autogeom 0.0.1__tar.gz

autogeom-0.0.1/LICENSE

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+MIT License
+
+Copyright (c) Andreas V. Copan
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

autogeom-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: autogeom
+Version: 0.0.1
+Author: Andreas V. Copan, Troy N. Smith
+Author-email: Andreas V. Copan <avcopan@uga.edu>, Troy N. Smith <troy.smith@uga.edu>
+License-Expression: MIT
+License-File: LICENSE
+Requires-Dist: numpy>=2.2
+Requires-Dist: pint>=0.24
+Requires-Dist: py3dmol>=2.5
+Requires-Dist: pydantic>=2.9
+Requires-Dist: pyparsing>=3.3.2
+Requires-Dist: rdkit>=2025.3.3
+Requires-Dist: scipy>=1.15
+Requires-Dist: xyzrender>=0.3.8
+Requires-Python: >=3.13
+Project-URL: Repository, https://github.com/avcopan/autogeom
+Project-URL: Documentation, https://avcopan.github.io/autogeom/
+Description-Content-Type: text/markdown
+
+# autogeom
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/licenses/MIT)
+[![Pixi Badge](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/prefix-dev/pixi/main/assets/badge/v0.json)](https://pixi.sh)
+[![Code style: ruff](https://img.shields.io/badge/code%20style-ruff-000000.svg)](https://github.com/astral-sh/ruff)
+[![Typing: ty](https://img.shields.io/badge/typing-ty-EFC621.svg)](https://github.com/astral-sh/ty)
+[![Copier](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/copier-org/copier/master/img/badge/badge-grayscale-border.json)](https://github.com/copier-org/copier)
+
+autogeom is a Python library for 3D molecular structures. It centers on a single `Geometry` model (atomic symbols, Cartesian coordinates, charge, and spin) and the functions that operate on it: xyz I/O, measurements, transformations, alignment, 3D visualization, and conversions to and from InChI, SMILES, and RDKit.
+
+See the [documentation](https://avcopan.github.io/autogeom/) for the user guide and API reference.
+
+autogeom continues the `Geometry` part of [automol](https://github.com/avcopan/automol) 0.0.31 under a new name. See the [changelog](https://github.com/avcopan/autogeom/blob/main/CHANGELOG.md) for what changed.
+
+## Installation
+
+autogeom requires Python 3.13 or later.
+With [Pixi](https://pixi.sh), add it from the [`avcopan/automech`](https://prefix.dev/channels/avcopan/automech) channel on prefix.dev:
+
+```bash
+pixi workspace channel add https://repo.prefix.dev/avcopan/automech
+pixi add autogeom
+pixi add --pypi xyzrender  # optional: only on PyPI, needed for render_svg/render_gif
+```
+
+Or install it from PyPI, which includes xyzrender:
+
+```bash
+pip install autogeom  # or: uv add autogeom
+```
+
+For local development, see [Contributing](https://github.com/avcopan/autogeom/blob/main/CONTRIBUTING.md).
+
+## Usage
+
+Everything is imported from the package root.
+
+### Geometry
+
+```python
+import autogeom
+from autogeom import Geometry
+
+water = Geometry(
+    symbols=["O", "H", "H"],
+    coordinates=[[0.0, 0.0, 0.0], [0.0, 0.0, 0.96], [0.93, 0.0, -0.24]],
+    charge=0,
+    spin=0,
+)
+
+com = autogeom.center_of_mass(water)
+angle = autogeom.angle(water, [1, 0, 2], degrees=True)
+```
+
+### InChI, SMILES, and RDKit
+
+```python
+autogeom.inchi(water)  # "InChI=1S/H2O/h1H2"
+autogeom.smiles(water)  # "O"
+autogeom.formula(water)  # "H2O"
+
+ethanol = autogeom.from_smiles("CCO")  # embeds 3D coordinates
+mol = autogeom.rdkit_mol(ethanol)  # rdkit.Chem.Mol
+```
+
+### Visualization
+
+```python
+from autogeom import View
+
+# Visualization (e.g. in a Jupyter notebook)
+view = View()
+view.add_geometry(water, label=True)
+```
+
+In a notebook, a `Geometry` also displays itself as a 3D view.
+
+See the [documentation](https://avcopan.github.io/autogeom/) for more on geometries, conversions, and visualization.
+
+## Contributing
+
+Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change. See [Contributing](https://github.com/avcopan/autogeom/blob/main/CONTRIBUTING.md) for the design rules and workflow.
+
+## License
+
+This project is licensed under the [MIT License](https://github.com/avcopan/autogeom/blob/main/LICENSE).
+
+## Credits
+
+This package was created with [copier](https://copier.readthedocs.io/) and the [avcopan/copier-pixi-python](https://github.com/avcopan/copier-pixi-python) project template.

