firecode 1.5.3__tar.gz → 2.0.0__tar.gz

{firecode-1.5.3 → firecode-2.0.0}/.coveragerc

@@ -1,6 +1,12 @@
 [run]
 source = prism_pruner
-omit = prism_pruner/__main__.py
+omit =
+    firecode/__main__.py
+    */.pixi/*
+    */tests/*
+    # */venv/*
+    # setup.py
+    # */__pycache__/*
 
 [report]
 exclude_lines =
@@ -20,4 +26,4 @@ exclude_lines =
     if __name__ == .__main__.:
 
     # Don't complain if an ellipsis isn't run (typically in an abstractmethod):
-    ^\s*\.\.\.
+    ^\s*\.\.\.

{firecode-1.5.3 → firecode-2.0.0}/.github/workflows/test.yml

@@ -6,6 +6,7 @@ on:
     branches:
     - main
     - feature/**
+    - bug/**
 
 jobs:
   test:
@@ -18,7 +19,7 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
 
       # - uses: actions/setup-python@v6
       #   with:
@@ -38,9 +39,14 @@ jobs:
       # - run: pixi run types
       - run: pixi run -e dev test_cov
 
+      - run: pixi run -e dev coverage report 
+
+      - run: head -5 coverage.xml
+
       - name: Upload Coverage to Codecov
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           files: ./coverage.xml
-        env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+          token: ${{ secrets.CODECOV_TOKEN }}
+          verbose: true
+          disable_search: true

{firecode-1.5.3 → firecode-2.0.0}/.gitignore

@@ -4,8 +4,9 @@ site/
 .vscode/
 .mypy_cache/
 firecode.egg-info/
-docs/
 
 firecode/calculators/uma-s-1p1.pt
+firecode/calculators/uma-s-1p2.pt
+firecode/calculators/esen_sm_conserving_all.pt
 coverage.xml
 .coverage

{firecode-1.5.3 → firecode-2.0.0}/.pre-commit-config.yaml

@@ -12,7 +12,7 @@ repos:
   hooks:
   - id: ruff
     name: ruff-format
-    stages: [pre-commit, pre-push]
+    stages: [pre-commit]
     language: system
     entry: pixi run fmt
     types: [python]
@@ -20,24 +20,24 @@ repos:
 
   - id: ruff
     name: ruff-check
-    stages: [pre-commit, pre-push]
+    stages: [pre-commit]
     language: system
     entry: pixi run lint
     types: [python]
     pass_filenames: false
 
-  # - id: Mypy
-  #   name: mypy
-  #   stages: [pre-commit, pre-push]
-  #   language: system
-  #   entry: pixi run types
-  #   types: [python]
-  #   pass_filenames: false
+  - id: Mypy
+    name: mypy
+    stages: [pre-commit]
+    language: system
+    entry: pixi run types
+    types: [python]
+    pass_filenames: false
 
   - id: pytest
     name: pytest
-    stages: [pre-commit, pre-push]
+    stages: [pre-push]
     language: system
-    entry: pixi run -e dev pytest -s -m codecov
+    entry: pixi run -e dev test_cov
     types: [python]
     pass_filenames: false

