Literature DB >> 34240979

stk: An extendable Python framework for automated molecular and supramolecular structure assembly and discovery.

Lukas Turcani1, Andrew Tarzia1, Filip T Szczypiński1, Kim E Jelfs1.   

Abstract

Computational software workflows are emerging as all-in-one solutions to speed up the discovery of new materials. Many computational approaches require the generation of realistic structural models for property prediction and candidate screening. However, molecular and supramolecular materials represent classes of materials with many potential applications for which there is no go-to database of existing structures or general protocol for generating structures. Here, we report a new version of the supramolecular toolkit, stk, an open-source, extendable, and modular Python framework for general structure generation of (supra)molecular structures. Our construction approach works on arbitrary building blocks and topologies and minimizes the input required from the user, making stk user-friendly and applicable to many material classes. This version of stk includes metal-containing structures and rotaxanes as well as general implementation and interface improvements. Additionally, this version includes built-in tools for exploring chemical space with an evolutionary algorithm and tools for database generation and visualization. The latest version of stk is freely available at github.com/lukasturcani/stk.

Entities:  

Year:  2021        PMID: 34240979     DOI: 10.1063/5.0049708

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  5 in total

1.  Automated Rational Design of Metal-Organic Polyhedra.

Authors:  Aleksandar Kondinski; Angiras Menon; Daniel Nurkowski; Feroz Farazi; Sebastian Mosbach; Jethro Akroyd; Markus Kraft
Journal:  J Am Chem Soc       Date:  2022-06-22       Impact factor: 16.383

Review 2.  Computational Modeling of Supramolecular Metallo-organic Cages-Challenges and Opportunities.

Authors:  Tomasz K Piskorz; Vicente Martí-Centelles; Tom A Young; Paul J Lusby; Fernanda Duarte
Journal:  ACS Catal       Date:  2022-05-02       Impact factor: 13.700

3.  ChemSpaX: exploration of chemical space by automated functionalization of molecular scaffold.

Authors:  Adarsh V Kalikadien; Evgeny A Pidko; Vivek Sinha
Journal:  Digit Discov       Date:  2022-01-06

Review 4.  Unlocking the computational design of metal-organic cages.

Authors:  Andrew Tarzia; Kim E Jelfs
Journal:  Chem Commun (Camb)       Date:  2022-03-18       Impact factor: 6.222

5.  Conformer-RL: A deep reinforcement learning library for conformer generation.

Authors:  Runxuan Jiang; Tarun Gogineni; Joshua Kammeraad; Yifei He; Ambuj Tewari; Paul M Zimmerman
Journal:  J Comput Chem       Date:  2022-08-24       Impact factor: 3.672

  5 in total

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