues"
+Changelog = "https://molcrafts.github.io/molpy/changelog/"
+
+[build-system]
+requires = [
+    "setuptools>=42",
+    "wheel",
+    "ninja",
+    "numpy",
+]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+"molpy.parser" = ["grammar/*.lark"]
+"molpy.parser.smiles" = ["grammars/*.lark"]
+"molpy.data" = ["README.md"]
+"molpy.data.forcefield" = ["*.xml"]
+
+[tool.black]
+line-length = 88
+target-version = ['py312']
+include = '\.pyi?$'
+extend-exclude = '''
+/(
+  # directories
+  \.eggs
+  | \.git
+  | \.hg
+  | \.mypy_cache
+  | \.tox
+  | \.venv
+  | build
+  | dist
+)/
+'''
+
+[tool.isort]
+profile = "black"
+line_length = 88
+multi_line_output = 3
+include_trailing_comma = true
+force_grid_wrap = 0
+use_parentheses = true
+ensure_newline_before_comments = true
+
+[tool.pytest.ini_options]
+markers = [
+    "external: tests requiring external network/resources or executables",
+]

molcrafts_molpy-0.2.2/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

molcrafts_molpy-0.2.2/src/molcrafts_molpy.egg-info/PKG-INFO

@@ -0,0 +1,137 @@
+Metadata-Version: 2.4
+Name: molcrafts-molpy
+Version: 0.2.2
+Summary: Modern Python framework for molecular simulation and analysis
+Author-email: Roy Kid <lijichen365@gmail.com>
+Maintainer-email: Roy Kid <lijichen365@gmail.com>
+License: BSD-3-Clause
+Project-URL: Homepage, https://github.com/MolCrafts/molpy
+Project-URL: Documentation, https://molcrafts.github.io/molpy
+Project-URL: Repository, https://github.com/MolCrafts/molpy.git
+Project-URL: Issues, https://github.com/MolCrafts/molpy/issues
+Project-URL: Changelog, https://molcrafts.github.io/molpy/changelog/
+Keywords: molecular-simulation,computational-chemistry,molecular-dynamics,force-fields,scientific-computing
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Typing :: Typed
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=2.0
+Requires-Dist: python-igraph>=1.0.0
+Requires-Dist: lark>=1.3.1
+Requires-Dist: h5py>=3.0.0
+Provides-Extra: dev
+Requires-Dist: pytest>=6.0.0; extra == "dev"
+Requires-Dist: pytest-cov>=3.0.0; extra == "dev"
+Requires-Dist: pytest-mock>=3.10.0; extra == "dev"
+Requires-Dist: pre-commit>=4.0.0; extra == "dev"
+Provides-Extra: doc
+Requires-Dist: mkdocs>=1.4.0; extra == "doc"
+Requires-Dist: mkdocs-material>=9.7.0; extra == "doc"
+Requires-Dist: mkdocstrings[python]>=0.24.0; extra == "doc"
+Requires-Dist: mkdocs-jupyter==0.24.7; extra == "doc"
+Requires-Dist: packmol; extra == "doc"
+Requires-Dist: rdkit; extra == "doc"
+Requires-Dist: matplotlib; extra == "doc"
+Requires-Dist: scienceplots; extra == "doc"
+Provides-Extra: all
+Requires-Dist: molcrafts-molpy[dev,doc]; extra == "all"
+Dynamic: license-file
+
+# 🚀 MolPy — A fast, clean, and composable toolkit for molecular modeling
+
+[![Python](https://img.shields.io/badge/python-3.12+-blue)](https://www.python.org/downloads/)
+[![License](https://img.shields.io/badge/license-BSD--3--Clause-green)](./LICENSE)
+[![Docs](https://img.shields.io/badge/docs-online-blue)](https://molcrafts.github.io/molpy)
+[![CI](https://github.com/MolCrafts/molpy/workflows/CI/badge.svg)](https://github.com/MolCrafts/molpy/actions)
+
+> **⚠️ MolPy is under active development.**
+> The API is evolving rapidly and may change between minor versions.
+
+**MolPy** is a modern, strongly typed, and extensible toolkit for molecular modeling.
+It provides a clean data model, flexible builders, explicit force-field typing, and lightweight analysis — a foundation designed for reproducible workflows and AI-assisted development.
+
+## 🚀 Installation
+
+```bash
+pip install molcrafts-molpy
+```
+
+For development:
+
+```bash
+git clone https://github.com/MolCrafts/molpy.git
+cd molpy
+pip install -e ".[dev]"
+```
+
+---
+
+## ✨ Features
+
+- **Unified Data Model** — `Frame` / `Block` / `Box` for molecular structures
+- **Explicit Topology** — `Atom`, `Bond`, `Angle`, `Dihedral` with typed metadata
+- **Force-Field Typing** — rule-based, engine-agnostic typifiers (OPLS-AA, custom SMARTS/SMIRKS)
+- **Polymer Builders** — automatic polymer assembly from BigSMILES/GBigSMILES/CGSmiles
+  - Linear, branched, and cyclic topologies
+  - Polydisperse systems with Schulz-Zimm, Poisson, Uniform, Flory-Schulz distributions
+  - Reaction-based crosslinking and network formation
+- **Chemistry Parsers** — SMILES, BigSMILES, GBigSMILES, and CGSmiles support
+- **Adapter System** — seamless integration with RDKit, LAMMPS, OpenMM, Packmol
+- **Reaction Framework** — explicit chemical reactions with leaving groups
+- **Lightweight Analysis** — composable compute operators
+- **Robust I/O** — PDB, XYZ, LAMMPS DATA, JSON-based formats
+- **AI-Friendly APIs** — predictable, strongly typed, minimal magic
+
+---
+
+## 📚 Documentation
+
+Full documentation: **[https://molcrafts.github.io/molpy](https://molcrafts.github.io/molpy)**
+
+---
+
+## 🌌 MolCrafts Ecosystem
+
+### **MolVis** — Interactive Molecular Visualization
+
+WebGL-based visualization and editing.
+
+### **MolRS** — High-Performance Rust Backend
+
+Typed array structures, compute kernels, and fast builders (native + WASM).
+
+---
+
+## 🤝 Contributing
+
+```bash
+pip install -e ".[dev]"
+pre-commit install
+pytest -q
+```
+
+We welcome issues and pull requests.
+
+---
+
+## 📄 License
+
+BSD-3-Clause — see [LICENSE](LICENSE).
+
+---
+
+**Built with ❤️ by MolCrafts.**