{firecode-1.5.3 → firecode-2.0.0}/CHANGELOG.md

@@ -1,10 +1,41 @@
 
-<!-- - Introduced compatibility of SADDLE and NEB keywords for scan> runs with both 2 indices (distance scans) and 4 indices (distance scans) -->
-
-<!-- - ... mep_relax> BETA
-- ... IMAGES kw, also implement it for neb>-->
-<!-- FINALSPLEVEL keyword? -->
- <!-- add documentation: SCRAMBLECHECK kw, fsm>, neb>, rdkit_search>, standalone optimizer-->
+<!-- add documentation: SCRAMBLECHECK kw, fsm>, neb>, rdkit_search>, standalone optimizer, non-inline constraints-->
+<!-- add number of active constraints printout for parallel multithread functions -->
+
+
+## FIRECODE 2.0.0 🔥 (WIP)
+- Restructured and expanded solvent module.
+- Implemented vibrational analysis via ASE including quasi-RRHO thermochemistry to get free energies.
+- Added Sella dependency to perform saddle points optimization with the `saddle>` operator.
+- Added FREQ keyword, computing free energies at the end of embedding or refine runs.
+- Added `freq>` operator for standalone frequency analysis on any ensemble.
+- Added T (temperature, in K), T_C (temperature, in °C), P (pressure, in atm), and C (concentration, in mol/L) keywords.
+- Updated CREST interface to version 3 of the program (see [paper](https://doi.org/10.1063/5.0197592) and [documentation](https://crest-lab.github.io/crest-docs/))
+- Added delta solvation implementation for gas-phase ML models, providing energies _and_ forces via TBLITE in the geometry optimization loop. Activate with environmental variable FIRECODE_SOLV_IMPLEM_FOR_ML="opt"
+- Dropped support for native XTB calculator, and XTB-pyhton interface, since TBLITE is the modern successor.
+- Added basic [racerts](https://github.com/digital-chemistry-laboratory/racerts) interface ("rdkit_search>" operator, alias of "racerts>").
+- Removed PROCS keyword.
+- Removed force field pre-optimization and related keywords (FFCALC, FFLEVEL)
+- Added basic interface to ORCA's [GOAT](https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.202500393) via the `goat>` operator (GFN2-xTB level with GFN-FF uphill steps).
+- Renamed "CRESTNCI" keyword to "NCI" to cater for both CREST and GOAT.
+- Significant restructuring of some core code organization (interfaces, context_manager.py, settings.py)
+- Separated interfaces with external programs in "interfaces".
+- Added the use of environmental variables throughout the codebase. Defaults in settings.py, specific context managers in utils.py.
+- Environment variables in settings.py can now be overridden by a local `.firecoderc` with key=value pairs in the same folder as the input file.
+- Added automated [packmol](https://github.com/m3g/packmol) solvator interface (`packmol>` operator, **preview**!).
+<!-- - Added MD equilibration of solvated boxes (`equilibrate>`) -->
+
+## FIRECODE 1.6.0 🔥 (March 11 2026)
+- Refreshed constraints handling in operators.
+- Added non-inline constraints specification after a molecule line. Syntax: "B/A/D i1 i2 [i3] [i4] [auto/value]"
+- These constraints can be fixed (default, same as uppercase in-line constraints) or temporary (like "interactions", i.e. "D 1 2 3 4 fixed=false")
+- Clearer, more explicit printouts for all constraints at any step.
+- the mtd>/mtd_search> operator now has more explicit synonyms: crest> and crest_search>
+- Added tests for the crest_search>, neb> and fsm> operators, as well as a "neb> scan>" chain.
+- Updated documentation: usage and operators (`neb>`, `fsm>`, `rdkit_search>`, `crest_search>`, ...) as well as keywords (general vs. legacy).
+- Type annotated the whole codebase(!).
+- Removed molecular bending and RIGID keyword.
+- Removed standalone ORCA calculator (can use ASE in the future, but throws NotImplementedError for now.)
 
