firecode 1.5.1__tar.gz → 1.5.2__tar.gz

firecode-1.5.2/.ase/gui.py

@@ -0,0 +1 @@
+gui_default_settings["show_bonds"] = True

firecode-1.5.2/.coveragerc

@@ -0,0 +1,23 @@
+[run]
+source = prism_pruner
+omit = prism_pruner/__main__.py
+
+[report]
+exclude_lines =
+    # Have to re-enable the standard pragma
+    pragma: no cover
+
+    # Don't complain about missing debug-only code:
+    def __repr__
+    if self\.debug
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise AssertionError
+    raise NotImplementedError
+
+    # Don't complain if non-runnable code isn't run:
+    if 0:
+    if __name__ == .__main__.:
+
+    # Don't complain if an ellipsis isn't run (typically in an abstractmethod):
+    ^\s*\.\.\.

firecode-1.5.2/.github/workflows/test.yml

@@ -0,0 +1,46 @@
+name: Test
+
+on:
+  pull_request: {}
+  push:
+    branches:
+    - main
+    - feature/**
+
+jobs:
+  test:
+    strategy:
+      matrix:
+        python-version: ['3.12']
+        os: [ubuntu-latest]
+
+    name: Python ${{ matrix.os }} ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v5
+
+      # - uses: actions/setup-python@v6
+      #   with:
+      #     python-version: ${{ matrix.python-version }}
+
+      - uses: prefix-dev/setup-pixi@v0.9.4
+        with:
+          pixi-version: v0.63.2
+          cache: true
+          environments: dev
+          # locked: false
+          locked: true
+
+      - run: pixi install -e dev --locked
+      # - run: pixi run fmt
+      # - run: pixi run lint
+      # - run: pixi run types
+      - run: pixi run -e dev test_cov 
+
+      - name: Upload Coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          files: ./coverage.xml
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

firecode-1.5.2/.gitignore

@@ -0,0 +1,11 @@
+__pycache__/
+build/
+site/
+.vscode/
+.mypy_cache/
+firecode.egg-info/
+docs/
+
+firecode/calculators/uma-s-1p1.pt
+coverage.xml
+.coverage

firecode-1.5.2/.pre-commit-config.yaml

@@ -0,0 +1,43 @@
+exclude: '.pixi/'
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0  # this is optional, use `pre-commit autoupdate` to get the latest rev!
+  hooks:
+    - id: check-yaml
+    - id: check-toml
+    - id: end-of-file-fixer
+    - id: trailing-whitespace
+
+- repo: local
+  hooks:
+  - id: ruff
+    name: ruff-format
+    stages: [pre-commit, pre-push]
+    language: system
+    entry: pixi run fmt
+    types: [python]
+    pass_filenames: false
+
+  - id: ruff
+    name: ruff-check
+    stages: [pre-commit, pre-push]
+    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: pytest
+    name: pytest
+    stages: [pre-commit, pre-push]
+    language: system
+    entry: pixi run test
+    types: [python]
+    pass_filenames: false

{firecode-1.5.1 → firecode-1.5.2}/CHANGELOG.md

@@ -4,14 +4,20 @@
 <!-- - ... mep_relax> BETA
 - ... IMAGES kw, also implement it for neb>-->
 <!-- FINALSPLEVEL keyword? -->
+ <!-- add documentation: SCRAMBLECHECK kw, fsm>, neb>, rdkit_search>, standalone optimizer-->
 
-## FIRECODE 1.5.0 🔥 (WIP)
-- Implemented an interface to [ML-FSM](https://github.com/thegomeslab/ML-FSM/tree/main).
-- Removed openbabel dependency.
+## FIRECODE 1.5.2 🔥 (WIP)
+- Broken up installation into dedicated modules: minimal (`firecode`) and MLIPs (`firecode[aimnet2]`, `firecode[uma]`, `firecode[full]`)
+- Updated tests infrastructure and added CodeCov CI.
+
+## FIRECODE 1.5.1 🔥 (February 17 2026)
 - Imports bugfixes.
 - Restructured setup to use [Pixi](https://pixi.prefix.dev/latest/).
-- Removed SMILES to 3D conversion.
- <!-- add documentation: SCRAMBLECHECK kw, fsm>, neb>, rdkit_search>-->
+- Removed openbabel dependency.
+- Removed SMILES to 3D conversion with Openbabel.
+- Implemented an interface to [ML-FSM](https://github.com/thegomeslab/ML-FSM/tree/main) with the "fsm>" operator.
+- Added the "rdkit_search>" operator (ETKDGv3).
+- Updated the AIMNET2 interface, which now relies exclusively on the "aimnet[ase]" library (see [repository](https://github.com/isayevlab/aimnetcentral)).
 