autogeom-0.0.1/README.md

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+# autogeom
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/licenses/MIT)
+[![Pixi Badge](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/prefix-dev/pixi/main/assets/badge/v0.json)](https://pixi.sh)
+[![Code style: ruff](https://img.shields.io/badge/code%20style-ruff-000000.svg)](https://github.com/astral-sh/ruff)
+[![Typing: ty](https://img.shields.io/badge/typing-ty-EFC621.svg)](https://github.com/astral-sh/ty)
+[![Copier](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/copier-org/copier/master/img/badge/badge-grayscale-border.json)](https://github.com/copier-org/copier)
+
+autogeom is a Python library for 3D molecular structures. It centers on a single `Geometry` model (atomic symbols, Cartesian coordinates, charge, and spin) and the functions that operate on it: xyz I/O, measurements, transformations, alignment, 3D visualization, and conversions to and from InChI, SMILES, and RDKit.
+
+See the [documentation](https://avcopan.github.io/autogeom/) for the user guide and API reference.
+
+autogeom continues the `Geometry` part of [automol](https://github.com/avcopan/automol) 0.0.31 under a new name. See the [changelog](https://github.com/avcopan/autogeom/blob/main/CHANGELOG.md) for what changed.
+
+## Installation
+
+autogeom requires Python 3.13 or later.
+With [Pixi](https://pixi.sh), add it from the [`avcopan/automech`](https://prefix.dev/channels/avcopan/automech) channel on prefix.dev:
+
+```bash
+pixi workspace channel add https://repo.prefix.dev/avcopan/automech
+pixi add autogeom
+pixi add --pypi xyzrender  # optional: only on PyPI, needed for render_svg/render_gif
+```
+
+Or install it from PyPI, which includes xyzrender:
+
+```bash
+pip install autogeom  # or: uv add autogeom
+```
+
+For local development, see [Contributing](https://github.com/avcopan/autogeom/blob/main/CONTRIBUTING.md).
+
+## Usage
+
+Everything is imported from the package root.
+
+### Geometry
+
+```python
+import autogeom
+from autogeom import Geometry
+
+water = Geometry(
+    symbols=["O", "H", "H"],
+    coordinates=[[0.0, 0.0, 0.0], [0.0, 0.0, 0.96], [0.93, 0.0, -0.24]],
+    charge=0,
+    spin=0,
+)
+
+com = autogeom.center_of_mass(water)
+angle = autogeom.angle(water, [1, 0, 2], degrees=True)
+```
+
+### InChI, SMILES, and RDKit
+
+```python
+autogeom.inchi(water)  # "InChI=1S/H2O/h1H2"
+autogeom.smiles(water)  # "O"
+autogeom.formula(water)  # "H2O"
+
+ethanol = autogeom.from_smiles("CCO")  # embeds 3D coordinates
+mol = autogeom.rdkit_mol(ethanol)  # rdkit.Chem.Mol
+```
+
+### Visualization
+
+```python
+from autogeom import View
+
+# Visualization (e.g. in a Jupyter notebook)
+view = View()
+view.add_geometry(water, label=True)
+```
+
+In a notebook, a `Geometry` also displays itself as a 3D view.
+
+See the [documentation](https://avcopan.github.io/autogeom/) for more on geometries, conversions, and visualization.
+
+## Contributing
+
+Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change. See [Contributing](https://github.com/avcopan/autogeom/blob/main/CONTRIBUTING.md) for the design rules and workflow.
+
+## License
+
+This project is licensed under the [MIT License](https://github.com/avcopan/autogeom/blob/main/LICENSE).
+
+## Credits
+
+This package was created with [copier](https://copier.readthedocs.io/) and the [avcopan/copier-pixi-python](https://github.com/avcopan/copier-pixi-python) project template.