 ## FIRECODE 1.5.3 🔥 (February 19 2026)
 - Fixes a bug with reactive_atoms_classes_dict and embedder.options.charge.

firecode-2.0.0/PKG-INFO

@@ -0,0 +1,151 @@
+Metadata-Version: 2.4
+Name: firecode
+Version: 2.0.0
+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,>=3.12
+Requires-Dist: ase
+Requires-Dist: inquirerpy
+Requires-Dist: matplotlib
+Requires-Dist: mlfsm
+Requires-Dist: networkx
+Requires-Dist: numpy
+Requires-Dist: prettytable
+Requires-Dist: prism-pruner
+Requires-Dist: psutil
+Requires-Dist: racerts>=0.1.6
+Requires-Dist: rdkit>=2025.9.3
+Requires-Dist: rich
+Requires-Dist: scipy
+Requires-Dist: sella>=2.4.2
+Provides-Extra: aimnet2
+Requires-Dist: aimnet[ase]; extra == 'aimnet2'
+Provides-Extra: full
+Requires-Dist: aimnet[ase]; extra == 'full'
+Requires-Dist: fairchem-core; extra == 'full'
+Provides-Extra: uma
+Requires-Dist: fairchem-core; extra == 'uma'
+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)
+[![Powered by: Pixi](https://img.shields.io/badge/Powered_by-Pixi-facc15)](https://pixi.sh)
+![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)
+[![codecov](https://codecov.io/gh/ntampellini/FIRECODE/graph/badge.svg?token=D9TM6S33D8)](https://codecov.io/gh/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 a computational chemistry workflow driver and hub for the generation, optimization and refinement of conformational ensembles, including  transition state and thermochemical utilities.
+
+
+
+<!-- It runs flexible workflows for conformer generation (via [CREST](https://github.com/crest-lab/crest), [RDKit](https://github.com/rdkit/rdkit)), double-ended TS search ([NEB](https://ase-lib.org/ase/neb.html) via [ASE](https://github.com/rosswhitfield/ase), [ML-FSM](https://github.com/thegomeslab/ML-FSM)), and (constrained) ensemble optimization through popular calculators like [XTB](https://github.com/grimme-lab/xtb), [TBLITE](https://github.com/tblite/tblite), [ORCA](https://www.orcasoftware.de/tutorials_orca/), and Pytorch Neural Network models ([AIMNET2](https://github.com/isayevlab/AIMNet2), [UMA](https://huggingface.co/facebook/UMA)) via [ASE](https://github.com/rosswhitfield/ase).
+
+Conformational pruning is performed with the now standalone [PRISM Pruner](https://github.com/ntampellini/prism_pruner).
+
+As a legacy feature from [TSCoDe](https://github.com/ntampellini/TSCoDe), FIRECODE can also assemble non-covalent adducts from conformational ensembles (embedding) programmatically. -->
+
+## Calculators
+
+- [xTB](https://github.com/grimme-lab/xtb) *(native)*
+- [tblite](https://github.com/tblite/tblite) *(via [ASE](https://github.com/rosswhitfield/ase))*
+- [AIMNET2](https://github.com/isayevlab/AIMNet2) *(via [ASE](https://github.com/rosswhitfield/ase))*
+- [UMA](https://huggingface.co/facebook/UMA) *(via [ASE](https://github.com/rosswhitfield/ase))*
+
+## Interfaces / utilities
+
+- [CREST](https://github.com/crest-lab/crest) *(conformational search)*
+- [GOAT](https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.202500393) *(conformational search)*
+- [racerts](https://github.com/digital-chemistry-laboratory/racerts) *(conformational search)*
