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Add missing repeat indices for Chai-1
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@amorehead
amorehead committed Sep 25, 2024
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51 changes: 34 additions & 17 deletions README.md
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Expand Up @@ -674,44 +674,61 @@ Run inference on each dataset

```bash
conda activate forks/chai-lab/chai-lab/
python3 posebench/models/chai_inference.py dataset=posebusters_benchmark
python3 posebench/models/chai_inference.py dataset=astex_diverse
python3 posebench/models/chai_inference.py dataset=dockgen
python3 posebench/models/chai_inference.py dataset=casp15
python3 posebench/models/chai_inference.py dataset=posebusters_benchmark repeat_index=1
...
python3 posebench/models/chai_inference.py dataset=astex_diverse repeat_index=1
...
python3 posebench/models/chai_inference.py dataset=dockgen repeat_index=1
...
python3 posebench/models/chai_inference.py dataset=casp15 repeat_index=1
...
conda deactivate
```

Extract predictions into separate files for proteins and ligands

```bash
python3 posebench/data/chai_output_extraction.py dataset=posebusters_benchmark
python3 posebench/data/chai_output_extraction.py dataset=astex_diverse
python3 posebench/data/chai_output_extraction.py dataset=dockgen
python3 posebench/data/chai_output_extraction.py dataset=casp15
python3 posebench/data/chai_output_extraction.py dataset=posebusters_benchmark repeat_index=1
...
python3 posebench/data/chai_output_extraction.py dataset=astex_diverse repeat_index=1
...
python3 posebench/data/chai_output_extraction.py dataset=dockgen repeat_index=1
...
python3 posebench/data/chai_output_extraction.py dataset=casp15 repeat_index=1
...
```

Relax the generated ligand structures inside of their respective protein pockets

```bash
python3 posebench/models/inference_relaxation.py method=chai-lab dataset=posebusters_benchmark remove_initial_protein_hydrogens=true
python3 posebench/models/inference_relaxation.py method=chai-lab dataset=astex_diverse remove_initial_protein_hydrogens=true
python3 posebench/models/inference_relaxation.py method=chai-lab dataset=dockgen remove_initial_protein_hydrogens=true
python3 posebench/models/inference_relaxation.py method=chai-lab dataset=posebusters_benchmark remove_initial_protein_hydrogens=true repeat_index=1
...
python3 posebench/models/inference_relaxation.py method=chai-lab dataset=astex_diverse remove_initial_protein_hydrogens=true repeat_index=1
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python3 posebench/models/inference_relaxation.py method=chai-lab dataset=dockgen remove_initial_protein_hydrogens=true repeat_index=1
...
```

Align predicted protein-ligand structures to ground-truth complex structures

```bash
python3 posebench/analysis/complex_alignment.py method=chai-lab dataset=posebusters_benchmark
python3 posebench/analysis/complex_alignment.py method=chai-lab dataset=astex_diverse
python3 posebench/analysis/complex_alignment.py method=chai-lab dataset=dockgen
python3 posebench/analysis/complex_alignment.py method=chai-lab dataset=posebusters_benchmark repeat_index=1
...
python3 posebench/analysis/complex_alignment.py method=chai-lab dataset=astex_diverse repeat_index=1
...
python3 posebench/analysis/complex_alignment.py method=chai-lab dataset=dockgen repeat_index=1
...
```

Analyze inference results for each dataset

```bash
python3 posebench/analysis/inference_analysis.py method=chai-lab dataset=posebusters_benchmark
python3 posebench/analysis/inference_analysis.py method=chai-lab dataset=astex_diverse
python3 posebench/analysis/inference_analysis.py method=chai-lab dataset=dockgen
python3 posebench/analysis/inference_analysis.py method=chai-lab dataset=posebusters_benchmark repeat_index=1
...
python3 posebench/analysis/inference_analysis.py method=chai-lab dataset=astex_diverse repeat_index=1
...
python3 posebench/analysis/inference_analysis.py method=chai-lab dataset=dockgen repeat_index=1
...
```

Analyze inference results for the CASP15 dataset
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4 changes: 2 additions & 2 deletions docs/source/acknowledgements.rst
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Expand Up @@ -2,5 +2,5 @@ Acknowledgements
================

.. mdinclude:: ../../README.md
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4 changes: 2 additions & 2 deletions docs/source/bonus.rst
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Expand Up @@ -2,8 +2,8 @@ Bonus
================

