v0.4.0 - flexible sidechains to RDKit mols

What's new

• Proper parsing of flexible sidechains and dockings with multiple simultaneous ligands
• Documentation for covalent docking. It consists of docking ligands as flexible sidechains, so translation and rotation do not take place. The only degrees of freedom are the rotatable bonds, and the input ligand is aligned with the protein by Meeko. This feature was present in v0.3.3.
• Renamed script mk_copy_coords.py to mk_export.py
• Changed license to LGPL-2.1

Fixes and other improvements

• Molecules with implicit hydrogens are skipped, warn if conformer not 3D
• API changes to RDKitMolCreate
• Fixed flexible_amides=True and PDBQTMolecule.__iter__
• Write docking energies to SDF