firecode 1.4.0__tar.gz → 1.5.0a0__tar.gz

firecode-1.5.0a0/.ase/gui.py

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+gui_default_settings['show_bonds'] = True

firecode-1.5.0a0/.gitignore

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+.vscode/
+.DS_Store
+cython
+old
+variables.md
+
+# Created by https://www.toptal.com/developers/gitignore/api/python
+# Edit at https://www.toptal.com/developers/gitignore?templates=python
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# End of https://www.toptal.com/developers/gitignore/api/python
+firecode/TEST_NOTEBOOK.ipynb
+*Zone.Identifier
+firecode/calculators/uma-s-1p1.pt

firecode-1.5.0a0/.readthedocs.yaml

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+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.8"
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  # fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+   install:
+   - requirements: docs/requirements.txt

{firecode-1.4.0 → firecode-1.5.0a0}/CHANGELOG.md

@@ -3,11 +3,21 @@
 
 <!-- - ... mep_relax> BETA
 - ... IMAGES kw, also implement it for neb>-->
+<!-- FINALSPLEVEL keyword? -->
+
+## FIRECODE 1.5.0 🔥 (WIP)
+- Implemented an interface to [ML-FSM](https://github.com/thegomeslab/ML-FSM/tree/main).
+- Removed openbabel dependency.
+- Imports bugfixes.
+- Restructured setup to use [Pixi](https://pixi.prefix.dev/latest/).
+ <!-- add documentation: SCRAMBLECHECK kw -->
+
 ## FIRECODE 1.4.0 🔥 (January 25 2026) - Big cleanup and reorganization!
 - Similarity pruning is now done via the standalone [PRISM](https://github.com/ntampellini/prism_pruner) library.
 - Removed dependencies: numba, cclib, periodictable.
 - Removed MOPAC, GAUSSIAN and OPENBABEL calculator interfaces completely.
 - Removed SADDLE, CSEARCH and NCI keywords, as well as the saddle> operator.
+- Restructured most functions taking coordinates and atomic numbers to atomic symbols and coordinates (ASE style). [coords, atomnos] -> [atoms, coords]
 - Bumped minimum Python version from 3.8 to 3.12.
 
 ## FIRECODE 1.3.0 🔥 (December 15 2025)

firecode-1.5.0a0/PKG-INFO

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+Metadata-Version: 2.4
+Name: firecode
+Version: 1.5.0a0
+Summary: FIRECODE: Filtering Refiner and Embedder for Conformationally Dense Ensembles
+Author-email: Nicolò Tampellini <nicolo.tampellini@yale.edu>
+License-Expression: LGPL-3.0-or-later
+License-File: LICENSE
+Requires-Python: <3.13,>=3.10
+Requires-Dist: ase
+Requires-Dist: fairchem-core
+Requires-Dist: importlib-metadata
+Requires-Dist: inquirerpy
+Requires-Dist: llvmlite
+Requires-Dist: matplotlib
+Requires-Dist: networkx
+Requires-Dist: numpy
+Requires-Dist: prettytable
+Requires-Dist: prism-pruner
+Requires-Dist: psutil
+Requires-Dist: rdkit>=2025.9.3
+Requires-Dist: rich
+Requires-Dist: scipy
+Requires-Dist: typing-extensions
+Description-Content-Type: text/markdown
+
+
+# FIRECODE - Filtering Refiner and Embedder for Conformationally Dense Ensembles
+
+<div align="center">
+
+[![License: GNU LGPL v3](https://img.shields.io/github/license/ntampellini/firecode)](https://opensource.org/licenses/LGPL-3.0)
+![Python Version](https://img.shields.io/badge/Python-3.12-blue)
+![Size](https://img.shields.io/github/languages/code-size/ntampellini/firecode)
+![Lines](https://sloc.xyz/github/ntampellini/firecode/)
+[![CodeFactor Grade](https://img.shields.io/codefactor/grade/github/ntampellini/firecode)](https://www.codefactor.io/repository/github/ntampellini/firecode)
+
+[![PyPI](https://img.shields.io/pypi/v/firecode)](https://pypi.org/project/firecode/)
+[![Wheel](https://img.shields.io/pypi/wheel/firecode)](https://pypi.org/project/firecode/)
+[![Documentation Status](https://readthedocs.org/projects/firecode/badge/?version=latest)](https://firecode.readthedocs.io/en/latest/?badge=latest)
+![PyPI - Downloads](https://img.shields.io/pypi/dm/firecode)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v1.json)](https://github.com/charliermarsh/ruff)
+
+![Twitter](https://img.shields.io/twitter/url?url=https%3A%2F%2Ftwitter.com%2Fntampellini_&label=%40ntampellini_&link=https%3A%2F%2Ftwitter.com%2Fntampellini_)
+
+</div>
+
+<p align="center">
+
+  <img src="docs/images/logo.png" alt="FIRECODE logo" class="center" width="500"/>
+
+</p>
+
+*FIRECODE is the expanded successor of [TSCoDe](https://github.com/ntampellini/TSCoDe).* 
+
+FIRECODE is a computational chemistry toolbox for the generation, optimization and refinement of conformational ensembles. It features many flexible and highly customizable workflow utilities including conformer generation (via [CREST](https://github.com/crest-lab/crest) or FIRECODE), constrained ensemble optimization through popular calculators like [XTB](https://github.com/grimme-lab/xtb), [ORCA](https://www.orcasoftware.de/tutorials_orca/), [GAUSSIAN](https://gaussian.com/) and Pytorch Neural Network models via [ASE](https://github.com/rosswhitfield/ase) ([AIMNET2](https://github.com/isayevlab/AIMNet2)). It implements a series of conformational pruning routines based on inertia tensors, RMSD, symmetry-corrected RMSD, and more. It can also assemble non-covalent adducts from conformational ensembles (embedding) for fast and automated generation and evaluation of ground and transtition state-like structures. CPU and GPU multithreading is implemented throughout the codebase and linear algebra-intensive modules are compiled at runtime via [Numba](https://github.com/numba/numba).
+
+
+## Documentation
+Documentation on how to install and use the program can be found on [readthedocs](https://firecode.readthedocs.io/en/latest/index.html).