+- [ETKDG](https://pubs.acs.org/doi/10.1021/acs.jcim.0c00025) *(via [rdkit](https://github.com/rdkit/rdkit), conformational search)*
+- [TSCoDe](https://github.com/ntampellini/TSCoDe) *(conformational embedding)*
+- [prism_pruner](https://github.com/ntampellini/prism_pruner) *(conformational pruning)*
+- [ML-FSM](https://pubs.acs.org/doi/10.1021/acs.jcim.0c00025) *(two-ended TS search)*
+- [Sella](https://github.com/zadorlab/sella) *(saddle point optimization)*
+<!-- - [packmol](https://github.com/m3g/packmol) *(explicit solvation)* -->
+
+...plus frequency calculation, NEB optimization, and more are all implemented in the code in a calculator-agnostic way.
+
+## Installation
+
+The package is distributed via `pip`, and the use of [`uv`](https://docs.astral.sh/uv/) is highly recommended. The default installation is minimalistic, and torch/GPU support requires dedicated installs:
+
+```python
+uv pip install firecode           # XTB, TBLITE, ORCA
+uv pip install firecode[aimnet2]  # + AIMNET2
+uv pip install firecode[uma]      # + UMA/OMOL
+uv pip install firecode[full]     # + AIMNET2, UMA/OMOL
+```
+
+More installation details in the documentation.
+
+## Usage
+
+Installation exposes the main program working on a plain text file as well as a standalone optimizer.
+
+```
+🔥 firecode [-h] [-s] [-t] input.txt [-n NAME] [-p]
+
+    positional arguments:
+      inpufile.txt            Input filename, can be any text file.
+
+    optional arguments:
+      -h, --help              Show this help message and exit.
+      -s, --setup             Guided setup of the calculation settings.
+      -n, --name NAME         Specify a custom name for the run.
+      -cl,--command_line      Read instructions from the command line instead of from an input file.
+      -p, --profile           Profile the run through cProfiler.
+```
+
+```
+🔥 firecode_opt [-h] [-i] [-t TEMPERATURE] [-c CALCULATOR] [-m METHOD] [-s SOLVENT] [-o] [-f] [--ts] [--irc] [--cfile CFILE] [-n] [--debug]
+                    filenames [filenames ...]
+
+positional arguments:
+  filenames             Input filename(s), in .xyz format
+
+options:
+  -h, --help            show this help message and exit
+  -i, --interactive     Set options interactively.
+  -t TEMPERATURE, --temperature TEMPERATURE
+                        Temperature, in degrees Celsius.
+  -c CALCULATOR, --calculator CALCULATOR
+                        Calculator (default UMA).
+  -m METHOD, --method METHOD
+                        Method (default OMOL for UMA).
+  -s SOLVENT, --solvent SOLVENT
+                        Solvent (default ch2cl2).
+  -o, --opt             Optimize the geometry.
+  -f, --freq            Perform vibrational analysis.
+  --ts, --saddle        Optimize to a TS.
+  --irc                 Run an IRC calculation.
+  --cfile CFILE         Uses a constraint file.
+  -n, --newfile         Write optimized structure to a new file (*_opt.xyz).
+  --debug               Does not delete optimization data.
+```
+
+## Documentation
+Documentation on how to install and use the program can be found on [readthedocs](https://firecode.readthedocs.io/en/latest/index.html).

