Issues

• Audit ambiguous tetrahedral P bond order before adding hypervalent H-placement fallback

  RosettaCommons/atomworks#106 · Filter by author kierandidi opened on Oct 2, 2026

• Support rebuilding declared P-H at five-coordinate centers: OMol phosphorane reproducer

  RosettaCommons/atomworks#105 · Filter by author kierandidi opened on Oct 2, 2026

• Dependency on biotite 1.4.0 requires pdbx_PDB_ins_code in atom_site type cifs

  RosettaCommons/atomworks#99 · Filter by author averyyyang opened on Aug 19, 2026
  

• Stale .ccd_codes_cache: components added under an existing letter dir are silently invisible

  RosettaCommons/atomworks#97 · Filter by author ssiddhantsharma opened on Aug 11, 2026

• atomworks should ignore obsoleted CCD codes

  RosettaCommons/atomworks#94 · Filter by author roccomoretti opened on Jul 20, 2026
  

• Do I need to setup CCD and PDB PATH mirrors, if I just want to prepare .cdf and .sdf files from .pdb for use in RF3?

  question
  RosettaCommons/atomworks#78 · Filter by author tsamdin opened on Mar 9, 2026
  5

  

• Lost string annotations because of array monkey patch

  RosettaCommons/atomworks#77 · Filter by author francois-rozet opened on Mar 6, 2026
  1

• Bug/documentation issue: Requesting altloc ("label_alt_id") in extra_fields gets overwritten by "first" if occupancy is not also in extra_fields

  RosettaCommons/atomworks#70 · Filter by author k-chrispens opened on Dec 16, 2025
  1

  

• Write better description of how to write tests in the contributor guide

  RosettaCommons/atomworks#54 · Filter by author nscorley opened on Oct 10, 2025
  

• IO examples improvements

  RosettaCommons/atomworks#47 · Filter by author rclune opened on Sep 20, 2025
  

• Can't run examples from PyPI version of atomworks

  RosettaCommons/atomworks#46 · Filter by author rclune opened on Sep 19, 2025

• Update Contributing docs page

  RosettaCommons/atomworks#44 · Filter by author rclune opened on Sep 19, 2025
  

• Create tutorial for ML usage

  RosettaCommons/atomworks#43 · Filter by author rclune opened on Sep 19, 2025
  

• Create Introductory Tutorial for IO tools

  RosettaCommons/atomworks#42 · Filter by author rclune opened on Sep 19, 2025
  

• Update AtomSelection to accept AtomArray query syntax

  enhancement
  Feature

  RosettaCommons/atomworks#40 · Filter by author nscorley opened on Sep 19, 2025

• bug: LIG from parse

  bug
  RosettaCommons/atomworks#37 · Filter by author nscorley opened on Sep 18, 2025

• Extend AtomWorks for sequence-based tasks

  enhancement
  Feature

  RosettaCommons/atomworks#27 · Filter by author nscorley opened on Sep 12, 2025

• Include inplace argument for all Transforms

  cleanup
  RosettaCommons/atomworks#26 · Filter by author nscorley opened on Sep 12, 2025

• Adopt Python 3.12 override decorator after dropping 3.11

  cleanup
  RosettaCommons/atomworks#24 · Filter by author Croydon-Brixton opened on Sep 11, 2025

• Expose parser defaults as direct arguments

  cleanupdocumentation
  RosettaCommons/atomworks#23 · Filter by author Croydon-Brixton opened on Sep 11, 2025