ParmEd v4.2.2

What's Changed

• Fix setup.py by @swails in #1327

Full Changelog: 4.2.1...4.2.2

ParmEd v4.2.1

What's Changed

• Support Python 3.12 by @mattwthompson in #1325
• Fix usage of lru_cache for cache in py38 by @swails in #1326

Full Changelog: 4.2.0...4.2.1

ParmEd v4.2.0

What's Changed

• Added 3D-RISM and GBNSR6 to mdin configuration by @Valdes-Tresanco-MS in #1305
• Basic routines for internal to cartesian coordinate conversion by @bradakta in #1311
• Transfer chain IDs to OpenMM topology. by @jpthompson17 in #1310
• Add a library of all CCD residues separate from modified amino/nucleic acids by @swails in #1315
• Fix Python 3.8 support by @swails in #1319
• Preserve residue IDs, insertion codes, and bond orders in OpenMM topology conversions by @jpthompson17 in #1316

New Contributors

• @bradakta made their first contribution in #1311

Full Changelog: 4.1.0...4.2.0

ParmEd v4.1.0

What's Changed

• set python_requires to >=3.8 by @njzjz in #1285
• switch out copy with deepcopy for structure.copy() method by @daico007 in #1290
• Drude psf where NUMANISO is zero by @florianjoerg in #1274
• lonepair refinement by @JohannesKarwou in #1266
• Set atomic number when applying a patch by @peastman in #1275
• Prefer patch versions that replace external bonds by @peastman in #1278
• Enable changing C4 terms in LJ pairs individually by @KevinMei-Github in #1277
• Fix an error with mdin changing by @swails in #1299
• Fix bug with adding positional restraints for OpenMM (#1301) by @nffaruk in #1302
• Fix bug with restart reporter for OpenMM minimization by @nffaruk in #1303
• Preserve formal charges from PDB and CIF files if present over templates by @swails in #1304

New Contributors

• @njzjz made their first contribution in #1285
• @daico007 made their first contribution in #1290
• @florianjoerg made their first contribution in #1274
• @JohannesKarwou made their first contribution in #1266
• @KevinMei-Github made their first contribution in #1277
• @nffaruk made their first contribution in #1302

Full Changelog: 4.0.0...4.1.0

ParmEd v4.0.0

This is a major ParmEd release with some minor backwards-incompatible changes:

• Python support has been restricted to Python v3.8 and newer (dropping support for Python 2.7)
• Support OpenMM 7.5 and older has been dropped. The OpenMM integration will now require OpenMM 7.6 or newer.
• The xparmed GUI has been removed

What's Changed

• Check to make sure CHARMM patch doesn't create empty residue by @jchodera in #1139
• Major cleanup and remove Python 2 support by @swails in #1138
• Bug in Atom.umass by @anabiman in #1141
• Remove duplicate definition by @swails in #1144
• Add Entos converters and add support for LJ-PME in OpenMM by @swails in #1145
• Add DL poly writers by @swails in #1146
• Add citation for ParmEd to README by @swails in #1147
• Add atomic number guessing based on mass for PSF files. by @swails in #802
• Add some tests for the checkValidity command by @swails in #1148
• Fix a bug where parm.save() would convert to a ChamberParm if CMAPs were present, even though Amber has CMAPs now by @swails in #1152
• fix wrong dim in box estimation by @anabiman in #1165
• Improving parameterized inference by @anabiman in #1162
• missing check for DihedralType in Dihedral.funct by @anabiman in #1170
• Add explicit hydrogens when loading in SMILES by @justinGilmer in #1172
• Fix/openmm namespace change by @mikemhenry in #1176
• Allow some 1-4 interactions to be unscaled by @peastman in #1149
• Bump recursion limit by @swails in #1180
• Base unscaled pairs on all atoms in a torsion by @peastman in #1182
• Prototype for heterogenous mass repartitioning by @bradakstx in #1186
• Perceive external bonds (necessary for glycam ffxml conversion) by @zhang-ivy in #1184
• nbfix_symmetry - gromacs test skip by @tjwatson-stx in #1196
• Fix issue with colliding atom types in structure addition by @swails in #1199
• Try to fix osx builds more permanently by @swails in #1200
• Converted AMOEBA code to work with OpenMM 7.6 by @peastman in #1201
• reading gromacs topologies with insertion codes fixed by @Valdes-Tresanco-MS in #1219
• Reading a Gromacs topology fails with insertion code or negative number by @Valdes-Tresanco-MS in #1225
• PBRadii by @Valdes-Tresanco-MS in #1230
• Fix energy printout by @swails in #1232
• Fix AmberParm.from_structure with CMAPs by @swails in #1233
• Add support for more CHARMM force fields by @swails in #1157
• Add an RDKit export utility by @swails in #1252
• Fix bond order assignment in structure copying and slicing by @swails in #1256
• Ignore blank lines in mol2 by @adw62 in #1263
• Delete test_parmed_visualization.py by @swails in #1269
• Fix bug reported by Alex Sodt by @swails in #1281
• Improve CIF and PDB parsing and add informatics fields to Atom and Bond by @swails in #1284

New Contributors

• @anabiman made their first contribution in #1141
• @justinGilmer made their first contribution in #1172
• @mikemhenry made their first contribution in #1176
• @bradakstx made their first contribution in #1186
• @zhang-ivy made their first contribution in #1184
• @tjwatson-stx made their first contribution in #1196
• @adw62 made their first contribution in #1263

Full Changelog: 3.4.0...4.0.0

ParmEd v3.4.4

Bugs fixed

• reading gromacs topologies with insertion codes fixed by @Valdes-Tresanco-MS in #1220
• Do not force CMAPs to write a ChamberParm instance by @swails in #1224
• Reading a Gromacs topology fails with insertion code or negative number by @Valdes-Tresanco-MS in #1222
• New pb radii sets by @Valdes-Tresanco-MS in #1227
• Fix AmberParm.from_structure with CMAPs v3.4 by @swails in #1234
• Added 3D-RISM with sander to mdin by @Valdes-Tresanco-MS in #1239
• write PDB conect records for S-S bridges and HETATM by @Valdes-Tresanco-MS in #1240
• Fix bug for nbfix/chamber in ParmEd v3.4 by @swails in #1282

Full Changelog: 3.4.3...3.4.4

ParmEd v3.4.3

Finish ParmEd fixes for OpenMM 7.6 compatibility

ParmEd v3.4.2

Fix support for OpenMM 7.6

ParmEd v3.4.1

This point-release update adds support for 12-6-4 parameters for additional water models.

ParmEd v3.4.0

• #1082 - Add support for Drude particles in parameter file reading and writing
• #1132 - Fix file detection errors for large NetCDF files and fix issue where modified RNA residue names get modified when writing PDB files
• #1122 - Fix conversions to GROMACS files when NBFIX terms are present from either Amber or CHARMM