firecode-2.0.0/README.md

@@ -0,0 +1,120 @@
+
+# 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)
+[![Powered by: Pixi](https://img.shields.io/badge/Powered_by-Pixi-facc15)](https://pixi.sh)
+![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)
+[![codecov](https://codecov.io/gh/ntampellini/FIRECODE/graph/badge.svg?token=D9TM6S33D8)](https://codecov.io/gh/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 a computational chemistry workflow driver and hub for the generation, optimization and refinement of conformational ensembles, including  transition state and thermochemical utilities.
+
+
+
+<!-- It runs flexible workflows for conformer generation (via [CREST](https://github.com/crest-lab/crest), [RDKit](https://github.com/rdkit/rdkit)), double-ended TS search ([NEB](https://ase-lib.org/ase/neb.html) via [ASE](https://github.com/rosswhitfield/ase), [ML-FSM](https://github.com/thegomeslab/ML-FSM)), and (constrained) ensemble optimization through popular calculators like [XTB](https://github.com/grimme-lab/xtb), [TBLITE](https://github.com/tblite/tblite), [ORCA](https://www.orcasoftware.de/tutorials_orca/), and Pytorch Neural Network models ([AIMNET2](https://github.com/isayevlab/AIMNet2), [UMA](https://huggingface.co/facebook/UMA)) via [ASE](https://github.com/rosswhitfield/ase).
+
+Conformational pruning is performed with the now standalone [PRISM Pruner](https://github.com/ntampellini/prism_pruner).
+
+As a legacy feature from [TSCoDe](https://github.com/ntampellini/TSCoDe), FIRECODE can also assemble non-covalent adducts from conformational ensembles (embedding) programmatically. -->
+
+## Calculators
+
+- [xTB](https://github.com/grimme-lab/xtb) *(native)*
+- [tblite](https://github.com/tblite/tblite) *(via [ASE](https://github.com/rosswhitfield/ase))*
+- [AIMNET2](https://github.com/isayevlab/AIMNet2) *(via [ASE](https://github.com/rosswhitfield/ase))*
+- [UMA](https://huggingface.co/facebook/UMA) *(via [ASE](https://github.com/rosswhitfield/ase))*
+
+## Interfaces / utilities
+
+- [CREST](https://github.com/crest-lab/crest) *(conformational search)*
+- [GOAT](https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.202500393) *(conformational search)*
+- [racerts](https://github.com/digital-chemistry-laboratory/racerts) *(conformational search)*
+- [ETKDG](https://pubs.acs.org/doi/10.1021/acs.jcim.0c00025) *(via [rdkit](https://github.com/rdkit/rdkit), conformational search)*
+- [TSCoDe](https://github.com/ntampellini/TSCoDe) *(conformational embedding)*
+- [prism_pruner](https://github.com/ntampellini/prism_pruner) *(conformational pruning)*
+- [ML-FSM](https://pubs.acs.org/doi/10.1021/acs.jcim.0c00025) *(two-ended TS search)*
+- [Sella](https://github.com/zadorlab/sella) *(saddle point optimization)*
+<!-- - [packmol](https://github.com/m3g/packmol) *(explicit solvation)* -->
+
+...plus frequency calculation, NEB optimization, and more are all implemented in the code in a calculator-agnostic way.
+
+## Installation
+
+The package is distributed via `pip`, and the use of [`uv`](https://docs.astral.sh/uv/) is highly recommended. The default installation is minimalistic, and torch/GPU support requires dedicated installs:
+
+```python
+uv pip install firecode           # XTB, TBLITE, ORCA
+uv pip install firecode[aimnet2]  # + AIMNET2
+uv pip install firecode[uma]      # + UMA/OMOL
+uv pip install firecode[full]     # + AIMNET2, UMA/OMOL
+```
+
+More installation details in the documentation.
+
+## Usage
+
+Installation exposes the main program working on a plain text file as well as a standalone optimizer.
+
+```
+🔥 firecode [-h] [-s] [-t] input.txt [-n NAME] [-p]
+
+    positional arguments:
+      inpufile.txt            Input filename, can be any text file.
+
+    optional arguments:
+      -h, --help              Show this help message and exit.
+      -s, --setup             Guided setup of the calculation settings.
+      -n, --name NAME         Specify a custom name for the run.
+      -cl,--command_line      Read instructions from the command line instead of from an input file.
+      -p, --profile           Profile the run through cProfiler.
+```
+
+```
+🔥 firecode_opt [-h] [-i] [-t TEMPERATURE] [-c CALCULATOR] [-m METHOD] [-s SOLVENT] [-o] [-f] [--ts] [--irc] [--cfile CFILE] [-n] [--debug]
+                    filenames [filenames ...]
+
+positional arguments:
+  filenames             Input filename(s), in .xyz format
+
+options:
+  -h, --help            show this help message and exit
+  -i, --interactive     Set options interactively.
+  -t TEMPERATURE, --temperature TEMPERATURE
+                        Temperature, in degrees Celsius.
+  -c CALCULATOR, --calculator CALCULATOR
+                        Calculator (default UMA).
+  -m METHOD, --method METHOD
+                        Method (default OMOL for UMA).
+  -s SOLVENT, --solvent SOLVENT
+                        Solvent (default ch2cl2).
+  -o, --opt             Optimize the geometry.
+  -f, --freq            Perform vibrational analysis.
+  --ts, --saddle        Optimize to a TS.
+  --irc                 Run an IRC calculation.
+  --cfile CFILE         Uses a constraint file.
+  -n, --newfile         Write optimized structure to a new file (*_opt.xyz).
+  --debug               Does not delete optimization data.
+```
+
+## Documentation
+Documentation on how to install and use the program can be found on [readthedocs](https://firecode.readthedocs.io/en/latest/index.html).

