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, poly-nuclear 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 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.Comment: 81 pages, 26 figures, 3 table