Commit Graph

11 Commits

Author SHA1 Message Date
Jasper Butcher
5e7b739ed3 Add initial RFD3 Files and passing tests
* Add initial files

* add files

* Move projects.aa_design -> rfd3

* Make format

* Delete test files

* Add configs

* Mc

* Fixed tests

* remove test files
2025-11-11 10:07:43 -08:00
ncorley
3e80413b0b fix: updates to fix RF3 2025-10-03 16:01:48 -07:00
ncorley
6891de148b chore: apptainers, ipd, rf3 runnable 2025-10-02 13:31:34 -07:00
ncorley
cbbe4c6a6d wip: save before letting Claude rip 2025-10-01 12:01:05 -07:00
Nathaniel Corley
2f0449d016 docs: readme update and cleanup (#477)
Co-authored-by: Nathaniel Corley <nscorley@Nathaniels-MacBook-Pro.local>
2025-08-15 16:37:25 +02:00
Simon Mathis
9ec23cd32e clean 2025-08-14 14:43:47 -07:00
Simon Mathis
9338d8bdc4 clean 2025-08-14 14:42:13 -07:00
Nathaniel Corley
7d108f7e25 fix: inference (#131)
* fix: update inference and apptainers

* fix ref_space_uid (#156)

* fix ref_space_uid

* remove chiral transforms as they are in datahub now

* copy datahub pipeline back into modelhub

---------

Co-authored-by: Rohith Krishna <rohith@digs>

* chore: MR conflicts

* chore: ruff

* fix: inference with confidence (#170)

* chore: ruff

* wip: inference with confidence

* chore: make inference work

* Add early stopping to inference (#157)

* Add early stopping to inference

* refactor: early stopping

* chore: ruff

* fix: remove is_real_atom from network input

---------

Co-authored-by: ncorley <ncorley@uw.edu>

* docs: update README

---------

Co-authored-by: Frank DiMaio <dimaio@uw.edu>

* chore: update paths to point to checkpoint symlink

* chore: NCAA example, bump submodules

* fix: inference with templates (#165)

* enable templating using old syntax

* rebase and reset datahub

* make the code fail when running from json

add tests for templating syntax

push up cifutils

* updated README

* reenable metrics after rebase

* fix typo

* Update src/modelhub/inference_engines/af3.py

---------

Co-authored-by: Rohith Krishna <rohith@digs>
Co-authored-by: Nathaniel Corley <ncorley@uw.edu>

* fix: minor inference changes with apptainers and chiral metrics

* chore: ruff, clean up comments

* chore: MR comments

---------

Co-authored-by: Rohith Krishna <rohith@uw.edu>
Co-authored-by: Rohith Krishna <rohith@digs>
Co-authored-by: Frank DiMaio <dimaio@uw.edu>
2025-04-29 02:03:01 +00:00
Simon Mathis
ec696acbed run make format on trunk and add CI for make format checks (#162)
* ci: add ci to trunk

* chore: fix linting issues

* ci: rename lint trunk workflow
2025-04-24 11:13:18 -07:00
Nathaniel Corley
5a492032d5 refactor: new modelhub (#109)
* Initial commit of chiral changes

Initial checkin of chiral feature code

Add chiral metric

* Update the way chiral features are incorporated into the model

Move initialization to new func

use default pytorch reset parameters

fix initialization for chirals

config

rename argument of confidence head

fix initialization for chirals

* refactor: src nest, rename rf2aa to modelhub

* refactor: initial commit without projects

* Initial commit of chiral changes

* Initial checkin of chiral feature code

* Add chiral metric

* Remove option for double residual connection.  Add kq_norm oiptions to base (20250125) config.

* Restoring flag

* config

* rename argument of confidence head

* Update the way chiral features are incorporated into the model

* config

* rename argument of confidence head

* Update the way chiral features are incorporated into the model

* Initial commit of chiral changes

Initial checkin of chiral feature code

Add chiral metric

* Update the way chiral features are incorporated into the model

Move initialization to new func

use default pytorch reset parameters

fix initialization for chirals

config

rename argument of confidence head

fix initialization for chirals

* refactor: new modelhub

---------

Co-authored-by: fdimaio <dimaio@uw.edu>
Co-authored-by: HaotianZhangAI4Science <haotianzhang@zju.edu.cn>
2025-04-08 13:33:17 -07:00
ncorley
719f3f8064 refactor: delete data, add makefile, environment yaml, apptainer, env 2025-02-04 21:07:15 -08:00