autogeom-0.0.1/pyproject.toml

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+[project]
+name = "autogeom"
+version = "0.0.1"
+readme = "README.md"
+license = "MIT"
+license-files = ["LICENSE"]
+dependencies = [
+    "numpy>=2.2",
+    "pint>=0.24",
+    "py3dmol>=2.5",
+    "pydantic>=2.9",
+    "pyparsing>=3.3.2",
+    "rdkit>=2025.3.3",
+    "scipy>=1.15",
+    "xyzrender>=0.3.8",
+]
+requires-python = ">= 3.13"
+
+[[project.authors]]
+name = "Andreas V. Copan"
+email = "avcopan@uga.edu"
+
+[[project.authors]]
+name = "Troy N. Smith"
+email = "troy.smith@uga.edu"
+
+[project.urls]
+Repository = "https://github.com/avcopan/autogeom"
+Documentation = "https://avcopan.github.io/autogeom/"
+
+[build-system]
+build-backend = "uv_build"
+requires = ["uv_build"]
+
+[tool.ruff]
+extend-exclude = [".claude"]
+
+[tool.ruff.lint]
+select = ["ALL"]
+ignore = [
+    "COM812",
+    "TID252",
+    "D203",
+    "D213",
+    "CPY001",
+]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/**.py" = [
+    "S101",
+    "PLR2004",
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = "google"
+
+[tool.ty.environment]
+python = ".pixi/envs/test/bin/python"
+
+[tool.ty.src]
+include = [
+    "src",
+    "tests",
+]
+
+[tool.importlinter]
+root_package = "autogeom"
+
+[[tool.importlinter.contracts]]
+name = "Module Layering"
+type = "layers"
+layers = [
+    "autogeom._view | autogeom._convert",
+    "autogeom._transform",
+    "autogeom._measure",
+    "autogeom._trajectory",
+    "autogeom._geometry",
+    "autogeom.rd",
+    "autogeom.element | autogeom.types | autogeom.units",
+    "autogeom.exc",
+]
+ignore_imports = ["autogeom._geometry -> autogeom._view"]
+
+[tool.pytest.ini_options]
+testpaths = [
+    "tests",
+    "src",
+]
+addopts = [
+    "--doctest-modules",
+    "--cov=autogeom",
+    "--cov-report=term-missing",
+    "--cov-report=html",
+]
+doctest_optionflags = "NORMALIZE_WHITESPACE"
+
+[tool.coverage.run]
+branch = true
+source = ["autogeom"]
+
+[tool.coverage.report]
+show_missing = true
+skip_covered = true
+fail_under = 80

autogeom-0.0.1/pyproject.toml.orig

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+[project]
+name = "autogeom"
+version = "0.0.1"
+readme = "README.md"  # the PyPI page
+license = "MIT"
+license-files = ["LICENSE"]
+authors = [
+    {name = "Andreas V. Copan", email = "avcopan@uga.edu"},
+    {name = "Troy N. Smith", email = "troy.smith@uga.edu"},
+]
+dependencies = [
+    "numpy>=2.2",
+    "pint>=0.24",
+    "py3dmol>=2.5",
+    "pydantic>=2.9",
+    "pyparsing>=3.3.2",
+    "rdkit>=2025.3.3",  # earlier releases fail to embed allenes (C=C=C)
+    "scipy>=1.15",
+    "xyzrender>=0.3.8",
+]
+requires-python = ">= 3.13"
+
+[project.urls]
+Repository = "https://github.com/avcopan/autogeom"
+Documentation = "https://avcopan.github.io/autogeom/"
+
+[build-system]
+build-backend = "uv_build"
+requires = ["uv_build"]
+
+# Ruff configurations
+[tool.ruff]
+extend-exclude = [".claude"]  # vendored agent skills
+
+[tool.ruff.lint]
+select = ["ALL"]
+ignore = [
+    "COM812",   # missing trailing comma (handled by format)
+    "TID252",   # relative import
+    "D203",     # conflict: incorrect blank line before class (uses D211 instead)
+    "D213",     # conflict: multi-line summary second line (uses D212 instead)
+    "CPY001",   # copyright notice
+]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/**.py" = ["S101", "PLR2004"]  # assert, magic values
+
+[tool.ruff.lint.pydocstyle]
+convention = "google"
+
+# Ty configurations
+[tool.ty.environment]
+python = ".pixi/envs/test/bin/python"
+
+[tool.ty.src]
+include = [
+    "src",
+    "tests",
+]
+
+# Import-linter configurations
+[tool.importlinter]
+root_package = "autogeom"
+
+[[tool.importlinter.contracts]]
+name = "Module Layering"
+type = "layers"
+layers = [
+    "autogeom._view | autogeom._convert",
+    "autogeom._transform",
+    "autogeom._measure",
+    "autogeom._trajectory",
+    "autogeom._geometry",
+    "autogeom.rd",
+    "autogeom.element | autogeom.types | autogeom.units",
+    "autogeom.exc",
+]
+ignore_imports = [
+    # `Geometry._repr_html_` imports `view` lazily to render itself in Jupyter
+    "autogeom._geometry -> autogeom._view",
+]
+
+# Pytest configurations
+[tool.pytest.ini_options]
+testpaths = ["tests", "src"]
+addopts = [
+    "--doctest-modules",
+    "--cov=autogeom",
+    "--cov-report=term-missing",
+    "--cov-report=html",
+]
+doctest_optionflags = "NORMALIZE_WHITESPACE"
+
+# Pytest-cov configurations
+[tool.coverage.run]
+branch = true
+source = ["autogeom"]
+
+[tool.coverage.report]
+show_missing = true
+skip_covered = true
+fail_under = 80

