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

v0.7.1

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
• Added pdbqt doc specification from autodock manual by @joanimato in #376
• 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
• update docs to remove empty ligand for adgpu tethered tutorial3 by @diogomart in #406
• add template to monomer JSON encoder by @diogomart in #408
• update version strings to v0.7.1 by @diogomart in #409

New Contributors

• @k-ujihara made their first contribution in #328
• @Chryzl made their first contribution in #365
• @joanimato made their first contribution in #376
• @itaneja2 made their first contribution in #379

Full Changelog: v0.6.1...v0.7.1

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

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.