{firecode-1.5.3 → firecode-2.0.0}/firecode/__main__.py

@@ -14,24 +14,31 @@ GNU General Public License for more details.
 
 https://github.com/ntampellini/firecode
 
-Nicolo' Tampellini - nicolo.tampellini@yale.edu
+Nicolo' Tampellini - ntamp@mit.edu
 
 """
 
 import argparse
 import os
 import sys
+from io import TextIOWrapper
 
 from rich.traceback import install
 
 install(show_locals=True)
 
 
-def main():
-    usage = """\n\n    🔥 python -m firecode [-h] [-s] [-t] input.txt [-n NAME] [-p]
-    🔥 python -m firecode -cl "refine> mtd> mol.xyz"
-    🔥 python -m firecode -c
-    🔥 python -m firecode -o mol.xyz
+def main() -> None:
+    # Redirect stdout and stderr to handle encoding errors
+    sys.stdout = TextIOWrapper(
+        sys.stdout.buffer, encoding="utf-8", errors="replace", write_through=True
+    )
+
+    sys.stderr = TextIOWrapper(
+        sys.stdout.buffer, encoding="utf-8", errors="replace", write_through=True
+    )
+
+    usage = """\n\n    🔥 firecode [-h] [-s] [-t] input.txt [-n NAME] [-p]
 
         positional arguments:
           inpufile.txt            Input filename, can be any text file.
@@ -39,12 +46,9 @@ def main():
         optional arguments:
           -h, --help              Show this help message and exit.
           -s, --setup             Guided setup of the calculation settings.
-          -t, --test              Perform some tests to check the software setup.
           -n, --name NAME         Specify a custom name for the run.
           -cl,--command_line      Read instructions from the command line instead of from an input file.
-          -c, --cite              Print citation links.
           -p, --profile           Profile the run through cProfiler.
-          -o, --optimize FILE     Run a standalone structure optimization tool.
 
           """
 
@@ -52,9 +56,6 @@ def main():
     parser.add_argument(
         "-s", "--setup", help="Guided setup of the calculation settings.", action="store_true"
     )
-    parser.add_argument(
-        "-t", "--test", help="Perform some tests to check the software setup.", action="store_true"
-    )
     parser.add_argument(
         "-cl",
         "--command_line",
@@ -71,13 +72,6 @@ def main():
     parser.add_argument(
         "-n", "--name", help="Specify a custom name for the run.", action="store", required=False
     )
-    parser.add_argument(
-        "-c",
-        "--cite",
-        help="Print the appropriate document links for citation purposes.",
-        action="store_true",
-        required=False,
-    )
     parser.add_argument(
         "-p",
         "--profile",
@@ -85,21 +79,13 @@ def main():
         action="store_true",
         required=False,
     )
-    parser.add_argument(
-        "-o",
-        "--optimize",
-        help="Run a standalone structure optimization tool.",
-        action="store",
-        required=False,
-        nargs="+",
-    )
 
     args = parser.parse_args()
 
-    if (
-        not (args.test or args.setup or args.command_line or args.optimize)
-    ) and args.inputfile is None:
-        parser.error("One of the following arguments are required: inputfile, -t, -s, -o.\n")
+    env_variables_handling()
+
+    if (not (args.setup or args.command_line)) and args.inputfile is None:
+        parser.error("One of the following arguments are required: inputfile, -t, -s.\n")
 
     if args.setup:
         from firecode.modify_settings import run_setup
@@ -107,24 +93,6 @@ def main():
         run_setup()
         sys.exit(0)
 