 ## 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.
@@ -24,7 +30,7 @@
 ## FIRECODE 1.3.0 🔥 (December 15 2025)
 - Added [UMA](https://fair-chem.github.io/core/uma.html) as a calculator with Meta MLIPs, via ASE and the fairchem-core library. The model path needs to be specified in the settings.py file.
 - Polished the neb> and scan> operators to work in sequence (neb> scan> start.xyz i1 i2).
-- Added standalone structure optimizer, called with "python -m firecode -o mol.xyz".
+- Added standalone structure optimizer, called with "firecode -o mol.xyz".
 - Corrected behavior of fixed constraints with no specified distance, which before would relax. Now they are kept fixed at the initial distance.
 - Moved tests to their own folders.
 <!-- - Added free energy calculation via ASE vibrational analysis. -->
@@ -67,7 +73,7 @@
 - Informative suggestions: keywords that are not understood can generate suggestion of known keywords to use instead.
 - Removed rmsd library dependency for local numba numpy implementation.
 - Increased similarity_refining thresholds for the maximum number of structures to be compared: 1E5 for RMSD and MOI, 1E4 for rotationally corrected RMSD. Added printouts in log if we skip a pruning stage because the ensemble is too large.
-- Fixed a bug in _get_rotation_mask that would rotate the wrong part of the molecule (spotted because prune_by_rmsd_rot_corr would not reject some molecules that it should have) 
+- Fixed a bug in _get_rotation_mask that would rotate the wrong part of the molecule (spotted because prune_by_rmsd_rot_corr would not reject some molecules that it should have)
 - Added a debug messages printout function for the Pruner class, which by default is set to embedder.debuglog
 - Added support for AIMNET2 Pytorch models, including GPU support, with the package aimnet2-firecode. If a solvent is specified, the ALPB ΔGsolv (XTB) is added to the vacuum SP EE.
 - Removed support for the THREADS keyword and command line setting, as the number of workers in every multithreaded parallelism is now automated.
@@ -97,10 +103,10 @@
 - Various small bugfixes/graphic restyling
 - Stuctures are optimized at embedder.options.theory_level before running the mtd_search> operator, and a FatalError is raised if they scramble during this process. This increases the robustness of the workflow by avoiding changes in the molecular graph if the input structure is bad.
 - Added a warning printout system to the Embedder class, via logging and appending strings to the embedder.warnings list.
-- Added a saturation and compenetration check for input molecules, that warns about potential bad geometries. 
+- Added a saturation and compenetration check for input molecules, that warns about potential bad geometries.
 
 ## 0.4.10 (February 24, 2024)
-- Reduced/summarized printouts for loose to tight optimization steps. 
+- Reduced/summarized printouts for loose to tight optimization steps.
 <!-- - Removed call to compenetration_refining() on input ensemble: it is usually already pruned for compenetration for embed runs, and other ensembles (for example from "refine> mtd>" runs coming from CREST) benefit from relaxing eventual clashes that are present. -->
 
 ## 0.4.9 (February 22, 2024)
@@ -338,4 +344,4 @@
 - If pivots decrease during a bend, an exception is raised. Future versions might have a different behavior in this scenario.
 
 ## 0.0.1 (August 10, 2021)
-- First release
+- First release

{firecode-1.5.1 → firecode-1.5.2}/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.4
 Name: firecode
-Version: 1.5.1
+Version: 1.5.2
 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-Python: <3.13,>=3.12
 Requires-Dist: ase
 Requires-Dist: inquirerpy
 Requires-Dist: matplotlib
@@ -33,9 +33,11 @@ Description-Content-Type: text/markdown
 
 [![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/)
@@ -53,10 +55,26 @@ Description-Content-Type: text/markdown
 
 </p>
 
-*FIRECODE is the expanded successor of [TSCoDe](https://github.com/ntampellini/TSCoDe).* 
+FIRECODE is a computational chemistry workflow driver for the generation, optimization and refinement of conformational ensembles, also implementing some transition state ultilities.
 
-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).
+It implements flexible and customizable 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.
+
+## 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.
 
 ## Documentation
-Documentation on how to install and use the program can be found on [readthedocs](https://firecode.readthedocs.io/en/latest/index.html).
+Additional documentation on how to install and use the program can be found on [readthedocs](https://firecode.readthedocs.io/en/latest/index.html).

firecode-1.5.2/README.md

@@ -0,0 +1,52 @@
+
+# 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 for the generation, optimization and refinement of conformational ensembles, also implementing some transition state ultilities.
+
+It implements flexible and customizable 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.
+
+## 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.
+
+## Documentation
+Additional documentation on how to install and use the program can be found on [readthedocs](https://firecode.readthedocs.io/en/latest/index.html).

