Merge pull request #4 from BioinfoMachineLearning/develop

Develop to Master Small Checkpoint

Author: amorehead

README.md

@@ -18,7 +18,7 @@ The Enhanced Database of Interacting Protein Structures for Interface Prediction
 
 ## Citation
 
-```
+```bibtex
 @misc{morehead2021dipsplus,
       title={DIPS-Plus: The Enhanced Database of Interacting Protein Structures for Interface Prediction}, 
       author={Alex Morehead and Chen Chen and Ada Sedova and Jianlin Cheng},
@@ -184,7 +184,7 @@ python3 project/datasets/builder/postprocess_pruned_pairs.py "$PROJDIR"/project/
 python3 project/datasets/builder/partition_dataset_filenames.py "$PROJDIR"/project/datasets/DIPS/final/raw --source_type rcsb --filter_by_atom_count True --max_atom_count 17500 --rank "$1" --size "$2"
 python3 project/datasets/builder/collect_dataset_statistics.py "$PROJDIR"/project/datasets/DIPS/final/raw --rank "$1" --size "$2"
 python3 project/datasets/builder/log_dataset_statistics.py "$PROJDIR"/project/datasets/DIPS/final/raw --rank "$1" --size "$2"
-python3 project/datasets/builder/impute_missing_feature_values.py "$PROJDIR"/project/datasets/DIPS/final/raw --impute_atom_features False --num_cpus 32 --rank "$1" --size "$2"
+python3 project/datasets/builder/impute_missing_feature_values.py "$PROJDIR"/project/datasets/DIPS/final/raw --impute_atom_features False --advanced_logging False --num_cpus 32 --rank "$1" --size "$2"
 
 # Optionally convert each postprocessed (final 'raw') complex into a pair of DGL graphs (final 'processed') with labels
 python3 project/datasets/builder/convert_complexes_to_graphs.py "$PROJDIR"/project/datasets/DIPS/final/raw "$PROJDIR"/project/datasets/DIPS/final/processed --num_cpus 32 --edge_dist_cutoff 15.0 --edge_limit 5000 --self_loops True --rank "$1" --size "$2"
@@ -223,7 +223,7 @@ python3 project/datasets/builder/postprocess_pruned_pairs.py "$PROJDIR"/project/
 python3 project/datasets/builder/partition_dataset_filenames.py "$PROJDIR"/project/datasets/DB5/final/raw --source_type db5 --rank "$1" --size "$2"
 python3 project/datasets/builder/collect_dataset_statistics.py "$PROJDIR"/project/datasets/DB5/final/raw --rank "$1" --size "$2"
 python3 project/datasets/builder/log_dataset_statistics.py "$PROJDIR"/project/datasets/DB5/final/raw --rank "$1" --size "$2"
-python3 project/datasets/builder/impute_missing_feature_values.py "$PROJDIR"/project/datasets/DB5/final/raw --impute_atom_features False --num_cpus 32 --rank "$1" --size "$2"
+python3 project/datasets/builder/impute_missing_feature_values.py "$PROJDIR"/project/datasets/DB5/final/raw --impute_atom_features False --advanced_logging False --num_cpus 32 --rank "$1" --size "$2"
 
 # Optionally convert each postprocessed (final 'raw') complex into a pair of DGL graphs (final 'processed') with labels
 python3 project/datasets/builder/convert_complexes_to_graphs.py "$PROJDIR"/project/datasets/DB5/final/raw "$PROJDIR"/project/datasets/DB5/final/processed --num_cpus 32 --edge_dist_cutoff 15.0 --edge_limit 5000 --self_loops True --rank "$1" --size "$2"

project/datasets/builder/generate_psaia_features.py

@@ -6,7 +6,7 @@
 import os
 
 import click
-from atom3.conservation import map_all_protrusion_indices
+import atom3.conservation as con
 
 from project.utils.utils import get_global_node_rank
 
@@ -39,7 +39,7 @@ def main(psaia_dir: str, psaia_config: str, pdb_dataset: str, pkl_dataset: str,
             os.environ["PATH"] += os.path.sep + PSAIA_PATH
 
         # Generate protrusion indices
-        map_all_protrusion_indices(psaia_config, pdb_dataset, pkl_dataset, pruned_dataset, output_dir, source_type)
+        con.map_all_protrusion_indices(psaia_config, pdb_dataset, pkl_dataset, pruned_dataset, output_dir, source_type)
 
 
 if __name__ == '__main__':