-    if args.cite:
-        print(
-            "No citation link is available for FIRECODE yet. You can link to the code on https://www.github.com/ntampellini/firecode"
-        )
-        sys.exit(0)
-
-    if args.test:
-        from firecode.tests import run_tests
-
-        run_tests()
-        sys.exit(0)
-
-    if args.optimize:
-        from firecode.standalone_optimizer import main
-
-        main(args.optimize)
-        sys.exit(0)
-
     if args.command_line:
         filename = "input_firecode.txt"
         with open(filename, "w") as f:
@@ -149,5 +117,49 @@ def main():
     # run the program
 
 
+def env_variables_handling() -> None:
+    """Handles global environment variables and associated processes.
+
+    Priority should be given to handling env vars with locally-scoped
+    context managers, if possible (see the env_override function).
+    """
+    from pathlib import Path
+    from shutil import rmtree
+
+    # remove compilation cache for jax: we might be running on different
+    # hardware from the last firecode run, and that might result in nasty
+    # compatibility issues with stale compilation of the jax library.
+    jax_comp_cache_dir = Path.home() / ".cache/sella/jax_cache"
+    rmtree(str(jax_comp_cache_dir), ignore_errors=True)
+
+    # export "FIRECODE_*" environment variables
+    from firecode.settings import ENV_VARS
+
+    for key, value in ENV_VARS.items():
+        os.environ.setdefault(key, value)
+
+    # override/add from global .firecoderc
+    if Path("~/.firecoderc").exists():
+        set_env_vars_from_file("~/.firecoderc")
+
+    # override/add from local .firecoderc
+    if ".firecoderc" in os.listdir(os.getcwd()):
+        set_env_vars_from_file(".firecoderc")
+
+
+def set_env_vars_from_file(filename: str) -> None:
+    """Set environment variable from a text file."""
+    with open(filename, "r") as f:
+        lines = f.readlines()
+
+    print(f"--> Setting environment variables from {filename}")
+    for line in lines:
+        key, value = line.split("=")
+        key = key.strip().upper()
+        value = value.strip()
+        os.environ[key] = value
+        print(f"  {key}={value}")
+
+
 if __name__ == "__main__":
     main()

firecode-2.0.0/firecode/algebra.py

@@ -0,0 +1,54 @@
+"""FIRECODE: Filtering Refiner and Embedder for Conformationally Dense Ensembles
+Copyright (C) 2021-2026 Nicolò Tampellini
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+"""
+
+import numpy as np
+from prism_pruner.algebra import normalize
+from scipy.spatial.distance import cdist
+
+from firecode.typing_ import Array1D_float, Array2D_float
+
+
+def point_angle(p1: Array1D_float, p2: Array1D_float, p3: Array1D_float) -> float:
+    """Returns the planar angle between three points in space, in degrees."""
+    return np.arccos(np.clip(normalize(p1 - p2) @ normalize(p3 - p2), -1.0, 1.0)) * 180 / np.pi  # type: ignore[no-any-return]
+
+
+def align_vec_pair(ref: Array2D_float, tgt: Array2D_float) -> Array2D_float:
+    """ref, tgt: iterables of two 3D vectors each
+
+    return: rotation matrix that when applied to tgt,
+            optimally aligns it to ref
+    """
+    B = np.zeros((3, 3))
+    for i in range(3):
+        for k in range(3):
+            tot = 0
+            for j in range(2):
+                tot += ref[j][i] * tgt[j][k]
+            B[i, k] = tot
+
+    u, s, vh = np.linalg.svd(B)
+
+    # Correct improper rotation if necessary (as in Kabsch algorithm)
+    if np.linalg.det(u @ vh) < 0:
+        s[-1] = -s[-1]
+        u[:, -1] = -u[:, -1]
+
+    return np.ascontiguousarray(np.dot(u, vh))
+
+
+def count_clashes(coords: Array2D_float) -> int:
+    """Returns the number of atomic distances between 0 and 0.5 Å."""
+    return int(np.count_nonzero((cdist(coords, coords) < 0.5) & (cdist(coords, coords) > 0)))