Meeko

Restores reactive docking, which is disabled in prior v0.6.0.alphas.
Fixes a bug that broke compatibility with Ringtail (https://github.com/forlilab/Ringtail/issues/28)

Enhanced receptor preparation. More information to come soon.

Enhanced receptor preparation. More information to come soon.

Enhanced receptor preparation. More information to come soon.

**What's new**
- Support for reactive docking ([chemrxiv](https://chemrxiv.org/engage/chemrxiv/article-details/6466fa77f2112b41e9c960c5), [instructions](https://github.com/forlilab/Meeko#reactive-docking))
- Easier to define new atom types from SMARTS 56
- Minimal support for receptor preparation ([instructions](https://github.com/forlilab/Meeko#2-prepare-protein-pdbqt))
- [Modified API](https://github.com/forlilab/Meeko#api-changes-in-v05)

**Fixes and other improvements**
- refuses to write PDBQT with Nan and Inf charges by default 55
- wildcards accepted by `mk_export.py`, e.g. `mk_export.py *.dlg` 43
- option `-c` in `mk_export.py` writes SDF with top pose from each cluster from autodock-gpu 38
- set grid box size and center based on existing ligand efb14bc532170491fcbf66fcaf6f177cfab97a98
- handle H isotopes 39
- `mk_export.py` reads gzipped files
- fix bond typing in `PDBQTMolecule` for single atom molecules 57
- other minor fixes and improvements

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