v0.7.0

What's Changed

• Use utility functions in jsonutils to fix #151 by @rwxayheee in #257
• Revision of default templates: Fixes and Disambiguation for inconsistent residue names in CHARMM by @rwxayheee in #256
• Add keyword argument rename_atoms to MoleculePreparation.prepare and make option avail in CLI script by @rwxayheee in #255
• Read Partial Charges from mol2 and SDF by @rwxayheee in #258
• docs: cli args override config file params by @diogomart in #265
• Format string in output file with plain line-ending character instead of os.linesep by @rwxayheee in #266
• don't max out substructure matches at 1000 by @diogomart in #270
• Catch prepare errors without interrupting batch processing by @rwxayheee in #272
• Remove dependencies from setup.py by @diogomart in #274
• Remove from class Ring the unused attributes to reduce overhead in molecule preparation by @rwxayheee in #276
• minor fixes and minor clean up by @diogomart in #289
• Adjust positions of hydrogen isotopes as if they were regular Hs by @rwxayheee in #296
• Introduce a base class for classes with JSON-interchange functions by @rwxayheee in #292
• add cycle_break attribute to molsetup Bond by @diogomart in #254
• Remove all uppercase types CL and BR from GPF file by @diogomart in #315
• Making Ala Gly Pro flexible doesn't raise error, simply writes to rigid part by @diogomart in #332
• Ranking passed templates by H_excess if tied with H_missing by @rwxayheee in #301
• Small Bugfixes in closed PR #259 by @rwxayheee in #325
• added function stitch from PR188, with options residues_to_add and bonds_to_use by @rwxayheee in #306
• add NumPy-style, Sphinx-compliant docstring to chemtempgen.py by @rwxayheee in #337
• Add capping group NHE to residue_chem_templates.json by @rwxayheee in #336
• Remove attribute MoleculeSetup.is_sidechain by @diogomart in #339
• Polymer from PQR by @rwxayheee in #285
• Improve test coverage for chemtempgen.py by @rwxayheee in #340
• espaloma torsion potentials in kcal/mol, not kJ/mol by @diogomart in #342
• --cache_templates for mk_prepare_receptor.py by @rwxayheee in #287
• Use warnings or logger rather than print by @k-ujihara in #328
• remove unused Atom.interaction_vectors by @diogomart in #346
• Forgive extra interresidue bonds by @diogomart in #347
• Fix mk_prepare_ligand.py --add_atom_types by @diogomart in #350
• add icode to BEGIN_RES by @diogomart in #349
• rigidify triple bonds (rigidify single bonds in single-triple-single) by @diogomart in #348
• support altloc B in PDB for mk_prepare_receptor.py --box_enveloping by @diogomart in #366
• Fix bond canonicalization bug in BondTyperLegacy for terminal triple bonds by @Chryzl in #365
• only single bonds are rotatable (mostly) by @diogomart in #361
• bugfix template matching for protonated NGLU by @diogomart in #374
• bugfix dihedrals overcounted by non-canonicalized atom indices by @diogomart in #375
• assign espaloma charges to single atom molecules by @diogomart in #377
• silly bug calling wrong mol by @itaneja2 in #379
• add vdW params for some metals to complement openff by @diogomart in #381
• Flexibilize then parameterize by @diogomart in #343
• (Fix #215) Update polymer/chorizo padded molecule with positions from adjacent residue when there are multiple bonds between a pair of residues by @rwxayheee in #341
• Gasteiger charges working for Iron-Sulfur clusters by @diogomart in #386
• Pass sdf as template (Fixes #385) by @allisonbarkdull in #389
• Rotatable terminal group option by @althea-hansel in #333
• better error msg when failing to write PDBQT with None atom_type by @diogomart in #395
• add template to monomer JSON encoder by @diogomart in #408

New Contributors

• @k-ujihara made their first contribution in #328
• @Chryzl made their first contribution in #365
• @itaneja2 made their first contribution in #379

Full Changelog: v0.6.1...v0.7.0