Commit Graph

19 Commits

Author SHA1 Message Date
Rohith Krishna
db7cbf37d1 fix: fix path in paths for pdb parsing (#715)
* refactor: change modelhub to foundry

* fix: fix path in paths for pdb parsing

* Update run_inf_tutorial.sh

---------

Co-authored-by: Rohith Krishna <rohith@localhost>
Co-authored-by: Raktim Mitra <timkartar7879@gmail.com>
2025-12-02 17:55:02 -08:00
ncorley
3e80413b0b fix: updates to fix RF3 2025-10-03 16:01:48 -07:00
ncorley
592de5b488 fix: working rf3 2025-10-01 23:52:01 -07:00
ncorley
cbbe4c6a6d wip: save before letting Claude rip 2025-10-01 12:01:05 -07:00
Kieran Didi
7f9f5244bd Fix iptm bug, add min ipae and ipde calc and ruff formatting 2025-09-18 18:43:18 -07:00
ncorley
f201cfa1cc fix: inference for RF3 2025-09-17 04:01:18 -07:00
ncorley
d89099b752 chore: documentations, cpu compatability, JSON inputs 2025-08-29 06:51:54 -07:00
Kieran Didi
e40c5c2168 fix: cli and inference config 2025-08-15 09:17:17 -07:00
Simon Mathis
da0a3b45e7 chore: ruff & remove outdated files 2025-08-14 13:53:20 -07:00
Simon Mathis
c7e588518b clean: swap cifutils/datahub backend for atomworks 2025-08-14 13:44:38 -07:00
Simon Mathis
739f09c820 clean: remove chemdata reliance 2025-08-13 01:30:57 +01:00
ncorley
1a9b71da2d tests: regression test 2025-08-11 16:06:08 -07:00
ncorley
7d32dcecf3 wip: stage 2, al working 2025-08-10 15:20:32 -07:00
Nathaniel Corley
26ed40fb07 feat: freeze weights, update resolvers (#199)
* feat: freeze weights, update resolvers

* chore: ruff
2025-05-12 14:15:15 -07:00
Nathaniel Corley
03a6dbb2b0 feat: RFScore arbitrary templating project (#179)
feat: updates to arbitrary templating, model loading support
2025-05-01 11:56:57 -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

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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
Nathaniel Corley
d801e186f3 ruff: format (#119) 2025-04-11 13:56:14 -07:00
Nathaniel Corley
8fc545c59b feat: distogram metrics, chiral metrics, path updates (#115)
* feat: distogram metrics

* wip: chirals

* feat: updated chiral metrics, comparative distogram metrics
2025-04-11 13:13:20 -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