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