RosettaCommons/atomworks

A generalized computational framework for biomolecular modeling.

Stars: 446
Forks: 52
Open beginner issues: 0
Indexed issues: 24

Dominant language: Python
License: BSD-3-Clause
Last GitHub push: Aug 20, 2026
Latest indexed: Sep 20, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

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24 open issues indexed

Dependency on biotite 1.4.0 requires pdbx_PDB_ins_code in atom_site type cifs Open

RosettaCommons/atomworks#99 · 1 assignee · Opened Aug 19, 2026
Stale .ccd_codes_cache: components added under an existing letter dir are silently invisible Open

Difficulty 3/5 1-2 days Newbie friendliness 64/100

RosettaCommons/atomworks#97 · Opened Aug 11, 2026
atomworks should ignore obsoleted CCD codes Open

RosettaCommons/atomworks#94 · 1 assignee · Opened Jul 20, 2026
Formal charge correction fails in the presence of bonds to metal ions Open

RosettaCommons/atomworks#80 · 1 comment · 2 assignees · Opened Apr 7, 2026
Metadata generation Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

RosettaCommons/atomworks#79 · Opened Mar 15, 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? Open

question

RosettaCommons/atomworks#78 · 5 comments · 1 assignee · Opened Mar 9, 2026
Lost string annotations because of array monkey patch Open

Difficulty 3/5 1-2 days Newbie friendliness 58/100

RosettaCommons/atomworks#77 · 1 comment · Opened Mar 6, 2026
Bug/documentation issue: Requesting altloc ("label_alt_id") in `extra_fields` gets overwritten by `"first"` if occupancy is not also in `extra_fields` Open

RosettaCommons/atomworks#70 · 1 comment · 1 assignee · Opened Dec 16, 2025
Preserve `extra_fields` when `add_missing_atoms` is set to True Open

RosettaCommons/atomworks#56 · 3 comments · 1 reaction · 1 assignee · Opened Oct 23, 2025
Write better description of how to write tests in the contributor guide Open

RosettaCommons/atomworks#54 · 2 assignees · Opened Oct 10, 2025
No such command 'metadata' Open

Difficulty 2/5 1-3 hours Newbie friendliness 52/100

RosettaCommons/atomworks#52 · Opened Oct 9, 2025
Import statements in examples are not working Open

RosettaCommons/atomworks#51 · 1 assignee · Opened Oct 8, 2025
IO examples improvements Open

RosettaCommons/atomworks#47 · 1 assignee · Opened Sep 20, 2025
Can't run examples from PyPI version of atomworks Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

RosettaCommons/atomworks#46 · Opened Sep 19, 2025
Update Contributing docs page Open

RosettaCommons/atomworks#44 · 1 assignee · Opened Sep 19, 2025
Create tutorial for ML usage Open

RosettaCommons/atomworks#43 · 1 assignee · Opened Sep 19, 2025
Create Introductory Tutorial for IO tools Open

RosettaCommons/atomworks#42 · 1 assignee · Opened Sep 19, 2025
Update `AtomSelection` to accept AtomArray query syntax Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 42/100

RosettaCommons/atomworks#40 · Opened Sep 19, 2025
Update `AtomArrayPlus` to natively support entry-level data Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

RosettaCommons/atomworks#39 · Opened Sep 19, 2025
bug: `LIG` from `parse` Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 35/100

RosettaCommons/atomworks#37 · Opened Sep 18, 2025
Extend `AtomWorks` for sequence-based tasks Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

RosettaCommons/atomworks#27 · Opened Sep 12, 2025
Include `inplace` argument for all `Transforms` Open

cleanup

Difficulty 4/5 3-5 days Newbie friendliness 40/100

RosettaCommons/atomworks#26 · Opened Sep 12, 2025
Adopt Python 3.12 override decorator after dropping 3.11 Open

cleanup

Difficulty 4/5 3-5 days Newbie friendliness 35/100

RosettaCommons/atomworks#24 · Opened Sep 11, 2025
Expose parser defaults as direct arguments Open

cleanup documentation

Difficulty 3/5 1-2 days Newbie friendliness 45/100

RosettaCommons/atomworks#23 · Opened Sep 11, 2025

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