tag:github.com,2008:https://github.com/ParmEd/ParmEd/releases 2025-06-18T09:45:24Z tag:github.com,2008:Repository/17307763/4.3.1 2026-01-12T14:20:20Z <p>Resolve issue/1386, fix `numpy.compat` deprecation warning (<a class="issue-link js-issue-link" href="https://github.com/ParmEd/ParmEd/pull/1387">#1387</a>)</p> <p>* Removed `numpy.compat` and added `asbytes` and `asstr`</p> <p>* Replaced FTP with HTTP requests</p> <p>* Skip test_parmed_genopen.py::TestGenopen::test_read_ftp_URL</p> <p>---------</p> <p>Co-authored-by: Matthew Burn &lt;[email protected]&gt; <br />Co-authored-by: Jason Swails &lt;[email protected]&gt;</p> swails tag:github.com,2008:Repository/17307763/4.3.0 2024-10-30T16:54:23Z swails tag:github.com,2008:Repository/17307763/4.2.2 2023-10-24T13:50:21Z swails tag:github.com,2008:Repository/17307763/4.2.1 2023-10-24T08:20:38Z swails tag:github.com,2008:Repository/17307763/4.2.0 2023-10-23T14:24:37Z <p>Preserve residue IDs, insertion codes, and bond orders in OpenMM topo…</p> <p>…logy conversions (<a class="issue-link js-issue-link" href="https://github.com/ParmEd/ParmEd/pull/1316">#1316</a>)</p> <p>* Preserve residue IDs, insertion codes, and bond orders in OpenMM topology conversions.</p> <p>* Remove type conversion.</p> <p>---------</p> <p>Co-authored-by: Jason Swails &lt;[email protected]&gt;</p> swails tag:github.com,2008:Repository/17307763/4.1.0 2023-04-07T13:55:39Z <p>Preserve formal charges from PDB and CIF files if present over templa…</p> <p>…tes (<a class="issue-link js-issue-link" href="https://github.com/ParmEd/ParmEd/pull/1304">#1304</a>)</p> swails tag:github.com,2008:Repository/17307763/4.0.0 2023-01-27T17:56:47Z <p>Improve CIF and PDB parsing and add informatics fields to Atom and Bo…</p> <p>…nd (<a class="issue-link js-issue-link" href="https://github.com/ParmEd/ParmEd/pull/1284">#1284</a>)</p> <p>* Add a comprehensive set of residue templates</p> <p>This adds all RNA, DNA, and protein/peptide residues as defined in the PDB <br />chemical component database that are "linking" residues</p> <p>* Add bond template and atom template property mapping to PDB/CIF parsing.</p> <p>* Fix atom serialization and fix a (poorly written) test.</p> <p>* Modernize some test stuff</p> <p>* Make sure we bundle a relevant JSON file.</p> <p>* Finish tests and fix remaining issues.</p> <p>Should be good to go now!</p> <p>* Oops - fix error after refactor.</p> <p>* Add missing ccd.js file</p> <p>* Update .gitignore</p> swails tag:github.com,2008:Repository/17307763/3.4.4 2023-01-17T03:21:20Z <p>Fix bug for nbfix/chamber in ParmEd v3.4 (<a class="issue-link js-issue-link" href="https://github.com/ParmEd/ParmEd/pull/1282">#1282</a>)</p> <p>* Fix bug for nbfix/chamber in ParmEd v3.4</p> <p>* Remove visualization tests</p> swails tag:github.com,2008:Repository/17307763/3.4.3 2021-08-31T14:16:21Z swails tag:github.com,2008:Repository/17307763/3.4.2 2021-08-28T01:55:58Z <p>support future namespace chane in openMM while keeping things backwar…</p> <p>…ds compatible (<a class="issue-link js-issue-link" href="https://github.com/ParmEd/ParmEd/pull/1176">#1176</a>) (<a class="issue-link js-issue-link" href="https://github.com/ParmEd/ParmEd/pull/1187">#1187</a>)</p> <p>Co-authored-by: Mike Henry &lt;[email protected]&gt;</p> swails