Releases: ParmEd/ParmEd
Releases · ParmEd/ParmEd
ParmEd v4.3.0
What's Changed
- Fixed Improper Method Call: Replaced
mktempby @fazledyn-or in #1328 - Add support for 12-6-4 models. by @swails in #1346
- Fix wildcard sorting when writing Amber parameter sets (fixes #1347) by @murfalo in #1348
- Match tleap by ensuring parm{10|99|15}.dat are loaded no more than once by @murfalo in #1353
- Ignore TURN comments in PDBs by @slochower in #1351
- fix
SyntaxWarning: invalid escape sequenceby @njzjz in #1350 - Fix output of changeLJSingleType by @swails in #1355
- Bugfixed AtomType equality operator by @murfalo in #1360
- Fix the build wrt RDKit package issues by @swails in #1370
- Fixed compatibility with NumPy 2.0+ by @vedranmiletic in #1374
- Fix serialization of structure with bond type attributes and add test by @swails in #1376
- Ensure PBC box vectors are in reduced form for OpenMM by @nffaruk in #1368
- Improve mdin parsing to not split restraintmask fields using '=' wildcard char by @nffaruk in #1369
- Fix velocity unit scale for existing vels passed to OpenMM by @nffaruk in #1367
- Switch to non-deprecated miniforge by @swails in #1378
New Contributors
- @fazledyn-or made their first contribution in #1328
- @murfalo made their first contribution in #1348
- @slochower made their first contribution in #1351
- @vedranmiletic made their first contribution in #1374
Full Changelog: 4.2.2...4.3.0
Contributors
vedranmiletic, swails, and 5 other contributors
Assets 2
ParmEd v4.2.2
Contributors
swails
Assets 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
Contributors
swails and mattwthompson
Assets 2
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
Full Changelog: 4.1.0...4.2.0
Contributors
swails, jpthompson17, and 2 other contributors
Assets 2
ParmEd v4.1.0
What's Changed
- set
python_requiresto>=3.8by @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
Contributors
swails, peastman, and 6 other contributors
Assets 2
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
Contributors
swails, anabiman, and 9 other contributors
Assets 2
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
Contributors
swails and Valdes-Tresanco-MS
Assets 2
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.