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Molassembler: Molecular Graph Construction, Modification, and Conformer Generation for Inorganic and Organic Molecules

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    Computational Chemistry

    Molassembler: Molecular Graph Construction, Modification, and Conformer Generation for Inorganic and Organic Molecules
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    Journal of Chemical Information and Modeling

    Cite this: J. Chem. Inf. Model. 2020, 60, 8, 3884–3900
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    https://doi.org/10.1021/acs.jcim.0c00503
    Published July 1, 2020
    Copyright © 2020 American Chemical Society
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    Abstract

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    We present the graph-based molecule software Molassembler for building organic and inorganic molecules. Molassembler provides algorithms for the construction of molecules built from any set of elements from the periodic table. In particular, polynuclear transition-metal complexes and clusters can be considered. Structural information is encoded as a graph. Stereocenter configurations are interpretable from Cartesian coordinates into an abstract index of permutation for an extensible set of polyhedral shapes. Substituents are distinguished through a ranking algorithm. Graph and stereocenter representations are freely modifiable, and the chiral state is propagated where possible through incurred ranking changes. Conformers are generated with full stereoisomer control by four spatial dimension Distance Geometry with a refinement error function including dihedral terms. Molecules are comparable by an extended graph isomorphism, and their representation is canonicalizeable. Molassembler is written in C++ and provides Python bindings.

    Copyright © 2020 American Chemical Society

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    • Shape classification, stereopermutation enumeration, and feasibility algorithm specifications; Derivative of Distance Geometry error function; and reproduction instructions for demonstration section (PDF)

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    Journal of Chemical Information and Modeling

    Cite this: J. Chem. Inf. Model. 2020, 60, 8, 3884–3900
    Click to copy citationCitation copied!
    https://doi.org/10.1021/acs.jcim.0c00503
    Published July 1, 2020
    Copyright © 2020 American Chemical Society
    Request reuse permissions

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