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

v0.3.2 - bugfix large macrocycles

Another macrocycle bugfix.

Previously, rings larger than max_ring_size were added to the rigid_rings list. Bonds that belong to rings in the rigid_rings list are prevented from being broken. For large macrocycles, such as vancomycin, some rings larger than max_ring_size encompass smaller rings that must be broken. The bugfix consists in not adding rings larger than max_ring_size to the rigid_rings list. The rigid_rings list is exclusive for rings smaller than min_ring_size.

The behavior of max_ring_size in unchanged from the user perspective: rings larger than the specified value will not be opened. This is because rings larger than max_ring_size are not listed as breakable rings.

This bug came into existence after we started using an exhaustive set of rings instead of a smallest set of smallest rings (SSSR), after migrating from OpenBabel to RDKit.

v0.3.1

Macrocycle related bug fixes that arose from differences in ring perception between OpenBabel and RDKit.

Since RDKit does not return an SSSR (smallest set of smallest rings), some macrocycles were not opened. For example, for "c1cc2ccc1CCCCCCO2", each aliphatic carbon would be perceived as belonging to two rings, which would not happen under SSSR because benzene is the smallest ring. Then, no bonds would be broken because the algorithm refused to break bonds belonging to more than a single SSSR ring. The ring perception is now performed by an external algorithm (Hanser, Jauffret and Kaufmann) and the procedure to define the bonds to break was redesigned to work with a exhaustive set of rings instead of an SSSR.

Also the --pH command line option was removed from mk_prepare_ligand.py.