{"id":13869925,"url":"https://github.com/lukasturcani/stk","last_synced_at":"2025-04-04T11:11:57.367Z","repository":{"id":31493379,"uuid":"125766929","full_name":"lukasturcani/stk","owner":"lukasturcani","description":"A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases.","archived":false,"fork":false,"pushed_at":"2024-03-28T15:56:50.000Z","size":46932,"stargazers_count":237,"open_issues_count":63,"forks_count":43,"subscribers_count":11,"default_branch":"master","last_synced_at":"2024-05-02T21:30:19.513Z","etag":null,"topics":["cheminformatics","chemistry","computational-chemistry","computational-science","materials-design","materials-discoveries","materials-science","materials-screening","molecular-evolution","molecular-modeling","molecular-structures","reactions"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/lukasturcani.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2018-03-18T20:57:46.000Z","updated_at":"2024-06-19T00:20:11.788Z","dependencies_parsed_at":"2023-11-09T16:26:48.651Z","dependency_job_id":"085d910d-1a29-4205-ba01-563631e442da","html_url":"https://github.com/lukasturcani/stk","commit_stats":{"total_commits":4460,"total_committers":15,"mean_commits":297.3333333333333,"dds":"0.11390134529147977","last_synced_commit":"80e138b6028a24b241219fbee6ddf22e7b32cbf4"},"previous_names":[],"tags_count":39,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lukasturcani%2Fstk","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lukasturcani%2Fstk/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lukasturcani%2Fstk/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lukasturcani%2Fstk/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lukasturcani","download_url":"https://codeload.github.com/lukasturcani/stk/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247166168,"owners_count":20894654,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["cheminformatics","chemistry","computational-chemistry","computational-science","materials-design","materials-discoveries","materials-science","materials-screening","molecular-evolution","molecular-modeling","molecular-structures","reactions"],"created_at":"2024-08-05T20:01:22.156Z","updated_at":"2025-04-04T11:11:57.333Z","avatar_url":"https://github.com/lukasturcani.png","language":"Python","funding_links":[],"categories":["Python","General Chemistry"],"sub_categories":[],"readme":":maintainers:\n  `lukasturcani \u003chttps://github.com/lukasturcani/\u003e`_,\n  `andrewtarzia \u003chttps://github.com/andrewtarzia/\u003e`_\n:documentation: https://stk.readthedocs.io\n:discord: https://discord.gg/zbCUzuxe2B\n\n.. figure:: docs/source/_static/stk.png\n\n.. image:: https://github.com/lukasturcani/stk/actions/workflows/tests.yml/badge.svg?branch=master\n  :target: https://github.com/lukasturcani/stk/actions?query=branch%3Amaster\n\n.. image:: https://readthedocs.org/projects/stk/badge/?version=latest\n  :target: https://stk.readthedocs.io\n\nOverview\n========\n\n``stk`` is a Python library which allows construction and\nmanipulation of complex molecules, as well as automatic\nmolecular design, and the creation of molecular, and molecular\nproperty, databases. The documentation of ``stk`` is available on\nhttps://stk.readthedocs.io and the project's Discord server can be\njoined through https://discord.gg/zbCUzuxe2B.\n\nInstallation\n============\n\nTo get ``stk``, you can install it with pip:\n\n.. code-block:: bash\n\n  pip install stk\n\nIf you would like to get updated when a new release of ``stk`` comes\nout, which happens pretty regularly, click on the ``watch`` button on\nthe top right corner of the GitHub page. Then select ``Releases only``\nfrom the dropdown menu.\n\nYou can see the latest releases here:\n\n  https://github.com/lukasturcani/stk/releases\n\nThere will be a corresponding release on ``pip`` for each release\non GitHub, and you can update your ``stk`` with:\n\n.. code-block:: bash\n\n  pip install stk --upgrade\n\nDeveloper Setup\n---------------\n\n1. Install `just`_.