# Nomodeco.py a normal mode decomposition tool
Nomodeco.py enables the automatic determination of an optimal internal coordinate set for a given molecular structure. Using the atomic coordinates of the given molecule Nomodeco.py constructs all possible primitive internal coordinates.
## Documentation
The following links provide further information and documentation about the package
[decomposing vibrations-docs](https://kemaloenen.github.io/decomposing-vibrations/)
## How to Use:
Nomodeco can be installed using pip:
```
pip install nomodeco
```
Make sure to use a python version >=3.12.5!
For further information and a version history see:
[Nomodeco on PyPI](https://pypi.org/project/nomodeco/)
Alternatively, Nomodeco can be installed using the [github-repository](https://github.com/KemalOenen/decomposing-vibrations). In the repository a enviroment.yml file is included which can be used to create a conda enviroment with python 3.12.5 and poetry installed.
```
conda env create -f enviroment.yml
```
Then using poetry the additional packages can be installed:
```
poetry update
```
With the usage of the enviroment.yml file also pymolpro is installed which runs jobs on the local molpro installation.
## Publication for further information:
Kemal Oenen, Dennis F. Dinu, Klaus R. Liedl; Determining internal coordinate sets for optimal representation of molecular vibration. J. Chem. Phys. 7 January 2024; 160 (1): 014104. https://doi.org/10.1063/5.0180657
Raw data
{
"_id": null,
"home_page": "https://github.com/KemalOenen/decomposing-vibrations",
"name": "nomodeco",
"maintainer": null,
"docs_url": null,
"requires_python": "<3.13,>=3.12.5",
"maintainer_email": null,
"keywords": "internal coordinates, quantum chemistry",
"author": "Kemal\u00d6nen",
"author_email": null,
"download_url": "https://files.pythonhosted.org/packages/af/67/6383d346d08acd3d17dfddffcb078ca4f6d10fc530d2e06fc3458466747d/nomodeco-0.2.6.tar.gz",
"platform": null,
"description": "# Nomodeco.py a normal mode decomposition tool\n\n\nNomodeco.py enables the automatic determination of an optimal internal coordinate set for a given molecular structure. Using the atomic coordinates of the given molecule Nomodeco.py constructs all possible primitive internal coordinates.\n\n## Documentation\n\nThe following links provide further information and documentation about the package\n\n[decomposing vibrations-docs](https://kemaloenen.github.io/decomposing-vibrations/)\n\n\n## How to Use:\n\nNomodeco can be installed using pip:\n\n```\npip install nomodeco\n```\n\nMake sure to use a python version >=3.12.5!\n\nFor further information and a version history see:\n\n[Nomodeco on PyPI](https://pypi.org/project/nomodeco/)\n\nAlternatively, Nomodeco can be installed using the [github-repository](https://github.com/KemalOenen/decomposing-vibrations). In the repository a enviroment.yml file is included which can be used to create a conda enviroment with python 3.12.5 and poetry installed.\n\n```\nconda env create -f enviroment.yml\n```\n\nThen using poetry the additional packages can be installed:\n\n```\npoetry update\n```\n\nWith the usage of the enviroment.yml file also pymolpro is installed which runs jobs on the local molpro installation.\n\n\n\n## Publication for further information:\nKemal Oenen, Dennis F. Dinu, Klaus R. Liedl; Determining internal coordinate sets for optimal representation of molecular vibration. J. Chem. Phys. 7 January 2024; 160 (1): 014104. https://doi.org/10.1063/5.0180657\n\n",
