molli: A General-Purpose Python Toolkit for Combinatorial Small Molecule Library Generation, Manipulation, and Feature Extraction. DOI Creative Commons
Alexander S. Shved, Blake E. Ocampo, Elena S. Burlova

и другие.

Опубликована: Авг. 12, 2024

The construction, management and analysis of large in silico molecular libraries is critical many areas modern chemistry. Herein, we introduce the MOLecular LIibrary toolkit, “molli”, which a Python 3 cheminformatics module that provides streamlined interface for manipulating libraries. Three-dimensional, combinatorial molecule can be expanded directly from two-dimensional chemical structure fragments stored CDXML files with high stereochemical fidelity. Geometry optimization, property calculation, conformer generation are executed by interfacing widely used computational chemistry programs such as OpenBabel, RDKit, ORCA, NWChem, xTB/CREST. Conformer-dependent grid-based feature calculators provide numerical representation, to robust three-dimensional visualization tools comprehensive images enhance human understanding thousands members. package includes command-line addition classes streamline frequently workflows. Parallel performance benchmarked on various hardware platforms, common workflows demonstrated different tasks ranging optimized descriptor calculation catalyst an NMR shift prediction workflow files.

Язык: Английский

molli: A General-Purpose Python Toolkit for Combinatorial Small Molecule Library Generation, Manipulation, and Feature Extraction. DOI Creative Commons
Alexander S. Shved, Blake E. Ocampo, Elena S. Burlova

и другие.

Опубликована: Авг. 12, 2024

The construction, management and analysis of large in silico molecular libraries is critical many areas modern chemistry. Herein, we introduce the MOLecular LIibrary toolkit, “molli”, which a Python 3 cheminformatics module that provides streamlined interface for manipulating libraries. Three-dimensional, combinatorial molecule can be expanded directly from two-dimensional chemical structure fragments stored CDXML files with high stereochemical fidelity. Geometry optimization, property calculation, conformer generation are executed by interfacing widely used computational chemistry programs such as OpenBabel, RDKit, ORCA, NWChem, xTB/CREST. Conformer-dependent grid-based feature calculators provide numerical representation, to robust three-dimensional visualization tools comprehensive images enhance human understanding thousands members. package includes command-line addition classes streamline frequently workflows. Parallel performance benchmarked on various hardware platforms, common workflows demonstrated different tasks ranging optimized descriptor calculation catalyst an NMR shift prediction workflow files.

Язык: Английский

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