v2.1.0-beta: Merge pull request #289 from X-lab-3D/development

The latest update to Pandora software now includes the implementation of reverse peptides for MHC-II.

v2.0.0

What's Changed

• Fixes to claculate LRMSD to match the atoms by @FarzanehParizi in #215
• Update README.md for MHCII example by @FarzanehParizi in #259
• Edit dbfolders structure zotero by @DarioMarzella in #266
• Extend allele name formatting in modelling_functions.py to include no… by @DarioMarzella in #268
• Fix GitHub pytest by @DarioMarzella in #269
• Update to version 2.0.0 by @DarioMarzella in #270

Full Changelog: v2.0.0-beta2.2...v2.0.0

v2.0.0-beta2.2

##What's changed:

• Fixed database loaded on zenodo. Updated zenodo link
• Fixed issues 251 and 252

Full Changelog: v2.0.0-beta2.1...v2.0.0-beta2.2

v2.0.0-beta2.1

What's Changed

*Update Zenodo link for database download
*Minor changed in documentation

New Contributors

• @jonasfoe made their first contribution in #241

v2.0.0-beta2

What's Changed

• Add fully flexible modeling by @DarioMarzella in #236
• Merge branch from PR 237 by @DarioMarzella in #238
• Issue 235 by @DarioMarzella in #239

Full Changelog: v2.0.0-beta1...v2.0.0-beta2

v2.0.0-beta1

What's Changed

• Add Docker recipe and instruction. by @DarioMarzella in #228
• Add Beta-2 microglobulin by @DarioMarzella in #231
• Update zenodo link. Hotfix cmd_pandora commands and default database… by @DarioMarzella in #233
• Improve docs and hotfix some workdir issues.

Full Changelog: v2.0.0-beta...v2.0.0-beta1

v2.0.0-beta

What's Changed

• Fix conda and pip installation. Move database default location. Add command line option to retrieve the external database. by @DarioMarzella in #222
• Add command-line options upon conda / pip installation. Update README. by @DarioMarzella in #223

Full Changelog: v2.0.0-alpha1...v2.0.0-beta

v2.0.0-alpha1

What's Changed

• Fix Issue 151. Update dependencies and README. Update setup.py by @DarioMarzella in #208
• change archiving so that only the case folder (one level) will be included inside the .tar files by @heleensev in #211
• Add PMHC.init.py and remove obsolete IMGT retrieving module by @DarioMarzella in #212
• Issue#204 by @Smaassen2 in #209
• Fix redundant imports in the package by @gcroci2 in #214
• Rename mhcseqs files and add blast database folder. by @DarioMarzella in #216

Full Changelog: v2.0.0-alpha...v2.0.0-alpha1

v2.0.0-alpha

What's Changed

• Template selection is now BLAST-based by default
• PANDORA now uses BLAST to retrieve the allele name (from IPD/MHC and IMGT/HLA databases)
• Made target sequence handling more robust. PANDORA can now take either the allele name or the MHC chain sequence and will try to retrieve the other automatically.
• Added an option to use template MHC sequence when no MHC sequence can be retrieved. Previously it was done by default, leading to incorrect models. Now, if no MHC sequence can be retrieved, the run will be stopped, unless the user sets use_templ_seq to True in their Target or Wrapper function.
• Database restructured. Now the user does not need to know the installation location and to handle any PANDORA-dependent path. By simply using functions like Database.construct_database() and Database.load() the user is able to generate and then load a database, without having to specify its location.
• Removed the need for Database.repath() function. Removed Database.repath() function.
• Parallelized and sped up database generation. Database generation takes now about 20~30 minutes on a single core, and it can be parallelized to reduce the time to less than one minute.
• Fixed multiple issues in netMHCpan interface. Now PANDORA does not need netMHC(II)pan to be installed internally anymore.
• Added clip_C_domain option to Pandora and Wrapper modules, to directly model only the G-domain
• Added the archiving option to the Wrapper, to allow users to model large batches of cases and immediately archive every folder in a .tar file.
• Extended pytest coverage
• Fixed numerous issues

Pull Requests

• Major updates to make MHCII, template selection and database download more robust. by @DarioMarzella in #128
• Development by @DarioMarzella in #129
• Merge mhcii_dm into development. by @DarioMarzella in #130
• Mhcii dm by @DarioMarzella in #149
• fixed an issue where the database creation script would crash by @DanLep97 in #152
• Update Wrapper and run_model.py to use a dictionary of arguments inst… by @DarioMarzella in #177
• Restructuring PANDORA's files by @gcroci2 in #164
• Update parallelize_db to development by @DarioMarzella in #178
• Parallelize templates cleaning by @gcroci2 in #169
• Add get_pdb_path() method to PMHC.template objects to replace static … by @DarioMarzella in #179
• tutorial example 3 changed name parameters by @Smaassen2 in #184
• Example 4 in tutorial has incorrect id by @Smaassen2 in #185
• Add get_pdb_path() method to PMHC.template objects to replace static … by @DarioMarzella in #187
• Fix pytest dev by @DarioMarzella in #189
• Add exception in run_model.py to prevent the Wrapper from crashing by @DarioMarzella in #191
• Fix Muscle version issue. Add blast to dependencies. Update README by @DarioMarzella in #193
• Issue 112 by @Smaassen2 in #196
• Fix/update of the test_pandora.py file by @Smaassen2 in #200
• Archiving by @heleensev in #199
• remove netMHCpan_install.py as obsolete. Update README. Fix an issue … by @DarioMarzella in #201
• Fix issue 202 by @DarioMarzella in #206

New Contributors

• @NicoRenaud made their first contribution in #108
• @DTRademaker made their first contribution in #114
• @DanLep97 made their first contribution in #152
• @gcroci2 made their first contribution in #164
• @Smaassen2 made their first contribution in #184
• @heleensev made their first contribution in #199

Full Changelog: https://github.com/X-lab-3D/PANDORA/commits/v2.0.0-alpha

v1.0.0

First Release of the PANDORA package, published with the Marzella, Parizi et. al Frontiers in immunology paper.