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amoreheadamorehead
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Fix README instructions' syntax and otherwise update in batch
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‎README.md‎

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@@ -229,7 +229,7 @@ Now that we know Docker is functioning properly, we can begin building our Docke
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1. Clone this repository and `cd` into it.
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```bash
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git clone https://github.com/amorehead/DeepInteract
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git clone https://github.com/BioinfoMachineLearning/DeepInteract
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cd DeepInteract/
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DI_DIR=$(pwd)
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```
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```bash
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# Clone this repository:
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git clone https://github.com/amorehead/DeepInteract
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git clone https://github.com/BioinfoMachineLearning/DeepInteract
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# Change to project directory:
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cd DeepInteract
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```bash
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# Download and extract preprocessed DGLGraphs for DIPS-Plus and CASP-CAPRI
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# Requires 7GB of free space
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# Requires ~55GB of free space
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mkdir -p project/datasets/DIPS/final
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cd project/datasets/DIPS/final
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# Download DIPS-Plus
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rm final_processed_dips.tar.gz.parta* final_raw_dips.tar.gz final_processed_dips.tar.gz
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# Download CASP-CAPRI
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mkdir -p ../../CASP_CAPRI/final
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cd ../../CASP_CAPRI/final
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wget https://zenodo.org/record/5546775/files/final_raw_casp_capri.tar.gz
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wget https://zenodo.org/record/5546775/files/final_processed_casp_capri.tar.gz
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rm final_raw_casp_capri.tar.gz final_processed_casp_capri.tar.gz
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```
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Navigate to the project directory and run the training script with the parameters desired:
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```bash
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cd project
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python3 lit_model_train.py --lr 1e-3 --weight_decay 1e-2
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cd ..
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```
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## Inference
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### Download trained model checkpoint
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```bash
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wget -P project/checkpoints https://zenodo.org/record/5546775/files/LitGINI-GeoTran-DilResNet.ckpt
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```
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Navigate to the project directory and run the training script with the parameters desired:
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```bash
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cd project
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python3 lit_model_train.py --lr 1e-3 --weight_decay --1e-2
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cd ..
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```
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## Inference
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### Predict interface contact probability maps
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Navigate to the project directory and run the prediction script

‎project/datasets/CASP_CAPRI/casp_capri_dgl_data_module.py‎

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# -------------------------------------------------------------------------------------------------------------------------------------
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# Following code curated for DeepInteract (https://github.com/amorehead/DeepInteract):
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# Following code curated for DeepInteract (https://github.com/BioinfoMachineLearning/DeepInteract):
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# -------------------------------------------------------------------------------------------------------------------------------------
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‎project/datasets/CASP_CAPRI/casp_capri_dgl_dataset.py‎

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"""Number of protein chains in each complex."""
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return 2
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@property
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def num_classes(self) -> int:
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"""Number of possible classes for each inter-chain residue pair in each complex."""
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return 2
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@property
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def num_node_features(self) -> int:
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"""Number of node feature values after encoding them."""

‎project/datasets/DIPS/dips_dgl_data_module.py‎

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# -------------------------------------------------------------------------------------------------------------------------------------
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# Following code curated for DeepInteract (https://github.com/amorehead/DeepInteract):
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# Following code curated for DeepInteract (https://github.com/BioinfoMachineLearning/DeepInteract):
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# -------------------------------------------------------------------------------------------------------------------------------------
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‎project/datasets/DIPS/dips_dgl_dataset.py‎

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# -------------------------------------------------------------------------------------------------------------------------------------
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# Following code curated for DeepInteract (https://github.com/amorehead/DeepInteract):
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# Following code curated for DeepInteract (https://github.com/BioinfoMachineLearning/DeepInteract):
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# -------------------------------------------------------------------------------------------------------------------------------------
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"""Number of protein chains in each complex."""
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return 2
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@property
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def num_classes(self) -> int:
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"""Number of possible classes for each inter-chain residue pair in each complex."""
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return 2
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@property
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def num_node_features(self) -> int:
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"""Number of node feature values after encoding them."""

‎project/datasets/PICP/picp_dgl_data_module.py‎

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# -------------------------------------------------------------------------------------------------------------------------------------
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# Following code curated for DeepInteract (https://github.com/amorehead/DeepInteract):
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# Following code curated for DeepInteract (https://github.com/BioinfoMachineLearning/DeepInteract):
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# -------------------------------------------------------------------------------------------------------------------------------------
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‎project/datasets/builder/check_percent_identity.py‎

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# -------------------------------------------------------------------------------------------------------------------------------------
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# Following code curated for DeepInteract (https://github.com/amorehead/DeepInteract):
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# Following code curated for DeepInteract (https://github.com/BioinfoMachineLearning/DeepInteract):
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# -------------------------------------------------------------------------------------------------------------------------------------
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‎project/datasets/builder/collect_dataset_statistics.py‎

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# -------------------------------------------------------------------------------------------------------------------------------------
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# Following code curated for DeepInteract (https://github.com/amorehead/DeepInteract):
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# Following code curated for DeepInteract (https://github.com/BioinfoMachineLearning/DeepInteract):
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# -------------------------------------------------------------------------------------------------------------------------------------
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‎project/datasets/builder/impute_missing_feature_values.py‎

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# -------------------------------------------------------------------------------------------------------------------------------------
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# Following code curated for DeepInteract (https://github.com/amorehead/DeepInteract):
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# Following code curated for DeepInteract (https://github.com/BioinfoMachineLearning/DeepInteract):
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# -------------------------------------------------------------------------------------------------------------------------------------
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@click.command()

‎project/datasets/builder/log_dataset_statistics.py‎

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# -------------------------------------------------------------------------------------------------------------------------------------
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# Following code curated for DeepInteract (https://github.com/amorehead/DeepInteract):
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# Following code curated for DeepInteract (https://github.com/BioinfoMachineLearning/DeepInteract):
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# -------------------------------------------------------------------------------------------------------------------------------------
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@click.command()

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