molcrafts_molpy-0.2.2/src/molcrafts_molpy.egg-info/SOURCES.txt

@@ -0,0 +1,163 @@
+LICENSE
+MANIFEST.in
+README.md
+pyproject.toml
+src/molcrafts_molpy.egg-info/PKG-INFO
+src/molcrafts_molpy.egg-info/SOURCES.txt
+src/molcrafts_molpy.egg-info/dependency_links.txt
+src/molcrafts_molpy.egg-info/requires.txt
+src/molcrafts_molpy.egg-info/top_level.txt
+src/molpy/__init__.py
+src/molpy/version.py
+src/molpy/adapter/__init__.py
+src/molpy/adapter/base.py
+src/molpy/adapter/rdkit.py
+src/molpy/adapter/utils.py
+src/molpy/builder/__init__.py
+src/molpy/builder/crystal.py
+src/molpy/builder/polymer/__init__.py
+src/molpy/builder/polymer/connectors.py
+src/molpy/builder/polymer/errors.py
+src/molpy/builder/polymer/growth_kernel.py
+src/molpy/builder/polymer/placer.py
+src/molpy/builder/polymer/polymer_builder.py
+src/molpy/builder/polymer/port_utils.py
+src/molpy/builder/polymer/sequence_generator.py
+src/molpy/builder/polymer/stochastic_generator.py
+src/molpy/builder/polymer/system.py
+src/molpy/builder/polymer/types.py
+src/molpy/compute/__init__.py
+src/molpy/compute/base.py
+src/molpy/compute/mcd.py
+src/molpy/compute/pmsd.py
+src/molpy/compute/rdkit.py
+src/molpy/compute/result.py
+src/molpy/compute/time_series.py
+src/molpy/core/__init__.py
+src/molpy/core/atomistic.py
+src/molpy/core/box.py
+src/molpy/core/cg.py
+src/molpy/core/config.py
+src/molpy/core/element.py
+src/molpy/core/entity.py
+src/molpy/core/forcefield.py
+src/molpy/core/frame.py
+src/molpy/core/logger.py
+src/molpy/core/region.py
+src/molpy/core/script.py
+src/molpy/core/selector.py
+src/molpy/core/topology.py
+src/molpy/core/trajectory.py
+src/molpy/core/units.py
+src/molpy/core/utils.py
+src/molpy/core/ops/__init__.py
+src/molpy/core/ops/geometry.py
+src/molpy/data/__init__.py
+src/molpy/data/__pycache__/__init__.cpython-312.pyc
+src/molpy/data/forcefield/__init__.py
+src/molpy/data/forcefield/oplsaa.xml
+src/molpy/data/forcefield/tip3p.xml
+src/molpy/data/forcefield/__pycache__/__init__.cpython-312.pyc
+src/molpy/engine/__init__.py
+src/molpy/engine/base.py
+src/molpy/engine/cp2k.py
+src/molpy/engine/lammps.py
+src/molpy/io/__init__.py
+src/molpy/io/readers.py
+src/molpy/io/utils.py
+src/molpy/io/writers.py
+src/molpy/io/data/__init__.py
+src/molpy/io/data/ac.py
+src/molpy/io/data/amber.py
+src/molpy/io/data/base.py
+src/molpy/io/data/gro.py
+src/molpy/io/data/h5.py
+src/molpy/io/data/lammps.py
+src/molpy/io/data/lammps_molecule.py
+src/molpy/io/data/mol2.py
+src/molpy/io/data/pdb.py
+src/molpy/io/data/top.py
+src/molpy/io/data/xsf.py
+src/molpy/io/data/xyz.py
+src/molpy/io/forcefield/__init__.py
+src/molpy/io/forcefield/amber.py
+src/molpy/io/forcefield/base.py
+src/molpy/io/forcefield/lammps.py
+src/molpy/io/forcefield/moltemplate.py
+src/molpy/io/forcefield/top.py
+src/molpy/io/forcefield/xml.py
+src/molpy/io/log/lammps.py
+src/molpy/io/trajectory/__init__.py
+src/molpy/io/trajectory/base.py
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