uibcdf/molsysmt

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Open source library to work with molecular systems

Stars: 14
Forks: 3
Open beginner issues: 2
Indexed issues: 50

Dominant language: Python
License: MIT
Last GitHub push: Sep 19, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

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49 open issues indexed

Migrate legacy MolSysMT trees into the Ruff gate Open

ci proposal

Difficulty 4/5 Over a week Newbie friendliness 42/100

uibcdf/molsysmt#212 · Opened Sep 12, 2026
info() has no mask, unlike get() and select(), so a scoped caller has to pre-resolve the intersection Open

Difficulty 3/5 1-2 days Newbie friendliness 68/100

uibcdf/molsysmt#206 · 1 comment · Opened Sep 4, 2026
Evaluate LTO and Rattler Build for native Conda latency Open

build ci in-progress performance proposal

Difficulty 4/5 3-5 days Newbie friendliness 25/100

uibcdf/molsysmt#205 · Opened Sep 4, 2026
A clean conda install of 0.22.0 cannot convert a PDB ID: 'mmcif' is undeclared and not on conda-forge Open

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

uibcdf/molsysmt#200 · 1 comment · Opened Sep 2, 2026
Regenerate the exported views once MolSysViewer 0.21.0 ships: the transparent-background fix lives in the HTML, not the runtime Open

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

uibcdf/molsysmt#199 · Opened Sep 2, 2026
Conda cannot resolve MolSysMT on supported Python 3.13 because MolSysViewer has no compatible build Open

bug build deps in-progress

Difficulty 4/5 3-5 days Newbie friendliness 45/100

uibcdf/molsysmt#195 · Opened Sep 1, 2026
The MolSysSuite positioning is absent from every public surface Open

api docs documentation

Difficulty 3/5 1-2 days Newbie friendliness 68/100

uibcdf/molsysmt#192 · Opened Aug 19, 2026
paper/main.tex is an unfilled template and the manuscript argument is unrecorded Open

docs proposal

Difficulty 4/5 3-5 days Newbie friendliness 55/100

uibcdf/molsysmt#191 · 1 comment · Opened Aug 19, 2026
The evidence matrix cannot show the surfaces the manuscript will lead with Open

build proposal tests

Difficulty 4/5 3-5 days Newbie friendliness 55/100

uibcdf/molsysmt#190 · Opened Aug 19, 2026
supported.forms() and info() return only styled tables, with no programmatic result Open

api basic proposal

Difficulty 3/5 1-2 days Newbie friendliness 68/100

uibcdf/molsysmt#188 · 1 comment · Opened Aug 19, 2026
The README presents experimental surfaces as headline capabilities Open

build docs documentation

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

uibcdf/molsysmt#186 · Opened Aug 19, 2026
No test workflow runs on a push to main and the CI badge names a missing workflow Open

bug ci

Difficulty 4/5 3-5 days Newbie friendliness 48/100

uibcdf/molsysmt#185 · 1 comment · Opened Aug 19, 2026
Execute every declared conversion edge in the test suite, not only audit it statically Open

convert enhancement form proposal tests

Difficulty 4/5 3-5 days Newbie friendliness 55/100

uibcdf/molsysmt#181 · Opened Aug 19, 2026
Integrate PROPKA for environment-dependent pKa instead of reimplementing it Open

build deps enhancement proposal

Difficulty 4/5 3-5 days Newbie friendliness 48/100

uibcdf/molsysmt#177 · Opened Aug 19, 2026
Add compact='molecule' to the wrapping functions Open

api pbc proposal

Difficulty 4/5 3-5 days Newbie friendliness 55/100

uibcdf/molsysmt#173 · Opened Aug 19, 2026
Audit PyUnitWizard fast-path adoption at quantity boundaries Open

argdigest performance units

Difficulty 4/5 3-5 days Newbie friendliness 48/100

uibcdf/molsysmt#155 · Opened Aug 13, 2026
Evaluate single-assessment delegation for public molecular-system predicates Open

basic proposal

Difficulty 4/5 3-5 days Newbie friendliness 48/100

uibcdf/molsysmt#154 · Opened Aug 13, 2026
Add an explicit source-form hint to convert Open

convert form proposal

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

uibcdf/molsysmt#151 · Opened Aug 13, 2026
Sphinx warning baseline and API reference debt Open

bug docs partial

Difficulty 4/5 3-5 days Newbie friendliness 48/100

uibcdf/molsysmt#144 · Opened Aug 9, 2026
Forms declare attributes they cannot deliver Open

attribute bug form partial

Difficulty 4/5 3-5 days Newbie friendliness 48/100

uibcdf/molsysmt#139 · Opened Aug 9, 2026
Add MolSys to CIF/BCIF conversion support for deterministic fixtures and offline workflows Open

