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yingyue2030699 wants to merge 89 commits into from
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Implement a new pdb pipeline and refactor old code #5

yingyue2030699 wants to merge 89 commits into from

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@yingyue2030699 yingyue2030699 commented Jul 18, 2025

Main features are:

  • PDB import and coarse-graining with distance based detection
  • Sequence alignment or structure superimposing for repeated chain detection
  • Graph theory based reaction system extraction
  • Tree struture based chain regularization

Minor changes include:

  • refactor the plationic solid, spherical assembly, and pdb class
  • collect a few commonly used geometry, energy, and force calculations and merge and put under ionerdss.math

thelordote and others added 30 commits June 4, 2025 13:24
@thelordote
Add simularium conversion support with a new function and lazyloader …
08d21d2 
…support
@thelordote
Added the simularium conversion function, with LazyLoader support, an…
3c28b60 
…d a jupyter notebook example along with sample data to run the code in the notebook.
@sangmk
Allow customize pdb directory
c6bbc1a
@sikaoguo22
Merge pull request #46 from mjohn218/main
d45dd6e 
Update README.md
@yingyue2030699
Switch ParseComplexes to standard naming, retain backwards compatibility
a9c7c56
@yingyue2030699
Delete version specification of pyqt
7ccb2d0
@sangmk
first commit of ProAffinity
e3b57ba
@sikaoguo22
reorder the interface list based on template list
a45b092
@sangmk
Merge branch 'main' into attach_ProAffinity_modified_by_Gabe
56be952
@sangmk
Merge pull request #52 from JohnsonBiophysicsLab/attach_ProAffinity_m…
4d7b34c 
…odified_by_Gabe

Attach Simularium converter and ProAffinity
@sangmk
ignore pdbfiles in proaffinity
07b101b
@sangmk
Delete proaffinity-gnn/pdbfiles directory
8df34eb 
This directory stores pdb files downloaded when testing
@sikaoguo22
update book chapter example
03bb758
@sikaoguo22
Merge branch 'main' of https://github.com/JohnsonBiophysicsLab/ionerdss
912fd8c
@jonathanfischer97
Update README.md
093e001
@sikaoguo22
Update book_chapter_example_system_1.ipynb
d006e44
@sikaoguo22
Merge branch 'main' of https://github.com/JohnsonBiophysicsLab/ionerdss
7535e02
@dependabot
Bump networkx from 3.0 to 3.2.1
96514ba 
Bumps [networkx](https://github.com/networkx/networkx) from 3.0 to 3.2.1.
- [Release notes](https://github.com/networkx/networkx/releases)
- [Commits](networkx/networkx@networkx-3.0...networkx-3.2.1)

---
updated-dependencies:
- dependency-name: networkx
  dependency-version: 3.2.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot
Bump nvidia-curand-cu12 from 10.3.2.106 to 10.3.10.19
a1df2a8 
Bumps [nvidia-curand-cu12](https://developer.nvidia.com/cuda-zone) from 10.3.2.106 to 10.3.10.19.

---
updated-dependencies:
- dependency-name: nvidia-curand-cu12
  dependency-version: 10.3.10.19
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>
@jonathanfischer97
Delete website/source/ionerdss_documentation_v1_1.rst
1834693
@sangmk
format usage in nerdss_analysis.py
8c0af0f
@jonathanfischer97
Create release-drafter.yml
aaed45c 
Automated release notes
@jonathanfischer97
Create release-drafter.yml config
c01554f 
Config file/template for release notes
@dependabot
Bump huggingface-hub from 0.32.2 to 0.33.2
efff670 
Bumps [huggingface-hub](https://github.com/huggingface/huggingface_hub) from 0.32.2 to 0.33.2.
- [Release notes](https://github.com/huggingface/huggingface_hub/releases)
- [Commits](huggingface/huggingface_hub@v0.32.2...v0.33.2)

---
updated-dependencies:
- dependency-name: huggingface-hub
  dependency-version: 0.33.2
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
@yingyue2030699
rename nerdss_model to model
bd0a2d9
@yingyue2030699
Add docstring to model.py
238d5d1
@yingyue2030699
Sam suggested renaming model.py to components.py
11f5320
@yingyue2030699
Change reactiontype to reaction
a64c51c
@yingyue2030699
Delete unused import in components.py
bbdaa00
@yingyue2030699
Add a new math module to put all the math, linalg related functions
e51cfd8
yingyue2030699 and others added 29 commits July 10, 2025 14:56
@yingyue2030699
Add ode specific environment
d93e9ef
@yingyue2030699
Update README for the environments
8d1ae3c
@yingyue2030699
Edit github workflow
b3599db
@yingyue2030699
Update environment
cdacec1
@yingyue2030699
Merge branch 'main' into graph_based_model
9d68d17
@yingyue2030699
Merge pull request #78 from JohnsonBiophysicsLab/graph_based_model
dc78bcb 
Implement graph thoery based model
@yingyue2030699
Add docstring to angles
cd3b4a0
@yingyue2030699
Unit test for angles
30d8531
@yingyue2030699
Add unittest for coords.py
30df52d
@yingyue2030699
Add rotation matrix and inertia tensor unittests
f171f2b
@jonathanfischer97
Merge pull request #79 from JohnsonBiophysicsLab/math_subpackage_test
ba7e6a2 
Add math subpackage unittest
@yingyue2030699
refactor pdb model
00f5d2c
@yingyue2030699
Change all dataclasses to manual classes
351487a
@yingyue2030699
delete unused import in components
6dcf125
@yingyue2030699
Update naming scheme in components
bad742e
@yingyue2030699
update reactions in components
b1dadbf
@yingyue2030699
update coarse_grain and testing
8b2e6c5
@yingyue2030699
Rename homolog to repeated chain
c5aa37a
@yingyue2030699
implement sequence alignment in structual analysis and unittest
a595da2
@yingyue2030699
Add custom aligner and change documentation
4a09206
@yingyue2030699
implement bond angles calculation
915385c
@yingyue2030699
Update bond geometry and test for edge cases
6ecbd4e
@yingyue2030699
angles.py refactored to math.bond_geometry
e67e2eb
@yingyue2030699
Rename translational / rotational diffusion constants
a1359be 
Rename diffusion_translation to translational_diffusion_constant
@yingyue2030699
move yiben's code to legacy
6342572
@yingyue2030699
update pdb.core with new pipeline
1c305fc
@yingyue2030699
move chain_int to legacy
b8cfd1f
@yingyue2030699
add unittest for bond angles calculation
76145e0
@yingyue2030699
create a standard file for spherical assemblies
d4f75bf
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5 participants

@yingyue2030699 @thelordote @sangmk @sikaoguo22 @jonathanfischer97