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.

v0.3.0

• RDKit replaces OpenBabel
• tertiary amides are rotatable if the nitrogen substituents are different
• fix OpenBabel inconsistency in which some anilines were kept rigid (#7)
• fix incorrect typing of nitrogens with +1 formal charge (ccsb-scripps/AutoDock-Vina#64)
• add Boron atom type
• aromatic sulfur now type S instead of SA (not H-bond acceptor anymore)
• drop pH option from MoleculePreparation

v0.2

• Bug fixes
• Add PDBQTMolecule and other post-docking analysis code
• SMARTS based atom typing
• RDKit dependency
• SMILES string in PDBQT files to create RDKit molecules from docking results