\n2. In a new virtual environment run:\n\n.. code-block:: bash\n\n  just dev\n\n3. Setup the `MongoDB`_ container (make sure ``docker`` is installed):\n\n.. code-block:: bash\n\n  just mongo\n\n4. Run code checks:\n\n.. code-block:: bash\n\n  just check\n\n\n.. _`just`: https://github.com/casey/just\n.. _`MongoDB`: https://www.mongodb.com/docs/manual/tutorial/install-mongodb-on-ubuntu/\n\nHow To Cite\n===========\n\nIf you use ``stk`` please cite\n\n  https://github.com/lukasturcani/stk\n\nand\n\n  https://aip.scitation.org/doi/10.1063/5.0049708\n\n\nPublications\n============\n\nabout stk\n---------\n\n* `stk: An Extendable Python Framework for Automated Molecular and\n  Supramolecular Structure Assembly and Discovery`__\n\n__ https://aip.scitation.org/doi/10.1063/5.0049708\n\n* Describing metal-organic cage usage: `Unlocking the computational design of metal–organic cages`__\n\n__ https://pubs.rsc.org/en/content/articlelanding/2022/CC/D2CC00532H\n\n* (Out of date) `stk: A Python Toolkit for Supramolecular Assembly`__\n  | chemrxiv__\n\n__ https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.25377\n__ https://chemrxiv.org/articles/STK_A_Python_Toolkit_for_Supramolecular_Assembly/6127826\n\nusing stk\n---------\n\n* Using stk for constructing larger numbers of coarse-grained models: `Systematic exploration of accessible topologies of cage molecules via minimalistic models`__\n\n__ https://pubs.rsc.org/en/content/articlelanding/2023/sc/d3sc03991a\n\n* `The effect of disorder in multi-component covalent organic frameworks`__\n\n__ https://pubs.rsc.org/en/content/articlehtml/2023/cc/d3cc01111a\n\n* `Tetramine Aspect Ratio and Flexibility Determine Framework Symmetry for Zn8L6 Self-Assembled Structures`__\n\n__ https://onlinelibrary.wiley.com/doi/10.1002/anie.202217987\n\n* `Orientational self-sorting in cuboctahedral Pd cages`__\n\n__ https://pubs.rsc.org/en/content/articlehtml/2022/sc/d2sc03856k\n\n* `Conformer-RL: A deep reinforcement learning library for conformer\n  generation`__\n\n__ https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.26984\n\n* `High-throughput Computational Evaluation of Low Symmetry Pd2L4\n  Cages to Aid in System Design`__\n\n__ https://onlinelibrary.wiley.com/doi/10.1002/anie.202106721\n\n* `Forecasting System of Computational Time of DFT/TDDFT Calculations\n  under the Multiverse Ansatz via Machine Learning and\n  Cheminformatics`__\n\n__ https://pubs.acs.org/doi/full/10.1021/acsomega.0c04981\n\n* `Using High-throughput Virtual Screening to Explore the\n  Optoelectronic Property Space of Organic Dyes; Finding\n  Diketopyrrolopyrrole Dyes for Dye-sensitized Water Splitting and\n  Solar Cells`__\n\n__ https://pubs.rsc.org/en/content/articlelanding/2021/SE/D0SE00985G#!divAbstract\n\n* `Accelerated Discovery of Organic Polymer Photocatalysts for Hydrogen\n  Evolution from Water through the Integration of Experiment and\n  Theory`__\n\n__ https://pubs.acs.org/doi/abs/10.1021/jacs.9b03591\n\n* `Structurally Diverse Covalent Triazine-Based Framework Materials for\n  Photocatalytic Hydrogen Evolution from Water`__\n\n__ https://pubs.acs.org/doi/full/10.1021/acs.chemmater.9b02825\n\n* `Mapping Binary Copolymer Property Space with Neural Networks`__\n\n__ https://pubs.rsc.org/ko/content/articlehtml/2019/sc/c8sc05710a\n\n* `An Evolutionary Algorithm for the Discovery of Porous Organic\n  Cages`__ | chemrxiv__\n\n__ https://pubs.rsc.org/en/content/articlelanding/2018/sc/c8sc03560a#!divAbstract\n__ https://chemrxiv.org/articles/An_Evolutionary_Algorithm_for_the_Discovery_of_Porous_Organic_Cages/6954557\n\n* `Machine Learning for Organic Cage Property Prediction`__\n  | chemrxiv__\n\n__ https://pubs.acs.org/doi/10.1021/acs.chemmater.8b03572\n__ https://chemrxiv.org/articles/Machine_Learning_for_Organic_Cage_Property_Prediction/6995018\n\n* `A High-Throughput Screening Approach for the Optoelectronic\n  Properties of Conjugated Polymers`__ | chemrxiv__\n\n__ https://pubs.acs.org/doi/abs/10.1021/acs.jcim.8b00256\n__ https://chemrxiv.org/articles/A_High-Throughput_Screening_Approach_for_the_Optoelectronic_Properties_of_Conjugated_Polymers/6181841\n\n* `Computationally-Inspired Discovery of an Unsymmetrical Porous\n  Organic Cage`__ | chemrxiv__\n\n__ https://pubs.rsc.org/en/content/articlelanding/2018/nr/c8nr06868b#!divAbstract\n__ https://chemrxiv.org/articles/Computationally-Inspired_Discovery_of_an_Unsymmetrical_Porous_Organic_Cage/6863684\n\n* `Maximising the Hydrogen Evolution Activity in Organic Photocatalysts\n  by co-Polymerisation`__\n\n__ https://pubs.rsc.org/en/Content/ArticleLanding/TA/2018/C8TA04186E#!divAbstract\n\n\nAcknowledgements\n================\n\nI began developing this code when I was working in the Jelfs group,\nhttp://www.jelfs-group.org/, whose members often provide me with\nvery valuable feedback, which I gratefully acknowledge.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flukasturcani%2Fstk","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flukasturcani%2Fstk","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flukasturcani%2Fstk/lists"}