Fix batching of missing_atom_masks, and clean up code (#160)

* Update filter_pdb_test_mmcifs.py

* Update filter_pdb_train_mmcifs.py

* Update inputs.py

* Update weighted_pdb_sampler.py

* Update inputs.py

Author: amorehead

alphafold3_pytorch/data/weighted_pdb_sampler.py

@@ -193,7 +193,7 @@ def __init__(
         alpha_nuc: float = 3.0,
         alpha_ligand: float = 1.0,
         pdb_ids_to_skip: List[str] = [],
-        subset_to_ids: list[int] | None = None,
+        pdb_ids_to_keep: list[str] | None = None,
     ):
         # Load chain and interface mappings
         if not isinstance(chain_mapping_paths, list):
@@ -226,28 +226,24 @@ def __init__(
             "Precomputing chain and interface weights. This may take several minutes to complete."
         )
 
-        # Subset to specific indices if provided
-        if exists(subset_to_ids):
-            chain_mapping = (
-                chain_mapping.with_row_index()
-                .filter(pl.col("index").is_in(subset_to_ids))
-                .select(["pdb_id", "chain_id", "molecule_id", "cluster_id"])
+        # Subset to specific PDB IDs if provided
+        if exists(pdb_ids_to_keep):
+            chain_mapping = chain_mapping.filter(pl.col("pdb_id").is_in(pdb_ids_to_keep)).select(
+                ["pdb_id", "chain_id", "molecule_id", "cluster_id"]
             )
-            interface_mapping = (
-                interface_mapping.with_row_index()
-                .filter(pl.col("index").is_in(subset_to_ids))
-                .select(
-                    [
-                        "pdb_id",
-                        "interface_chain_id_1",
-                        "interface_chain_id_2",
-                        "interface_molecule_id_1",
-                        "interface_molecule_id_2",
-                        "interface_chain_cluster_id_1",
-                        "interface_chain_cluster_id_2",
-                        "interface_cluster_id",
-                    ]
-                )
+            interface_mapping = interface_mapping.filter(
+                pl.col("pdb_id").is_in(pdb_ids_to_keep)
+            ).select(
+                [
+                    "pdb_id",
+                    "interface_chain_id_1",
+                    "interface_chain_id_2",
+                    "interface_molecule_id_1",
+                    "interface_molecule_id_2",
+                    "interface_chain_cluster_id_1",
+                    "interface_chain_cluster_id_2",
+                    "interface_cluster_id",
+                ]
             )
 
         chain_mapping.insert_column(

alphafold3_pytorch/inputs.py

@@ -63,7 +63,7 @@
     is_polymer,
 )
 from alphafold3_pytorch.utils.model_utils import exclusive_cumsum
-from alphafold3_pytorch.utils.utils import default, exists, first, identity
+from alphafold3_pytorch.utils.utils import default, exists, first
 
 # silence RDKit's warnings
 
@@ -166,7 +166,8 @@ def inner(x, *args, **kwargs):
 }
 
 ATOM_DEFAULT_PAD_VALUES = dict(
-    molecule_atom_lens = 0
+    molecule_atom_lens = 0,
+    missing_atom_mask = True
 )
 
 @typecheck
@@ -2678,10 +2679,6 @@ def __init__(
         assert folder.exists() and folder.is_dir(), f"{str(folder)} does not exist for PDBDataset"
         self.folder = folder
 
-        self.files = {
-            os.path.splitext(os.path.basename(file.name))[0]: file
-            for file in folder.glob(os.path.join("**", "*.cif"))
-        }
         self.sampler = sampler
         self.sample_type = sample_type
         self.training = training
@@ -2700,9 +2697,14 @@ def __init__(
         if exists(self.sampler):
             sampler_pdb_ids = set(self.sampler.mappings.get_column("pdb_id").to_list())
             self.files = {
-                file: filepath
-                for (file, filepath) in self.files.items()
-                if file in sampler_pdb_ids
+                os.path.splitext(os.path.basename(filepath.name))[0]: filepath
+                for filepath in folder.glob(os.path.join("**", "*.cif"))
+                if os.path.splitext(os.path.basename(filepath.name))[0] in sampler_pdb_ids
+            }
+        else:
+            self.files = {
+                os.path.splitext(os.path.basename(file.name))[0]: file
+                for file in folder.glob(os.path.join("**", "*.cif"))
             }
 
         if exists(sample_only_pdb_ids):

scripts/filter_pdb_test_mmcifs.py

@@ -24,7 +24,6 @@
 import glob
 import os
 from datetime import datetime
-from typing import List, Tuple
 
 import timeout_decorator
 from tqdm.contrib.concurrent import process_map

scripts/filter_pdb_train_mmcifs.py

@@ -37,7 +37,6 @@
 import random
 from datetime import datetime
 from operator import itemgetter
-from typing import Dict, List, Set, Tuple
 
 import numpy as np
 import timeout_decorator