Replace the pyMBE Pandas dataframe for a canonical pyMBE database#147

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pm-blanco wants to merge 55 commits intopyMBE-dev:mainfrom

pm-blanco:change_storage

Commits on Nov 21, 2025

first draft
pmblanco
committed

Commits on Nov 25, 2025

Database with reactions and states disentangled
pmblanco
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first complete draft of the database for particles
pmblanco
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Commits on Dec 2, 2025

add all pmb_types
pmblanco
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Commits on Dec 3, 2025

clean up and document storage code
pmblanco
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Commits on Dec 4, 2025

start refactoring pyMBE to use the new database
pmblanco
committed

Commits on Dec 5, 2025

updated residue and bond management in pyMBE
Pablo
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Commits on Dec 6, 2025

finish refactoring of residues, molecules and peptides
Pablo
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updated create_protein
Pablo
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Commits on Dec 8, 2025

refactor hydrogels
Pablo
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Commits on Dec 9, 2025

Commits on Dec 17, 2025

update methods to work with the new database
Pablo
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Commits on Jan 10, 2026

fix test for define and create molecules
Pablo
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Commits on Jan 11, 2026

modernize molecule tests, start cleaning lj tests
Pablo
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Commits on Jan 13, 2026

implement lj templates, fix tests
pmblanco
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Commits on Jan 16, 2026

add demo, add functions to load/save the database to the pyMBE API
pmblanco
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Commits on Jan 18, 2026

fix unit test
Pablo
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fix bug in create_counterions, fix unittest
Pablo
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update copyright
Pablo
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Commits on Jan 20, 2026

disentagle particle states from particle templates
pmblanco
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Commits on Jan 21, 2026

fix wrong handling of espresso types and acidity test
pmblanco
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fix molecule position test
pmblanco
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fix test
pmblanco
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fix seed test and load_interaction_parameters
pmblanco
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Commits on Jan 22, 2026

add metadata management, small cleanup
pmblanco
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clean up gcmc functional test
pmblanco
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fix bugs in setup bond, fix unittest
pmblanco
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fix net charge test
pmblanco
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fix parameter test
pmblanco
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Commits on Jan 23, 2026

Commits on Jan 24, 2026

fix protein framework and unit test
Pablo
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adapt cpH method
Pablo
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Commits on Jan 25, 2026

adapt reaction methods to the new database, fix docs
Pablo
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standarize docs
Pablo
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Commits on Jan 28, 2026

clean up repo, fix bug in setup of rigid object
pmblanco
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increase coverage
pmblanco
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Commits on Jan 29, 2026

improve coverage, clean docs
pmblanco
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Commits on Jan 30, 2026

add missing test
pmblanco
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increase coverage manager io, fix bug in lj
pmblanco
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Commits on Feb 4, 2026

remove dead ends in database io
Pablo
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improve docs
Pablo
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increase coverage of the database manager
Pablo
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Commits on Feb 6, 2026

reach full coverage
pmblanco
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solve issues detected by pylint
pmblanco
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fix bug
pmblanco
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solve dependency issues on the CI
pmblanco
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fix new bug in unit test
pmblanco
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lower requierements for pydantic to comply with current EESSI
pmblanco
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Commits on Feb 9, 2026

Commits on Feb 10, 2026

clean up tutorial
pmblanco
committed
update changelog
pmblanco
committed