autogeom-0.0.1/src/autogeom/__init__.py

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+"""Molecular geometries: the `Geometry` model and the functions that operate on it."""
+
+__version__ = "0.0.1"
+
+from . import element, rd, types
+from ._convert import (
+    formula,
+    from_inchi,
+    from_rdkit_mol,
+    from_smiles,
+    inchi,
+    rdkit_mol,
+    smiles,
+)
+from ._geometry import (
+    Geometry,
+    from_xyz_block,
+    from_xyz_file,
+    join,
+    remove_atoms,
+    select_atoms,
+    xyz_block,
+    xyz_file,
+)
+from ._measure import (
+    adjacency_matrix,
+    angle,
+    angles,
+    bonds,
+    center_of_mass,
+    dihedral,
+    dihedrals,
+    distance,
+    distance_keys,
+    distance_matrix,
+    inertia_tensor,
+    inertial_frame_rotation,
+    principal_axes,
+)
+from ._trajectory import (
+    from_xyz_trajectory_block,
+    from_xyz_trajectory_file,
+    xyz_trajectory_block,
+    xyz_trajectory_comments,
+    xyz_trajectory_file,
+)
+from ._transform import (
+    alignment_rotation,
+    axis_alignment_rotation,
+    center,
+    reflect,
+    rotate,
+    translate,
+    twist,
+    twist_angle,
+)
+from ._view import View, render_gif, render_svg, view
+from .exc import ElementNotFoundError, GeometryConversionError, XYZFormatError
+from .units import ureg
+
+__all__ = [
+    "ElementNotFoundError",
+    "Geometry",
+    "GeometryConversionError",
+    "View",
+    "XYZFormatError",
+    "adjacency_matrix",
+    "alignment_rotation",
+    "angle",
+    "angles",
+    "axis_alignment_rotation",
+    "bonds",
+    "center",
+    "center_of_mass",
+    "dihedral",
+    "dihedrals",
+    "distance",
+    "distance_keys",
+    "distance_matrix",
+    "element",
+    "formula",
+    "from_inchi",
+    "from_rdkit_mol",
+    "from_smiles",
+    "from_xyz_block",
+    "from_xyz_file",
+    "from_xyz_trajectory_block",
+    "from_xyz_trajectory_file",
+    "inchi",
+    "inertia_tensor",
+    "inertial_frame_rotation",
+    "join",
+    "principal_axes",
+    "rd",
+    "rdkit_mol",
+    "reflect",
+    "remove_atoms",
+    "render_gif",
+    "render_svg",
+    "rotate",
+    "select_atoms",
+    "smiles",
+    "translate",
+    "twist",
+    "twist_angle",
+    "types",
+    "ureg",
+    "view",
+    "xyz_block",
+    "xyz_file",
+    "xyz_trajectory_block",
+    "xyz_trajectory_comments",
+    "xyz_trajectory_file",
+]