Data

Tools

Indexes

Applications

Experiments

Open Source Science

Recent Releases of parmed

parmed - ParmEd v4.2.2

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

- Python
Published by swails over 2 years ago

parmed - ParmEd v4.2.1

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

- Python
Published by swails over 2 years ago

parmed - ParmEd v4.2.0

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

- Python
Published by swails over 2 years ago

parmed - ParmEd v4.1.0

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 (ParmEd#1301) 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

- Python
Published by swails about 3 years ago

parmed - 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 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 testparmedvisualization.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

- Python
Published by swails over 3 years ago

parmed - ParmEd v3.4.4

Bugs fixed

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

Full Changelog: https://github.com/ParmEd/ParmEd/compare/3.4.3...3.4.4

- Python
Published by swails over 3 years ago

parmed - ParmEd v3.4.3

Finish ParmEd fixes for OpenMM 7.6 compatibility

- Python
Published by swails almost 5 years ago

parmed - ParmEd v3.4.2

Fix support for OpenMM 7.6

- Python
Published by swails almost 5 years ago

parmed - ParmEd v3.4.1

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

- Python
Published by swails about 5 years ago

parmed - 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

- Python
Published by swails over 5 years ago

parmed - ParmEd v3.3.0

  • #1079 - Fixes a rare divide-by-zero error sometimes seen with LMOD in Amber
  • #1072 - Make lxml an optional dependency by falling back to built-in xml module
  • #1035 - Fixes parsing PSF files that do not have an NNB section and some CHARMM -> GROMACS conversions
  • #1060 - Fixes Cl GB radius to match tleap
  • #1059 - Fixes PSF parsing when residue IDs are not strict integers
  • #1055 - Make the default PDB chain ID "Z" instead of "*"
  • #1054 - Fixes a DeprecationWarning when importing collection ABCs

- Python
Published by swails over 5 years ago

parmed - ParmEd v3.2.0

  • Started parsing, storing, and writing LINK records from PDB files in the PDB parser and writer
  • Improve handling of duplicate templates when converting to OpenMM force field/residue template XML files
  • Fix building C++ extensions on macOS Mojave systems with Anaconda or Miniconda Python
  • Fixes #1030 - Improve converting from OpenMM-generated force field systems to GROMACS files
  • Add parmed.read_pdb and parmed.write_pdb as aliases to parmed.read_PDB and parmed.write_PDB
  • Overhauled the PDB parser so it is more robust for official RCSB files (but drops some support for storing all of the data in non-conforming PDB files, although all atoms from those are still parsed)
  • Fixed CHARMM parameter parsers to avoid failing when reading unsupported parameters (only fails when trying to use them).
  • Added support to reading CMAP terms in Amber topology files

- Python
Published by swails about 7 years ago

parmed - ParmEd v3.1.0

There are a number of fixes to this release. In particular:

  • Fix building with PGI compilers
  • Fixes #979
  • Fixes #977
  • Fixes #915
  • Fixes #756, #840, and #952 (all the same bug)
  • Fixes #988
  • Fixes #993
  • Fixes #991 -- reading Amber topology files now releases the GIL for improved multithreading
  • Provides option to write all PDB atom records as ATOM instead of some as HETATM
  • Fixes #999
  • Fixes NBFIX handling in GROMACS topology files
  • Fixes #970
  • Fixes writing GROMACS GRO files so that it matches the reordering done in GROMACS topology files.

- Python
Published by swails over 7 years ago

parmed - ParmEd v3.0.3

A small bugfix release that fixes bond determination in PDB files and PDB file parsing for large files that use a base-36 number system when atom and residue counts pass the allowed limits in the PDB format.

This is the same version released as part of AmberTools 18

- Python
Published by swails over 8 years ago

parmed - ParmEd v3.0.1

This release fixes a handful of issues including:

  • Updates to work with the latest version of PyRosetta (thanks to @dww100)
  • Fixes to improve converting CHARMM parameter and topology files into OpenMM-compatible force field XML files (thanks to @jchodera)
  • Support for reading raw GROMACS ITP files (without a parent topology) (thanks to @SGenheden)
  • Fixes sign of torsional angle calculation (thanks to @SGenheden)
  • Fixes assigning constraints in OpenMM involving angles and for certain rigid waters (thanks to @nvidic)

Thanks to everyone for their help with this!

- Python
Published by swails over 8 years ago

parmed - Version 3.0.0

- Python
Published by swails over 8 years ago

parmed - ParmEd version 2.7.3

This is a small feature-enhancement release with one small fix - parmed.load_file and Structure.save convenience methods now work with file-like objects that support seek and tell operations - Copying or slicing a Structure preserves TER cards when writing to a PDB file - Atom type names are taken from OpenMM's Atom.id attribute where applicable

- Python
Published by swails over 9 years ago

parmed - ParmEd version 2.7.1

This release has improved support for converting between different formats, including OpenMM, Amber, CHARMM, and GROMACS.

It has numerous bug fixes, and all users are encouraged to upgrade to this version.

