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

Abstract

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.