"bugtrack_url": null,
"license": null,
"summary": "a python package for the determination of optimal internal coordinate systems for molecular structures",
"version": "0.2.6",
"project_urls": {
"Homepage": "https://github.com/KemalOenen/decomposing-vibrations",
"Repository": "https://github.com/KemalOenen/decomposing-vibrations"
},
"split_keywords": [
"internal coordinates",
" quantum chemistry"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "1a3deaddc91c177c3a46810ae12d0d0f295112c8c12ca707db4a5fea7072d5fa",
"md5": "df7ae6ab4b3581196794f7afd5771e64",
"sha256": "831a88cb2a39157193ad6c72f90fccc8dbec7210e065ab0b9baf4608984b3a43"
},
"downloads": -1,
"filename": "nomodeco-0.2.6-py3-none-any.whl",
"has_sig": false,
"md5_digest": "df7ae6ab4b3581196794f7afd5771e64",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": "<3.13,>=3.12.5",
"size": 63877,
"upload_time": "2024-10-12T09:31:39",
"upload_time_iso_8601": "2024-10-12T09:31:39.098979Z",
"url": "https://files.pythonhosted.org/packages/1a/3d/eaddc91c177c3a46810ae12d0d0f295112c8c12ca707db4a5fea7072d5fa/nomodeco-0.2.6-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "af676383d346d08acd3d17dfddffcb078ca4f6d10fc530d2e06fc3458466747d",
"md5": "7de6c3e1f158e35a11a5b808b4b3dfa1",
"sha256": "f1aeee57d0b63e6aa8716f1948b1353e4866575557eb32cdb37a39fc2acf9722"
},
"downloads": -1,
"filename": "nomodeco-0.2.6.tar.gz",
"has_sig": false,
"md5_digest": "7de6c3e1f158e35a11a5b808b4b3dfa1",
"packagetype": "sdist",
"python_version": "source",
"requires_python": "<3.13,>=3.12.5",
"size": 186673,
"upload_time": "2024-10-12T09:31:41",
"upload_time_iso_8601": "2024-10-12T09:31:41.090098Z",
"url": "https://files.pythonhosted.org/packages/af/67/6383d346d08acd3d17dfddffcb078ca4f6d10fc530d2e06fc3458466747d/nomodeco-0.2.6.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-10-12 09:31:41",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "KemalOenen",
"github_project": "decomposing-vibrations",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"requirements": [
{
"name": "ase",
"specs": [
[
"==",
"3.23.0"
]
]
},
{
"name": "black",
"specs": [
[
"==",
"24.8.0"
]
]
},
{
"name": "blessed",
"specs": [
[
"==",
"1.20.0"
]
]
},
{
"name": "Brotli",
"specs": []
},
{
"name": "certifi",
"specs": []
},
{
"name": "cffi",
"specs": []
},
{
"name": "charset-normalizer",
"specs": []
},
{
"name": "chemcoord",
"specs": []
},
{
"name": "click",
"specs": [
[
"==",
"8.1.7"
]
]
},
{
"name": "colorama",
"specs": []
},
{
"name": "contourpy",
"specs": []
},
{
"name": "cycler",
"specs": []
},
{
"name": "editor",
"specs": [
[
"==",
"1.6.6"
]
]
},
{
"name": "fonttools",
"specs": []
},
{
"name": "future",
"specs": []
},
{
"name": "gmpy2",
"specs": []
},
{
"name": "greenlet",
"specs": [
[
"==",
"3.1.0"
]
]
},
{
"name": "h2",
"specs": []
},
{
"name": "hpack",
"specs": [
[
"==",
"4.0.0"
]
]
},
{
"name": "hyperframe",
"specs": []
},
{
"name": "idna",
"specs": []
},
{
"name": "importlib_metadata",
"specs": []
},
{
"name": "importlib_resources",
"specs": []