- Python
Published by swails over 9 years ago

parmed - ParmEd version 2.6.1

This is a minor bugfix release: - Fixes a nuisance parsing some PDB files with insertion codes and ANISOU records (#762)

- Python
Published by swails almost 10 years ago

parmed - ParmEd version 2.6.0

There are a number of improvements and bug fixes including: - Improved atomic number determination for mol2 files (#695) - Fix OFF file writing for solvent boxes (#702) - Fix bug in storing angle types for CHARMM systems (#704) - Eliminate severe performance degradation of OpenMM simulations with the NetCDF reporter (#722) - Support loading molecules from the rdkit package - Update for small changes to OpenMM API - Support native visualization through the nglview backend - Support reading SDF-format files (through rdkit)

And many other small improvements.

- Python
Published by swails almost 10 years ago

parmed - ParmEd version 2.5.1

- Python
Published by swails about 10 years ago

parmed - ParmEd v2.0.5

This is a major new stable release of ParmEd since version 1.1. An abbreviated list of changes and improvements are listed below: - Unified object model built on Structure that facilitates file format translations and integration with OpenMM - Support for reading and writing GROMACS topology and GRO files - Automatic file loading based on file contents (rather than filename extension) - Read many new file formats, including Mol2, GROMACS topology, GRO, PDBx/mmCIF, Amber OFF libraries, Amber parameter and leaprc files, CHARMM residue templates, OpenMM XML files, and more - Expressive selection syntax for slicing substructures and views of Structure - Flexible molecule splitting functionality within Structure - Support Python 2 and Python 3 in the same code base through the six module - Overhauled the coordinate and unit cell handling functionality, creating a unified interface for all objects based on the n-dimensional array in numpy - C++-accelerated Amber topology file reader - Abstract file reader capable of reading compressed and remote files (and remote compressed files) - Convenient Structure.save method that converts between different file formats automatically - Added gromber action to ParmEd interpreter to facilitate converting from GROMACS to AMBER file formats - Added ability to instantiate parametrized Structure from OpenMM Topology and System objects - Added robust unit handling and dimensional analysis through the unit package that is part of OpenMM - New package organization -- there is now a single subpackage parmed that contains all of the modules and packages. chemistry has been renamed parmed and ParmedTools has been moved to parmed.tools - Renamed scripts from parmed.py and xparmed.py to parmed and xparmed. - New, extensive API documentation generated automatically by Sphinx - Many bug fixes and stability improvements - Added serialization support (so that the objects in ParmEd can now be pickled)

This release brings some substantial changes and API stability. The major changes here that will affect users upgrading from older versions are 1. Python 2.7 or later is now required. Support for earlier versions of Python has been discontinued. 2. The numpy package is now required and is used for coordinate and unit cell handling 3. OpenMM support requires version 6.3 or later of the OpenMM library 4. The following packages have been renamed: - chemistry -> parmed - ParmedTools -> parmed.tools - ParmedTools.ParmedActions -> parmed.tools.actions

Making the above substitutions should be sufficient to fix existing scripts or programs to work with the newest version of ParmEd.

- Python
Published by swails over 10 years ago

parmed - ParmEd v. 2.0 Beta1

This is a major upgrade from the last release (version 1.1), and is also a substantial update from the version released with AmberTools 15. There have been over

This code is tested on Python 2.7, 3.3, and 3.4, and is expected to work for any later versions of Python 3.

Many big changes are enumerated below: - New package organization [1] - Support for reading and writing Gromacs topology files - Unified object model, permitting interconversion between file formats and integration with OpenMM for all of them - Support for reading more file formats (Amber OFF file, residue templates from CHARMM, mol2 files, PDBx/mmCIF -files, Gromacs GRO and topology files, and many more) - Flexible and powerful Structure manipulation features (fancy indexing of Structure, splitting, merging, and replicating Structure) - Accelerated Amber topology file reader - Arbitrary unit handling and dimensional analysis - Support Python 2 and Python 3 in the same code base without doing source code conversion - API and user documentation generated by Sphinx (http://parmed.github.io/ParmEd)

and many more...

[1] This release introduces a new Python package layout compared to previous releases. In particular, the chemistry package has been renamed to parmed, and the ParmedTools package has been renamed to parmed.tools.

A special thanks to Lee-Ping Wang and David Mobley for their help adding Gromacs support.

- Python
Published by swails about 11 years ago

parmed - ParmEd v1.1

This release adds a comprehensive test suite, a number of small bug fixes, and updated support for newer Amber force fields including: 1. The 12-6-4 potential for treating divalent metal ions 2. The ff14ipq force field that utilizes modified off-diagonal Lennard-Jones terms.

Also added is support for NBFIX modifications in CHARMM parameter and stream files. However, the long-range correction for these systems requires OpenMM 6.1 (not 6.0.1) or greater to use.

The APIs for the trajectory reporters are also significantly simplified, but this is a backwards-incompatible change.

- Python
Published by swails almost 12 years ago