{firecode-1.5.1 → firecode-1.5.2}/firecode/__main__.py

@@ -1,7 +1,5 @@
 # coding=utf-8
-'''
-
-FIRECODE: Filtering Refiner and Embedder for Conformationally Dense Ensembles
+"""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
@@ -18,23 +16,23 @@ https://github.com/ntampellini/firecode
 
 Nicolo' Tampellini - nicolo.tampellini@yale.edu
 
-'''
+"""
+
 import argparse
 import os
 import sys
+
 from rich.traceback import install
+
 install(show_locals=True)
 
-__version__ = '1.5.0'
 
 def main():
-
-
-    usage = '''\n\n    🔥 python -m firecode [-h] [-s] [-t] input.txt [-n NAME] [-p]
+    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
-        
+
         positional arguments:
           inpufile.txt            Input filename, can be any text file.
 
@@ -48,46 +46,88 @@ def main():
           -p, --profile           Profile the run through cProfiler.
           -o, --optimize FILE     Run a standalone structure optimization tool.
 
-          '''
+          """
 
     parser = argparse.ArgumentParser(usage=usage)
-    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", help="Read instructions from the command line instead of from an input file.", action="store")
-    parser.add_argument("inputfile", help="Input filename, can be any text file.", action='store', nargs='?', default=None)
-    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", help="Profile the run through cProfiler.", action='store_true', required=False)
-    parser.add_argument("-o", "--optimize", help="Run a standalone structure optimization tool.", action='store', required=False, nargs='+')
+    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",
+        help="Read instructions from the command line instead of from an input file.",
+        action="store",
+    )
+    parser.add_argument(
+        "inputfile",
+        help="Input filename, can be any text file.",
+        action="store",
+        nargs="?",
+        default=None,
+    )
+    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",
+        help="Profile the run through cProfiler.",
+        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:
+    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")
 
     if args.setup:
         from firecode.modify_settings import run_setup
+
         run_setup()
-        sys.exit()
+        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()
+        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()
+        sys.exit(0)
 
     if args.optimize:
         from firecode.standalone_optimizer import main
+
         main(args.optimize)
-        sys.exit()
+        sys.exit(0)
 
     if args.command_line:
-        
-        filename = 'input_firecode.txt'
-        with open(filename, 'w') as f:
+        filename = "input_firecode.txt"
+        with open(filename, "w") as f:
             f.write(args.command_line)
 
         args.inputfile = filename
@@ -98,8 +138,9 @@ def main():
 
     if args.profile:
         from firecode.profiler import profiled_wrapper
+
         profiled_wrapper(filename, args.name)
-        sys.exit()
+        sys.exit(0)
 
     embedder = Embedder(filename, stamp=args.name)
     # initialize embedder from input file
@@ -107,5 +148,6 @@ def main():
     embedder.run()
     # run the program
 
+
 if __name__ == "__main__":
-    main()
+    main()

{firecode-1.5.1 → firecode-1.5.2}/firecode/algebra.py

@@ -1,6 +1,4 @@
-'''
-
-FIRECODE: Filtering Refiner and Embedder for Conformationally Dense Ensembles
+"""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
@@ -13,7 +11,8 @@ 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
 
@@ -21,10 +20,8 @@ norm_of = np.linalg.norm
 
 
 def point_angle(p1, p2, p3):
-    '''
-    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
+    """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
 
 
 def kronecker_delta(i, j) -> int:
@@ -34,20 +31,18 @@ def kronecker_delta(i, j) -> int:
 
 
 def align_vec_pair(ref, tgt):
-    '''
-    ref, tgt: iterables of two 3D vectors each
-    
+    """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))
+    """
+    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
+                tot += ref[j][i] * tgt[j][k]
+            B[i, k] = tot
 
     u, s, vh = np.linalg.svd(B)
 
@@ -62,7 +57,7 @@ def align_vec_pair(ref, tgt):
 def cart_prod_idx(sizes: np.ndarray):
     """Generates ids tuples for a cartesian product"""
     assert len(sizes) >= 2
-    tuples_count  = np.prod(sizes)
+    tuples_count = np.prod(sizes)
     tuples = np.zeros((tuples_count, len(sizes)), dtype=np.int32)
     tuple_idx = 0
     # stores the current combination
@@ -91,9 +86,7 @@ def cart_prod_idx(sizes: np.ndarray):
 
 
 def vector_cartesian_product(x, y):
-    '''
-    Cartesian product, but with vectors instead of indices
-    '''
+    """Cartesian product, but with vectors instead of indices"""
     indices = cart_prod_idx(np.asarray((x.shape[0], y.shape[0]), dtype=np.int32))
     dim = x.shape[-1] if len(x.shape) > 1 else 1
     new_arr = np.zeros((*indices.shape, dim), dtype=x.dtype)
@@ -104,11 +97,10 @@ def vector_cartesian_product(x, y):
 
 
 def transform_coords(coords, rot, pos):
-    '''
-    Returns the rotated and tranlated
+    """Returns the rotated and tranlated
     coordinates. Slightly faster than
     Numpy, uses memory-contiguous arrays.
-    '''
+    """
     t = np.transpose(coords)
     m = rot @ t
     f = np.transpose(m)