Science Score: 26.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
-
○Academic publication links
-
○Committers with academic emails
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (13.3%) to scientific vocabulary
Last synced: 11 months ago
·
JSON representation
Repository
Cheminformatics tools for astrochemistry
Basic Info
- Host: GitHub
- Owner: laserkelvin
- License: mit
- Language: Python
- Default Branch: main
- Size: 126 KB
Statistics
- Stars: 2
- Watchers: 1
- Forks: 1
- Open Issues: 1
- Releases: 1
Created over 4 years ago
· Last pushed over 4 years ago
Metadata Files
Readme
Changelog
Contributing
License
Citation
Authors
README.rst
============
Astrochem ML
============
.. image:: https://img.shields.io/pypi/v/astrochem_ml.svg
:target: https://pypi.python.org/pypi/astrochem_ml
.. image:: https://img.shields.io/travis/laserkelvin/astrochem_ml.svg
:target: https://travis-ci.com/laserkelvin/astrochem_ml
.. image:: https://readthedocs.org/projects/astrochem-ml/badge/?version=latest
:target: https://astrochem-ml.readthedocs.io/en/latest/?version=latest
:alt: Documentation Status
Doing astrochemistry with robots.
The `astrochem_ml` package is designed for bringing accessible cheminformatics to
astrochemical discovery. The main features, some of which are currently active
development, are interfaces to common operations using RDKit that are relevant
to astrochemistry, and pre-trained embedding models ready for machine learning
projects that combine molecules and astrophysics.
The plan is to deliver a general purpose library, in addition to providing a
command line interface to several common tasks.
* Free software: MIT license
* Documentation: https://astrochem-ml.readthedocs.io.
Installation
------------
Not yet on PyPI, and so for now you can install `astrochem_ml` via:
```pip install git+https://github.com/laserkelvin/astrochem_ml```
Features
--------
Molecule generation
===================
A significant amount of functionality wraps the `rdkit` package, the main library
for doing cheminformatics in Python. For all molecule interactions, we go back
and forth between the native `rdkit` objects and SMILES/SMARTS strings.
* Exhaustive isotopologue generation in SMILES
.. code-block:: python
>>> from astrochem_ml.smiles import isotopes
# exhaustively enumerate all possible combinations isotopologues
# user can set the threshold for natural abundance and whether
# to include hydrogens
>>> isotopes.generate_all_isos("c1ccccc1", explicit_h=False)
['c1[13cH]c[13cH][13cH][13cH]1', ... 'c1ccccc1', '[13cH]1[13cH][13cH][13cH][13cH][13cH]1','c1c[13cH][13cH][13cH]c1']
* Functional group substitutions
Replace substructures with other ones in a tree data structure!
.. code-block:: python
>>> from astrochem_ml.smiles import MoleculeGenerator
# randomly grow out possible structures starting from benzene,
# and iteratively replace structures with other functional groups
>>> benzene = MoleculeGenerator("c1ccccc1", substructs=["c", "cC#N", "cC=O", "cN"])
>>> benzene.grow_tree(50)
100%|██████████████████████████████████████████████████████████████████| 50/50 [00:00<00:00, 237.44it/s]
>>> print(benzene)
c1ccccc1
├── Nc1ccccc1
├── N#Cc1ccccc1
└── O=Cc1ccccc1
├── Nc1ccccc1C=O
│ └── N#Cc1ccccc1C=O
├── Nc1cccc(C=O)c1
│ ├── Nc1cccc(C=O)c1N
│ │ ├── Nc1c(C=O)ccc(C=O)c1N
│ │ ├── Nc1cc(C=O)cc(C=O)c1N
...
This provides a high level interface to view every structure generated,
and from which parent.
Credits
-------
This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
Owner
- Name: Kelvin Lee
- Login: laserkelvin
- Kind: user
- Location: Hillsboro, OR
- Company: Intel Corporation
- Website: https://laserkelvin.github.io
- Twitter: cmmmsubmm
- Repositories: 95
- Profile: https://github.com/laserkelvin
HPC AI/ML engineer at Intel AXG. Previously postdoc at MIT, CfA/SAO. Interests in astrochemistry and physical chemistry.
Citation (CITATION.cff)
GitHub Events
Total
Last Year
Committers
Last synced: over 3 years ago
All Time
- Total Commits: 74
- Total Committers: 1
- Avg Commits per committer: 74.0
- Development Distribution Score (DDS): 0.0
Top Committers
| Name | Commits | |
|---|---|---|
| Kelvin Lee | k****e@g****m | 74 |
Issues and Pull Requests
Last synced: over 1 year ago
All Time
- Total issues: 2
- Total pull requests: 1
- Average time to close issues: 2 minutes
- Average time to close pull requests: 1 minute
- Total issue authors: 1
- Total pull request authors: 1
- Average comments per issue: 0.5
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- laserkelvin (2)
Pull Request Authors
- laserkelvin (1)
Top Labels
Issue Labels
enhancement (1)
bug (1)
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 22 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 2
- Total maintainers: 1
pypi.org: astrochem-ml
Cheminformatics tools for astrochemistry
- Homepage: https://github.com/laserkelvin/astrochem_ml
- Documentation: https://astrochem-ml.readthedocs.io/
- License: MIT
-
Latest release: 0.1.1
published over 4 years ago
Rankings
Dependent packages count: 10.1%
Forks count: 22.7%
Stargazers count: 31.9%
Average: 35.3%
Downloads: 44.5%
Dependent repos count: 67.3%
Maintainers (1)
Last synced:
11 months ago
Dependencies
poetry.lock
pypi
- atomicwrites 1.4.0 develop
- attrs 21.2.0 develop
- backports.entry-points-selectable 1.1.1 develop
- black 21.11b0 develop
- cfgv 3.3.1 develop
- click 8.0.3 develop
- distlib 0.3.3 develop
- filelock 3.4.0 develop
- flake8 4.0.1 develop
- identify 2.3.6 develop
- iniconfig 1.1.1 develop
- mccabe 0.6.1 develop
- mypy-extensions 0.4.3 develop
- nodeenv 1.6.0 develop
- packaging 21.0 develop
- pathspec 0.9.0 develop
- platformdirs 2.4.0 develop
- pluggy 1.0.0 develop
- pre-commit 2.15.0 develop
- py 1.11.0 develop
- pycodestyle 2.8.0 develop
- pyflakes 2.4.0 develop
- pytest 6.2.5 develop
- pyyaml 6.0 develop
- regex 2021.11.10 develop
- toml 0.10.2 develop
- tomli 1.2.2 develop
- typing-extensions 4.0.0 develop
- virtualenv 20.10.0 develop
- anytree 2.8.0
- colorama 0.4.4
- joblib 1.1.0
- numpy 1.21.1
- periodictable 1.6.0
- pyparsing 3.0.6
- rdkit-pypi 2021.9.2.1
- scikit-learn 1.0.1
- scipy 1.6.1
- selfies 2.0.0
- six 1.16.0
- threadpoolctl 3.0.0
- tqdm 4.62.3
pyproject.toml
pypi
- black ^21.11b0 develop
- flake8 * develop
- pre-commit ^2.15.0 develop
- pytest ^6.2.4 develop
- anytree ^2.8.0
- periodictable ^1.6.0
- python ^3.8
- rdkit-pypi ^2021.9.2
- scikit-learn ^1.0.1
- selfies ^2.0.0
- tqdm ^4.62.3