Major re-factorization in process. Main changes include:
Split PLComplex class into Ligand and Protein class.
Ligand is a wrapper around an rdkit molecule and provides methods to prepare ligands such as adding hydrogens and fixing its bond orders.
Protein represents a molecular system that can be a single structure or multiple structures from a MD trajectory. It makes use of the new Topology class.
The Topology class is a wrapper around an mdtraj topology.
New BindingSite classes handle extraction of the binding site and finding chemical features in it.
Note: Integration tests are not passing because the new methods and functions have not been implemented completely.
Description
Major re-factorization in process. Main changes include:
PLComplexclass intoLigandandProteinclass.Ligandis a wrapper around an rdkit molecule and provides methods to prepare ligands such as adding hydrogens and fixing its bond orders.Proteinrepresents a molecular system that can be a single structure or multiple structures from a MD trajectory. It makes use of the newTopologyclass.Topologyclass is a wrapper around an mdtraj topology.BindingSiteclasses handle extraction of the binding site and finding chemical features in it.Note: Integration tests are not passing because the new methods and functions have not been implemented completely.