v0.8.0

What's changed

• nagl charges from latest version of openff by @joanimato in #412
• feat: optionally move vdW volume when merging terminal atoms by @diogomart in #419
• Nagl charges by @joanimato in #420
• Fix: rotatable terminal groups use user-defined mk_config by @diogomart in #421
• feat: arg only_hs_with_coords exports mols with only Hs present in docking by @diogomart in #418
• fix: do not uniquify SMARTS matches by default (for OpenFF compat) by @diogomart in #424
• error message added if pdb res not built into rdkit mol by @itaneja2 in #426
• Move functions to parse residue IDs (from command line input) to utils by @diogomart in #429
• feat: inflexibilize polymer sidechains by @diogomart in #428
• fix: avoid likely RDKit issues in update_H_positions() by @diogomart in #433
• Feat: Add option to ignore https certificate for PDB download by @atillack in #434
• json receptors inputs for mk_prepare_receptor.py by @joanimato in #431
• Rename allow bad res by @diogomart in #414
• Docs anchored tutorial by @diogomart in #290
• feat: rewrite find_inter_mols_bonds function with faster kdtree implementation by @joanimato in #436
• Docs update by @joanimato in #437
• fix: Polymer.to_pdb() reads positions from MoleculeSetups, not Monomer.rdkit_mol by @diogomart in #438
• Precomputed charges by @joanimato in #435
• Fix pytest failing test by @joanimato in #441
• make forgiving of extra bonds optional by @diogomart in #383
• feat: add pytest workflow by @joanimato in #442
• docs: update installation instructions by @diogomart in #444
• feat: speed up (and rename) polymer.stitch function. by @joanimato in #443
• feat: added PR template by @joanimato in #447
• Template charges fix by @joanimato in #446
• allow polymer creation without suppling template and mk_prep by @joanimato in #445
• Update pull request template file location by @joanimato in #448
• fix: enable specifying openff version by @diogomart in #449
• chore: remove prints and progress bar from polymer by @diogomart in #450
• feat: package scofu1 config for mk_prepare_receptor.py --mk_config by @diogomart in #451
• fix: prevent division by zero in charge corrections by @diogomart in #452
• feat: gb mbondi parameters by @diogomart in #453
• docs: fix links to readthedocs by @diogomart in #455
• feat: add crippen values to molsetup by @diogomart in #456
• Consolidate gasteiger into ad4sol par by @diogomart in #457
• feat: exclude parameters in UniqAtomParams by @diogomart in #460
• feat: add copper (CU) to residue templates by @diogomart in #462
• fix: set covalent radious of Cu and K to zero by @diogomart in #463
• better help message for mk_prepare_receptor.py --add_templates by @diogomart in #464
• fix: support add_atom_types with multiple groups in load_atom_params by @diogomart in #465
• feat: crippen values as solvation parameters by @diogomart in #466
• fix: Polymer.to_rdkit_mol with user specified residues - thanks Andreas by @diogomart in #471
• Fix PDBQT writer formatting by @PabloPauling in #476
• feat: added bad_res_radius feature, allowing to specify cutoff distance by @joanimato in #474
• fix: bug fix in delete_bad_res_from_box_radius feature. padding was b… by @allisonbarkdull in #479
• feat: merge_these_atom_params by @diogomart in #469
• fix: Update add_rotamers_to_polymer_molsetup to work with current Monomers. by @atillack in #481
• fix: box_size needs to be defined because it is required by @joanimato in #482
• fix: use args.padding in --box_enveloping box branch by @JustinKyleKirkland in #487
• Adjacent padding by @joanimato in #486
• Fixes excessive verbosity of #492 by @diogomart in #493

New Contributors

• @atillack made their first contribution in #434
• @PabloPauling made their first contribution in #476
• @JustinKyleKirkland made their first contribution in #487

Full Changelog: v0.7.1...v0.8.0