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

uibcdf/molsysmt#135 · Opened Mar 11, 2026
Add weighted RMSD support (least_rmsd functions) Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

uibcdf/molsysmt#134 · Opened Feb 6, 2026
Improve the selection strategy in convert() Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

uibcdf/molsysmt#132 · Opened Dec 23, 2025
add_missing_terminal_cappings() takes too long Open

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

uibcdf/molsysmt#130 · Opened Nov 29, 2025
molsysmt.MolSys.info() and molsysmt.MolSys.get() should be shortcuts Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

uibcdf/molsysmt#128 · 1 comment · Opened Nov 25, 2025
Can we play with cDKTrees to improve the functions to get minimum and máximum distances? Open

enhancement optimization TODO

uibcdf/molsysmt#125 · 1 comment · 1 assignee · Opened Nov 11, 2025
Basic tools inside molsysmt.MolSys objects. Open

enhancement TODO

uibcdf/molsysmt#124 · 1 assignee · Opened Nov 10, 2025
The CI with skipping option Open

enhancement TODO

uibcdf/molsysmt#123 · 1 assignee · Opened Nov 10, 2025
Profile and reduce test-suite runtime without weakening coverage Open

enhancement performance proposal tests TODO

uibcdf/molsysmt#122 · 1 comment · 1 assignee · Opened Nov 8, 2025
Add copy(), __copy__(), and __deepcopy__() to native objects Open

enhancement TODO

uibcdf/molsysmt#121 · 1 assignee · Opened Nov 8, 2025
Add __repr__(self) to native objects Open

enhancement TODO

uibcdf/molsysmt#120 · 1 assignee · Opened Nov 8, 2025
Check function to make labels Open

enhancement TODO

uibcdf/molsysmt#119 · 1 assignee · Opened Nov 6, 2025
Improving the h5msm file format Open

uibcdf/molsysmt#114 · 1 assignee · Opened Apr 18, 2025
Title: Post-1.0: Integrate code quality tools (ruff, docstr-coverage, docstring checks) Open

enhancement

uibcdf/molsysmt#113 · 1 assignee · Opened Apr 7, 2025
Correct the output of getting empty alternate locations Open

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

uibcdf/molsysmt#112 · Opened Mar 30, 2025
basic.select method can be faster when `element` is diferent from 'atom' and `syntax='MolSysMT'` Open

optimization

Difficulty 4/5 3-5 days Newbie friendliness 42/100

uibcdf/molsysmt#110 · Opened Apr 22, 2024
We need OpenMM reporters with atom_indices as input argument. Open

Sobre Interfaz Gráfica

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

uibcdf/molsysmt#106 · Opened Oct 17, 2023
Is there a way to add a color bar to an nglview.NGLWidget? Open

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

uibcdf/molsysmt#95 · Opened Oct 21, 2022
A tool to work with the whole PDB database Open

enhancement

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

uibcdf/molsysmt#47 · Opened Jul 16, 2021
Wrong topology in mdtraj.Topology from nv.datafiles.GRO Open

bug

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

uibcdf/molsysmt#30 · Opened May 21, 2021
Including extended PDB and CCD ID codes Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 25/100

uibcdf/molsysmt#28 · Opened May 18, 2021
An auxiliary library to cite everything that was used along a workflow has to be included Open

enhancement

uibcdf/molsysmt#27 · 2 comments · 2 assignees · Opened May 6, 2021
Proteins, small molecules and entities names Open

bug

uibcdf/molsysmt#25 · 2 comments · 1 assignee · Opened May 6, 2021
Hbonds output formats Open

enhancement

uibcdf/molsysmt#22 · 1 comment · 1 assignee · Opened Apr 16, 2021
Other Python libraries to be checked Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

uibcdf/molsysmt#12 · 8 comments · Opened Jan 13, 2021
Pytraj objects, syntaxis and engines in MolSysMT Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

uibcdf/molsysmt#9 · Opened Jun 25, 2020
There are faster libraries to make queries in a DataFrame Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

uibcdf/molsysmt#8 · 2 comments · Opened Jun 25, 2020
Faster graph tools Open

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

uibcdf/molsysmt#7 · Opened Jun 24, 2020
Secondary structure prediction for sequence segments Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

uibcdf/molsysmt#1 · 1 comment · Opened Feb 20, 2019

uibcdf/molsysmt

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