molassembler¶
Molassembler is a C++ library that aims to facilitate conversions between Cartesian and graph representations of molecules. It provides the necessary functionality to represent a molecule as a graph, modify it in graph space, and generate new coordinates from graphs. It can capture the absolute configuration of inorganic molecules with multidentate and haptic ligands from Cartesian coordinates and enumerate non-superposable stereopermutations at non-terminal atoms and non-isotropic bonds at arbitrary local shapes ranging up to the icosahedron and cuboctahedron.
This is the documentation for molassembler’s Python bindings which bind the core functionality of the library for quick prototyping.
Core features¶
Molecules can be constructed from many types of information.
Stereocenters are treated in shapes ranging from monovacant tetrahedron all the way up to the icosahedron and cuboctahedron.
A high-temperature approximation is invoked by default to avoid considering inverting nitrogen centers as stereocenters, but this is optional. Even in the high-temperature approximation, nitrogen centers whose substituents form a strained cycle and hence do not invert rapidly are considered a stereocenter.
All stereocenter permutations are generated with relative statistical occurrence weights. Linking of ligands (denticity) is properly considered. Several classes of haptic ligands are supported.
Editing of molecules preservers chiral information by default, and is highly configurable.
Molecules can be canonicalized for fast isomorphism tests. Canonicalization can be customized to use subsets of the available information for vertex coloring if desired.
Ranking algorithms are nearly fully IUPAC Blue Book 2013 compliant, extended to larger symmetries.
Stochastic conformer generation with Distance Geometry
Directed conformer generation through enumeration of rotamers