Nathaniel Corley
8cbf11ea23
feat: predict and score ( #599 )
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Add ability to predict then run a set of metrics
2025-10-29 12:25:28 -07:00
ncorley
74e879a373
refactor: move datasets to common
2025-10-27 17:40:12 -07:00
Rafael Brent
4325878f17
feat: Conditional application of Metrics ( #585 )
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* feat: enable conditional application of Metrics based on tags passed through the Transform pipeline
* chore: ruff
---------
Co-authored-by: Rafi Brent <rafi.brent@gmail.com >
2025-10-25 21:29:50 -07:00
ncorley
d0ea2bad5d
hotfix: input parsing
2025-10-24 20:32:12 -07:00
Nathaniel Corley
44cd199837
fix: datasets ( #583 )
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* docs: README warning update
Added notices regarding bug fixes and upcoming changes.
* fix: inference for RF3
* chore: reomve submodules
* feat: update ligand templating, bump atomworks version
* Fix iptm bug, add min ipae and ipde calc and ruff formatting
* refactor: rf3 lab
* wip: save before letting Claude rip
* fix: working rf3
* chore: apptainers, ipd, rf3 runnable
* fix: README, environment, conftest
* add laproteina training and inference with new rf3 structure
* fix: updates to fix RF3
* feat: updates from proteina pipeline, squashfs manager
* fix: updates to support latest Run10 RF3
* fix: element type bug, utils, conformers
* update: ckpt path
* fix: add symlinked apptainer
* fix: MSAs for inference
* fix: apptainers, submodule bump for atomworks
* fix: apptainers
* Wip/attention improvements (#554 )
* feat: inference sharding; folders
* refactor: attention module reorganization and cleanup
* fix: regression tests
* feature: RF3 inference with atom arrays
* refactor: move datasets
* tests: additional regression tests
* fix: moving datasets aroudn
---------
Co-authored-by: Kieran Didi <kieran.didi@gmail.com >
Co-authored-by: Kieran Didi <kdidi@nvidia.com >
2025-10-24 16:35:05 -07:00
Tuscan R Thompson
de64112d89
Feat: cyclic inference ( #552 )
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* feat: inference for cyclic peptides
* chore: update README
* chore: lint
* chore: lint
* chore: cleanup if statement
2025-10-24 16:27:42 -07:00
Nathaniel Corley
d10cc62c69
test: additional regression tests ( #581 )
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* docs: README warning update
Added notices regarding bug fixes and upcoming changes.
* fix: inference for RF3
* chore: reomve submodules
* feat: update ligand templating, bump atomworks version
* Fix iptm bug, add min ipae and ipde calc and ruff formatting
* refactor: rf3 lab
* wip: save before letting Claude rip
* fix: working rf3
* chore: apptainers, ipd, rf3 runnable
* fix: README, environment, conftest
* add laproteina training and inference with new rf3 structure
* fix: updates to fix RF3
* feat: updates from proteina pipeline, squashfs manager
* fix: updates to support latest Run10 RF3
* fix: element type bug, utils, conformers
* update: ckpt path
* fix: add symlinked apptainer
* fix: MSAs for inference
* fix: apptainers, submodule bump for atomworks
* fix: apptainers
* Wip/attention improvements (#554 )
* feat: inference sharding; folders
* refactor: attention module reorganization and cleanup
* fix: regression tests
* feature: RF3 inference with atom arrays
* refactor: move datasets
* tests: additional regression tests
---------
Co-authored-by: Kieran Didi <kieran.didi@gmail.com >
Co-authored-by: Kieran Didi <kdidi@nvidia.com >
2025-10-24 14:57:12 -07:00
Nathaniel Corley
6a5c1964b0
refactor: move datasets ( #579 )
...
* docs: README warning update
Added notices regarding bug fixes and upcoming changes.
* fix: inference for RF3
* chore: reomve submodules
* feat: update ligand templating, bump atomworks version
* Fix iptm bug, add min ipae and ipde calc and ruff formatting
* refactor: rf3 lab
* wip: save before letting Claude rip
* fix: working rf3
* chore: apptainers, ipd, rf3 runnable
* fix: README, environment, conftest
* add laproteina training and inference with new rf3 structure
* fix: updates to fix RF3
* feat: updates from proteina pipeline, squashfs manager
* fix: updates to support latest Run10 RF3
* fix: element type bug, utils, conformers
* update: ckpt path
* fix: add symlinked apptainer
* fix: MSAs for inference
* fix: apptainers, submodule bump for atomworks
* fix: apptainers
* Wip/attention improvements (#554 )
* feat: inference sharding; folders
* refactor: attention module reorganization and cleanup
* fix: regression tests
* feature: RF3 inference with atom arrays
* refactor: move datasets
---------
Co-authored-by: Kieran Didi <kieran.didi@gmail.com >
Co-authored-by: Kieran Didi <kdidi@nvidia.com >
2025-10-23 15:55:48 -07:00
maxkazman
8f0ac4a263
feat: Multiple GPU inference and LOCAL_MSA_DIRS env variable usage ( #563 )
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* feat: support for multi-gpu inference and proper results gathering
* feat: utils for multi-gpu inference and multithreaded input parsing
* feat: use LOCAL_MSA_DIRS environment variable for msa dir override if available
* feat: automatically check shard depth and extension for msas during inference
2025-10-20 15:06:53 -07:00
Nathaniel Corley
31deb1ab3c
Wip/attention improvements ( #554 )
...
