v0.6.1

Fix broken links to https://meeko.readthedocs.io in README.
Add parameter files to MANIFEST.in to have them installed from conda-forge and PyPI.

v0.6.0 - polymers

v0.6.0 introduces several major updates:

• refactored code for receptor preparation
• refactored core class, the MoleculeSetup and RDKitMoleculeSetup
• renamed LinkedRDKitChorizo to Polymer, and ChorizoResidue to Monomer
• several templates for nucleic acids
• automatically generate templates from the Chemical Component Dictionary (CCD)
• critical classes can be (de)serialized to/from JSON
• dropped openbabel, including the template option in mk_export.py
• handle alternate locations in receptor preparation
• export PDB of full receptor including docked positions of flexible sidechains

See the documentation at meeko.readthedocs.io

v0.5.1

What's Changed

• Update classifier by @fabaff in #119

New Contributors

• @fabaff made their first contribution in #119

Full Changelog: v0.5.0...v0.5.1

v0.6.0-alpha.3 - receptor prep

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

v0.6.0-alpha.2 - receptor prep

Enhanced receptor preparation. More information to come soon.

v0.6.0-alpha.1 - receptor prep

Enhanced receptor preparation. More information to come soon.

v0.6.0-alpha - receptor prep

Enhanced receptor preparation. More information to come soon.

v0.5.0 - reactive docking

What's new

• Support for reactive docking (chemrxiv, instructions)
• Easier to define new atom types from SMARTS #56
• Minimal support for receptor preparation (instructions)
• Modified API

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 efb14bc
• 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

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

v0.3.3 - bugfix cycle detection

Fixes bug that causes small cycles, such as 6-member rings, to be modeled flexibly without glue atoms (e.g. CG0/G0).

Example: O1CC2C(CC1)C1C(C2)CCCC1 sdf

First reported in ccsb-scripps/AutoDock-Vina#106

New feature: support for covalent docking