Parmed

What's Changed
* Fix setup.py by swails in https://github.com/ParmEd/ParmEd/pull/1327


**Full Changelog**: https://github.com/ParmEd/ParmEd/compare/4.2.1...4.2.2

What's Changed
* Support Python 3.12 by mattwthompson in https://github.com/ParmEd/ParmEd/pull/1325
* Fix usage of lru_cache for cache in py38 by swails in https://github.com/ParmEd/ParmEd/pull/1326


**Full Changelog**: https://github.com/ParmEd/ParmEd/compare/4.2.0...4.2.1

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

New Contributors
* bradakta made their first contribution in https://github.com/ParmEd/ParmEd/pull/1311

**Full Changelog**: https://github.com/ParmEd/ParmEd/compare/4.1.0...4.2.0

What's Changed
* set `python_requires` to `>=3.8` by njzjz in https://github.com/ParmEd/ParmEd/pull/1285
* switch out copy with deepcopy for structure.copy() method by daico007 in https://github.com/ParmEd/ParmEd/pull/1290
* Drude psf where NUMANISO is zero by florianjoerg in https://github.com/ParmEd/ParmEd/pull/1274
* lonepair refinement by JohannesKarwou in https://github.com/ParmEd/ParmEd/pull/1266
* Set atomic number when applying a patch by peastman in https://github.com/ParmEd/ParmEd/pull/1275
* Prefer patch versions that replace external bonds by peastman in https://github.com/ParmEd/ParmEd/pull/1278
* Enable changing C4 terms in LJ pairs individually by KevinMei-Github in https://github.com/ParmEd/ParmEd/pull/1277
* Fix an error with mdin changing by swails in https://github.com/ParmEd/ParmEd/pull/1299
* Fix bug with adding positional restraints for OpenMM (ParmEd1301) by nffaruk in https://github.com/ParmEd/ParmEd/pull/1302
* Fix bug with restart reporter for OpenMM minimization by nffaruk in https://github.com/ParmEd/ParmEd/pull/1303
* Preserve formal charges from PDB and CIF files if present over templates by swails in https://github.com/ParmEd/ParmEd/pull/1304

New Contributors
* njzjz made their first contribution in https://github.com/ParmEd/ParmEd/pull/1285
* daico007 made their first contribution in https://github.com/ParmEd/ParmEd/pull/1290
* florianjoerg made their first contribution in https://github.com/ParmEd/ParmEd/pull/1274
* JohannesKarwou made their first contribution in https://github.com/ParmEd/ParmEd/pull/1266
* KevinMei-Github made their first contribution in https://github.com/ParmEd/ParmEd/pull/1277
* nffaruk made their first contribution in https://github.com/ParmEd/ParmEd/pull/1302

**Full Changelog**: https://github.com/ParmEd/ParmEd/compare/4.0.0...4.1.0

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 https://github.com/ParmEd/ParmEd/pull/1139
* Major cleanup and remove Python 2 support by swails in https://github.com/ParmEd/ParmEd/pull/1138
* Bug in Atom.umass by anabiman in https://github.com/ParmEd/ParmEd/pull/1141
* Remove duplicate definition by swails in https://github.com/ParmEd/ParmEd/pull/1144
* Add Entos converters and add support for LJ-PME in OpenMM by swails in https://github.com/ParmEd/ParmEd/pull/1145
* Add DL poly writers by swails in https://github.com/ParmEd/ParmEd/pull/1146
* Add citation for ParmEd to README by swails in https://github.com/ParmEd/ParmEd/pull/1147
* Add atomic number guessing based on mass for PSF files. by swails in https://github.com/ParmEd/ParmEd/pull/802
* Add some tests for the checkValidity command by swails in https://github.com/ParmEd/ParmEd/pull/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 https://github.com/ParmEd/ParmEd/pull/1152
* fix wrong dim in box estimation by anabiman in https://github.com/ParmEd/ParmEd/pull/1165
* Improving parameterized inference by anabiman in https://github.com/ParmEd/ParmEd/pull/1162
* missing check for DihedralType in Dihedral.funct by anabiman in https://github.com/ParmEd/ParmEd/pull/1170
* Add explicit hydrogens when loading in SMILES by justinGilmer in https://github.com/ParmEd/ParmEd/pull/1172
* Fix/openmm namespace change by mikemhenry in https://github.com/ParmEd/ParmEd/pull/1176
* Allow some 1-4 interactions to be unscaled by peastman in https://github.com/ParmEd/ParmEd/pull/1149
* Bump recursion limit by swails in https://github.com/ParmEd/ParmEd/pull/1180
* Base unscaled pairs on all atoms in a torsion by peastman in https://github.com/ParmEd/ParmEd/pull/1182
* Prototype for heterogenous mass repartitioning by bradakstx in https://github.com/ParmEd/ParmEd/pull/1186
* Perceive external bonds (necessary for glycam ffxml conversion) by zhang-ivy in https://github.com/ParmEd/ParmEd/pull/1184
* nbfix_symmetry - gromacs test skip by tjwatson-stx in https://github.com/ParmEd/ParmEd/pull/1196
* Fix issue with colliding atom types in structure addition by swails in https://github.com/ParmEd/ParmEd/pull/1199
* Try to fix osx builds more permanently by swails in https://github.com/ParmEd/ParmEd/pull/1200
* Converted AMOEBA code to work with OpenMM 7.6 by peastman in https://github.com/ParmEd/ParmEd/pull/1201
* reading gromacs topologies with insertion codes fixed by Valdes-Tresanco-MS in https://github.com/ParmEd/ParmEd/pull/1219
* Reading a Gromacs topology fails with insertion code or negative number by Valdes-Tresanco-MS in https://github.com/ParmEd/ParmEd/pull/1225
* PBRadii by Valdes-Tresanco-MS in https://github.com/ParmEd/ParmEd/pull/1230
* Fix energy printout by swails in https://github.com/ParmEd/ParmEd/pull/1232
* Fix AmberParm.from_structure with CMAPs by swails in https://github.com/ParmEd/ParmEd/pull/1233
* Add support for more CHARMM force fields by swails in https://github.com/ParmEd/ParmEd/pull/1157
* Add an RDKit export utility by swails in https://github.com/ParmEd/ParmEd/pull/1252
* Fix bond order assignment in structure copying and slicing by swails in https://github.com/ParmEd/ParmEd/pull/1256
* Ignore blank lines in mol2 by adw62 in https://github.com/ParmEd/ParmEd/pull/1263
* Delete test_parmed_visualization.py by swails in https://github.com/ParmEd/ParmEd/pull/1269
* Fix bug reported by Alex Sodt by swails in https://github.com/ParmEd/ParmEd/pull/1281
* Improve CIF and PDB parsing and add informatics fields to Atom and Bond by swails in https://github.com/ParmEd/ParmEd/pull/1284

New Contributors
* anabiman made their first contribution in https://github.com/ParmEd/ParmEd/pull/1141
* justinGilmer made their first contribution in https://github.com/ParmEd/ParmEd/pull/1172
* mikemhenry made their first contribution in https://github.com/ParmEd/ParmEd/pull/1176
* bradakstx made their first contribution in https://github.com/ParmEd/ParmEd/pull/1186
* zhang-ivy made their first contribution in https://github.com/ParmEd/ParmEd/pull/1184
* tjwatson-stx made their first contribution in https://github.com/ParmEd/ParmEd/pull/1196
* adw62 made their first contribution in https://github.com/ParmEd/ParmEd/pull/1263

**Full Changelog**: https://github.com/ParmEd/ParmEd/compare/3.4.0...4.0.0