* feat: inference sharding; folders
* refactor: attention module reorganization and cleanup
* fix: regression tests
* feature: RF3 inference with atom arrays
2025-10-09 22:53:53 -07:00
ncorley
d048cc887e
fix: apptainers
2025-10-08 15:45:09 -07:00
ncorley
2abd193d47
fix: apptainers, submodule bump for atomworks
2025-10-08 13:57:07 -07:00
ncorley
f2a9d502b5
fix: MSAs for inference
2025-10-07 22:57:35 -07:00
ncorley
30da9e6e6b
fix: add symlinked apptainer
2025-10-07 17:02:31 -07:00
ncorley
628c2bda5f
update: ckpt path
2025-10-07 16:36:10 -07:00
ncorley
423ff10a89
fix: element type bug, utils, conformers
2025-10-07 16:22:28 -07:00
ncorley
bcd3c527cd
fix: updates to support latest Run10 RF3
2025-10-07 13:49:42 -07:00
ncorley
606420436d
feat: updates from proteina pipeline, squashfs manager
2025-10-03 17:22:14 -07:00
ncorley
3e80413b0b
fix: updates to fix RF3
2025-10-03 16:01:48 -07:00
Kieran Didi
77c995cc11
add laproteina training and inference with new rf3 structure
2025-10-02 17:47:14 -07:00
ncorley
7a66a96a29
fix: README, environment, conftest
2025-10-02 17:38:03 -07:00
ncorley
6891de148b
chore: apptainers, ipd, rf3 runnable
2025-10-02 13:31:34 -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
ncorley
ac17c5f3c8
refactor: rf3 lab
2025-09-29 16:44:02 -07:00
Nathaniel Corley
b5c9685c73
Merge pull request #12 from RosettaCommons/fix/inference
...
fix: inference
2025-09-19 16:19:47 -07:00
Nathaniel Corley
b124517882
fix: iptm
...
Fix iptm bug, add min ipae and ipde calc and ruff formatting
2025-09-19 16:18:22 -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
Nathaniel Corley
f7289e9e5f
feat: inference examples
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Additional inference examples and functionality for RF3
2025-09-17 21:42:47 -07:00
ncorley
2e218aafc2
feat: update ligand templating, bump atomworks version
2025-09-17 21:41:57 -07:00
ncorley
b3e9466b52
chore: reomve submodules
2025-09-17 04:03:01 -07:00
ncorley
f201cfa1cc
fix: inference for RF3
2025-09-17 04:01:18 -07:00
Nathaniel Corley
5c8ba5f2a1
docs: README warning update
...
Added notices regarding bug fixes and upcoming changes.
2025-09-03 15:12:03 +03:00
Nathaniel Corley
a6060d7a45
fix: JSON inputs and arbitrary atomic-level templating support
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Includes major bug fix to running inference via JSON inputs; unfortunately, prior outputs using JSONs may not be valid and should be re-run
2025-08-29 17:02:20 +03:00
Nathaniel
ce9769be79
chore: clean up inference engine
2025-08-29 16:59:59 +03:00
Nathaniel
662605a56e
chore: format
2025-08-29 16:58:53 +03:00
Nathaniel
586ae4b28d
fix: add back template selection
2025-08-29 16:58:38 +03:00
Nathaniel
c7b3a5e073
chore: commit empty .env
2025-08-29 16:54:30 +03:00
ncorley
d89099b752
chore: documentations, cpu compatability, JSON inputs
2025-08-29 06:51:54 -07:00
Nathaniel Corley
e7430b11c5
fix(readme): formatting
2025-08-19 21:45:41 +02:00
Nathaniel Corley
0b914395f5
docs: update README disclaimer
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Clarify that training code is not yet supported
2025-08-19 21:45:23 +02:00
Kieran Didi
849281ef99
chore: remove submodules in favor of pip package
2025-08-15 11:30:19 -07:00
Kieran Didi
9d47095f72
chore: updated readme
2025-08-15 09:30:52 -07:00
Nathaniel Corley
1ba98a9a52
fix: PDB_MIRROR variable error catching
2025-08-15 18:27:18 +02:00
Kieran Didi
e40c5c2168
fix: cli and inference config
2025-08-15 09:17:17 -07:00
Nathaniel Corley
05ecfbf046
docs: graphics
2025-08-15 17:27:53 +02:00
Nathaniel Corley
2f0449d016
docs: readme update and cleanup ( #477 )
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Co-authored-by: Nathaniel Corley <nscorley@Nathaniels-MacBook-Pro.local >
2025-08-15 16:37:25 +02:00
Rohith Krishna
0e415316b7
reinit README
2025-08-15 02:07:08 -07:00
Rohith Krishna
a0ebd6b51a
format
2025-08-15 02:02:36 -07:00
Rohith Krishna
7707677613
enable rf3 fold syntax
2025-08-15 01:59:08 -07:00
