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Merge upstream #5

Merged
merged 39 commits into from
Oct 15, 2024
Merged

Merge upstream #5

merged 39 commits into from
Oct 15, 2024

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donbyron02
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  • first commit v1.1
  • Add Dockerfile for creating container. Also add web app code for simple gradio app. Refine requirements.txt/environment.yml. Automatically download models if not present.
  • Minor bugfix in Dockerfile (old paths)
  • Add examples
  • Rename default_inference_args.yaml to inference_args.yaml
  • Rename inference_args.yaml to default_inference_args.yaml
  • Update README.md
  • Break from download loop once the model has been downloaded.
  • Fix conda install instructions in README.
  • Update README.md
  • Add example CSV file
  • Improved logging
  • Improve memory efficiency of graph convolution operation.
  • Various bugfixes
  • fix a typo
  • Set any nans/infs in model scores to a small value.
  • Pin setuptools version
  • Add init files to all python modules. There were import failures in some cases, when project not in root directory without own virtual env
  • fix issue with different sequences and order
  • changing zero to nan to allow filtering of nan in new_extract_receptor_structure
  • fix docker build command in README.md
  • update README with GPU instructions
  • Fix environment.yml
  • Update README.md

gcorso and others added 30 commits February 28, 2024 11:21
@gcorso
first commit v1.1
001c4fa
@jsilter
Add Dockerfile for creating container.
d9114a4 
Also add web app code for simple gradio app.
Refine requirements.txt/environment.yml.
Automatically download models if not present.
@jsilter
Merge pull request gcorso#182 from gcorso/dev_v1.1
8c36c48 
Version 1.1
@jsilter
Minor bugfix in Dockerfile (old paths)
ecfc980
@jsilter
Add examples
d3791a8
@amorehead
Rename default_inference_args.yaml to inference_args.yaml
59b9313
@amorehead
Rename inference_args.yaml to default_inference_args.yaml
3964223
@amorehead
Update README.md
94a6d29
@gcorso
Merge pull request gcorso#188 from BioinfoMachineLearning/amorehead-p…
ff4ad1b 
…atch-inference-args

Rename `inference_args.yaml` to `default_inference_args.yaml` in `README.md`
@jsilter
Break from download loop once the model has been downloaded.
df3708b
@jsilter
Fix conda install instructions in README.
0b0f676 
Closes #gcorsoGH-185
@gcorso
Update README.md
6f5d4b1
@jsilter
Add example CSV file
e259429 
Meant to rename it earlier, accidentally just removed it.
@jsilter
Improved logging
3995b24 
* Change many print statements to logging statements, for better control
* Save log file to web app zip file for easier debugging
@jsilter
Improve memory efficiency of graph convolution operation.
2c867df
@jsilter
Various bugfixes
561f70a 
* Ensure we calculate rotatable bonds on the version of the ligand with no hydrogens. Also fix spelling of rotable -> rotatable. Closes gcorsoGH-220 (@Nobody-Zhang)

* Vectorize SO3 calculations. Closes PR gcorsoGH-218 (@tornikeo)

* Pin pytorch-lightning version. Closes gcorsoGH-193 (@mikael-h-christensen)

* Guard against divide by zero in torus.py. Closes gcorsoGH-161 (@amorehead)

* Update e3nn version to 0.5.1. Closes gcorsoGH-155 (@amorehead)

* Add a little more info on docker container to README.md
@deepsatflow
fix a typo
a87faaf
@jsilter
Merge pull request gcorso#222 from satishgaurav/patch-1
5238b18 
fix a typo in readme
@jsilter
Set any nans/infs in model scores to a small value.
9d0bf3d 
    With some low (but non-trivial) frequency, processing through the convolutional layers diverge and node attributes become a mixture of nan and inf (which seem to all turn to nan). This later throws an exception during the Kabsch transform, which ruins results for the whole complex. Setting these to 0 basically skips an iteration, at worst it ruins one of the sampled complexes, but leaves the others. Note this is only applied to the main model, *not* the confidence model.
@jsilter
Pin setuptools version
a487ef8
Add __init__ files to all python modules. There were import failures …
be0f0f5 
…in some cases, when project not in root directory without own virtual env
@gcorso
fix issue with different sequences and order
6d065cd
@bamattsson
changing zero to nan to allow filtering of nan in new_extract_recepto…
8c0b943 
…r_structure
@juliocesar-io
fix docker build command in README.md
a95a6b8
@juliocesar-io
update README with GPU instructions
0c1ab69
@jsilter
Merge pull request gcorso#236 from burn-in-soul/feat/inits
5c2e633 
Add __init__ files to all python modules
@jsilter
Merge pull request gcorso#248 from juliocesar-io/main
b65b59a 
Upated docker commands instructions in README.md
@jsilter
Merge pull request gcorso#241 from bamattsson/fixing_bug_in_atom_prep…
3e80ffd 
…rocessing

Fixing bug leading to atom graph containing a lot of incorrect atoms
@jsilter
Fix environment.yml
9a22cbc 
Install prody with conda and not pip.
@gcorso
Update README.md
b4704d9
@donbyron02 donbyron02 merged commit b547693 into main Oct 15, 2024
@donbyron02 donbyron02 deleted the dbryan/merge-upstream branch October 15, 2024 22:07
@donbyron02 donbyron02 mentioned this pull request Oct 15, 2024
Closed
@donbyron02 donbyron02 changed the title dbryan/merge upstream Merge upstream Oct 15, 2024
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7 participants
@donbyron02 @gcorso @jsilter @amorehead @deepsatflow @bamattsson @juliocesar-io