.. mdinclude:: ../../README.md
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.. image:: ./_static/WorkBench.jpeg
:alt: My brain after building PoseBench
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4 changes: 2 additions & 2 deletions docs/source/citing_this_work.rst
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Expand Up @@ -2,5 +2,5 @@ Citing this work
================

.. mdinclude:: ../../README.md
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4 changes: 2 additions & 2 deletions docs/source/comparative_plots.rst
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Expand Up @@ -2,5 +2,5 @@ How to create comparative plots of inference results
================

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4 changes: 2 additions & 2 deletions docs/source/ensemble_inference.rst
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Expand Up @@ -2,8 +2,8 @@ How to run inference with a method ensemble
================

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.. note::
In addition to having `consensus` as an available value for `ensemble_ranking_method`, one can also set `ensemble_ranking_method=ff` to have the method ensemble's top-ranked predictions selected using the criterion of "minimum (molecular dynamics) force field energy" (albeit while incurring a very large runtime complexity).
4 changes: 2 additions & 2 deletions docs/source/for_developers.rst
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Expand Up @@ -2,5 +2,5 @@ For developers
================

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2 changes: 1 addition & 1 deletion docs/source/method_inference.rst
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Expand Up @@ -3,4 +3,4 @@ How to run inference with individual methods

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10 changes: 5 additions & 5 deletions scripts/build_inference_script.py
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Expand Up @@ -136,20 +136,20 @@
],
"run_inference": [
"conda activate forks/chai-lab/chai-lab/",
"python3 posebench/models/chai_inference.py dataset={dataset} cuda_device_index={cuda_device_index} pocket_only_baseline={pocket_only_baseline}",
"python3 posebench/models/chai_inference.py dataset={dataset} cuda_device_index={cuda_device_index} pocket_only_baseline={pocket_only_baseline} repeat_index={repeat_index}",
"conda deactivate",
],
"extract_outputs": [
"python3 posebench/data/chai_output_extraction.py dataset={dataset} pocket_only_baseline={pocket_only_baseline}",
"python3 posebench/data/chai_output_extraction.py dataset={dataset} pocket_only_baseline={pocket_only_baseline} repeat_index={repeat_index}",
],
"relax": [
"python3 posebench/models/inference_relaxation.py method=chai-lab dataset={dataset} cuda_device_index={cuda_device_index} pocket_only_baseline={pocket_only_baseline} relax_protein={relax_protein} remove_initial_protein_hydrogens=true",
"python3 posebench/models/inference_relaxation.py method=chai-lab dataset={dataset} cuda_device_index={cuda_device_index} pocket_only_baseline={pocket_only_baseline} relax_protein={relax_protein} remove_initial_protein_hydrogens=true repeat_index={repeat_index}",
],
"align_complexes": [
"python3 posebench/analysis/complex_alignment.py method=chai-lab dataset={dataset} pocket_only_baseline={pocket_only_baseline}",
"python3 posebench/analysis/complex_alignment.py method=chai-lab dataset={dataset} pocket_only_baseline={pocket_only_baseline} repeat_index={repeat_index}",
],
"analyze_results": [
"python3 posebench/analysis/inference_analysis.py method=chai-lab dataset={dataset} pocket_only_baseline={pocket_only_baseline} relax_protein={relax_protein}",
"python3 posebench/analysis/inference_analysis.py method=chai-lab dataset={dataset} pocket_only_baseline={pocket_only_baseline} relax_protein={relax_protein} repeat_index={repeat_index}",
],
"assemble_casp15": [
"python3 posebench/models/ensemble_generation.py ensemble_methods=[chai-lab] ensemble_ranking_method={ensemble_ranking_method} input_csv_filepath=data/test_cases/casp15/ensemble_inputs.csv output_dir=data/test_cases/casp15/top_chai-lab_ensemble_predictions_{repeat_index} skip_existing=true relax_method_ligands_post_ranking=false relax_protein={relax_protein} export_file_format=casp15 export_top_n=5 combine_casp_output_files=true max_method_predictions=40 method_top_n_to_select=5 resume=true ensemble_benchmarking=true ensemble_benchmarking_dataset=casp15 cuda_device_index={cuda_device_index} ensemble_benchmarking_repeat_index={repeat_index}",
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