},
{
"name": "inquirer",
"specs": [
[
"==",
"3.4.0"
]
]
},
{
"name": "jax",
"specs": [
[
"==",
"0.4.33"
]
]
},
{
"name": "jaxlib",
"specs": [
[
"==",
"0.4.33"
]
]
},
{
"name": "joblib",
"specs": []
},
{
"name": "kiwisolver",
"specs": []
},
{
"name": "latexcodec",
"specs": []
},
{
"name": "llvmlite",
"specs": [
[
"==",
"0.43.0"
]
]
},
{
"name": "lxml",
"specs": []
},
{
"name": "matplotlib",
"specs": [
[
"==",
"3.9.2"
]
]
},
{
"name": "mendeleev",
"specs": [
[
"==",
"0.17.0"
]
]
},
{
"name": "ml_dtypes",
"specs": [
[
"==",
"0.5.0"
]
]
},
{
"name": "monty",
"specs": []
},
{
"name": "mpmath",
"specs": []
},
{
"name": "munkres",
"specs": [
[
"==",
"1.1.4"
]
]
},
{
"name": "mypy-extensions",
"specs": [
[
"==",
"1.0.0"
]
]
},
{
"name": "ndim",
"specs": []
},
{
"name": "networkx",
"specs": []
},
{
"name": "numba",
"specs": []
},
{
"name": "numpy",
"specs": []
},
{
"name": "opt-einsum",
"specs": [
[
"==",
"3.3.0"
]
]
},
{
"name": "orthopy",
"specs": []
},
{
"name": "packaging",
"specs": []
},
{
"name": "palettable",
"specs": []
},
{
"name": "pandas",
"specs": []
},
{
"name": "pathspec",
"specs": [
[
"==",
"0.12.1"
]
]
},
{
"name": "pillow",
"specs": []
},
{
"name": "platformdirs",
"specs": [
[
"==",
"4.3.6"
]
]
},
{
"name": "plotly",
"specs": []
},
{
"name": "prompt-tool-kit",
"specs": [
[
"==",
"1.0.14"
]
]
},
{
"name": "prompt-toolkit",
"specs": [
[
"==",
"1.0.14"
]
]
},
{
"name": "PubChemPy",
"specs": [
[
"==",
"1.0.4"
]
]
},
{
"name": "pybtex",
"specs": []
},
{
"name": "pycparser",
"specs": []
},
{
"name": "pyfiglet",
"specs": [
[
"==",
"0.8.post1"
]
]
},
{
"name": "Pygments",
"specs": [
[
"==",
"2.18.0"
]
]
},
{
"name": "PyInquirer",
"specs": [
[
"==",
"1.0.3"
]
]
},
{
"name": "pymatgen",
"specs": []
},
{
"name": "pymolpro",
"specs": []
},
{
"name": "pyparsing",
"specs": []
},
{
"name": "pysjef",
"specs": []
},
{
"name": "PySocks",
"specs": []
},
{
"name": "python-dateutil",
"specs": []
},
{
"name": "python-inquirer",
"specs": [
[
"==",
"1.0.3"
]
]
},
{
"name": "pytz",
"specs": []
},
{
"name": "PyYAML",
"specs": []
},
{
"name": "quadpy",
"specs": []
},
{
"name": "readchar",
"specs": [
[
"==",
"4.2.0"
]
]
},
{
"name": "regex",
"specs": []
},
{
"name": "requests",
"specs": []
},
{
"name": "ruamel.yaml",
"specs": []
},
{
"name": "ruamel.yaml.clib",
"specs": []
},
{
"name": "runs",
"specs": [
[
"==",
"1.2.2"
]
]
},
{
"name": "scipy",
"specs": []
},
{
"name": "seaborn",
"specs": [
[
"==",
"0.13.2"
]
]
},
{
"name": "setuptools",
"specs": [
[
"==",
"73.0.1"
]
]
},
{
"name": "six",
"specs": []
},
{
"name": "sortedcontainers",
"specs": []
},
{
"name": "spglib",
"specs": []
},
{
"name": "SQLAlchemy",
"specs": [
[
"==",
"2.0.35"
]
]
},
{
"name": "sympy",
"specs": []
},
{
"name": "tabulate",
"specs": []
},
{
"name": "tenacity",
"specs": []
},
{
"name": "tqdm",
"specs": []
},
{
"name": "typing_extensions",
"specs": []
},
{
"name": "tzdata",
"specs": []
},
{
"name": "uncertainties",
"specs": []
},
{
"name": "urllib3",
"specs": []
},
{
"name": "wcwidth",
"specs": [
[
"==",
"0.2.13"
]
]
},
{
"name": "wheel",
"specs": [
[
"==",
"0.44.0"
]
]
},
{
"name": "xmod",
"specs": [
[
"==",
"1.8.1"
]
]
},
{
"name": "zipp",
"specs": []
},
{
"name": "zstandard",
"specs": [
[
"==",
"0.23.0"
]
]
}
],
"lcname": "nomodeco"
}
