fast folding updates

moleculib/protein/dataset.py

@@ -426,29 +426,32 @@ class FastFoldingDataset:
 
     def __init__(
         self, 
-        base = "/mas/projects/molecularmachines/db/FastFoldingProteins/untar/",
+        base = "/mas/projects/molecularmachines/db/FastFoldingProteins/memmap/",
         proteins=None, 
         tau=0,
         shuffle=True,
         stride=1,
         preload=False,
         epoch_size=10000,
         padded=True,
+        num_folders=1,
     ):
-        proteins = list(FAST_FOLDING_PROTEINS.keys())
+        if proteins == None:
+            proteins = list(FAST_FOLDING_PROTEINS.keys())
 
         self.base_path = base 
         self.proteins = proteins 
         self.tau = tau
         self.time_sort = True
         self.stride = stride
         self.epoch_size = epoch_size * len(proteins)
-
+        self.num_folders = num_folders
+
         self.describe()
 
         self.atom_arrays = {
             protein: pdb.PDBFile.read(
-                self.base_path + protein + "_trajectories/0/filtered.pdb"
+                self.base_path + protein + "/0/filtered.pdb"
             ).get_structure()[0] for protein in proteins
         }
         self.atom_arrays = {
@@ -468,8 +471,8 @@ def describe(self):
         self.num_frames = defaultdict(int)
 
         for protein in self.proteins:
-            protein_path = self.base_path + protein + "_trajectories/"
-            for trajectory in os.listdir(protein_path):
+            protein_path = self.base_path + protein + "/"
+            for idx, trajectory in enumerate(os.listdir(protein_path)):
                 if trajectory.startswith("."): continue
                 self.num_trajectories[protein] += 1
                 trajectory_path = protein_path + trajectory + "/"
@@ -481,6 +484,10 @@ def describe(self):
                     if self.files[protein].get(int(trajectory)) is None:
                         self.files[protein][int(trajectory)] = []
                     self.files[protein][int(trajectory)].append(trajectory_path + supframe)
+                if idx == self.num_folders - 1:
+                    break
+
+
         for protein in self.proteins:
             print(f"{protein}: {self.num_trajectories[protein]} trajectories, {self.num_frames[protein]} total frames")
             # print(f"Trajectory lengths: {self.num_frames_per_traj[protein]}")
@@ -491,14 +498,15 @@ def __len__(self):
     def __getitem__(self, idx):
         protein = self.proteins[idx % len(self.proteins)]
 
-        # sample traj and sample file
+        # need to check if len(coord) > self.tau + 1
         while True:
             traj_idx = np.random.randint(0, self.num_trajectories[protein])
             subtraj_idx = np.random.randint(0, self.num_frames_per_traj[protein][traj_idx])
 
             mmap_path = self.files[protein][traj_idx][subtraj_idx]
             coord = open_memmap(mmap_path, mode='r', dtype=np.float32)       
             template = self.atom_arrays[protein]
+
             if len(coord) > self.tau + 1: break
 
         idx1 = np.random.randint(0, len(coord) - self.tau - 1)
@@ -509,7 +517,7 @@ def __getitem__(self, idx):
         p1 = ProteinDatum.from_atom_array(
             aa1,
             header=dict(
-                idcode=None,
+                idcode=protein,
                 resolution=None,
             ),
         )
@@ -524,10 +532,11 @@ def __getitem__(self, idx):
         p2 = ProteinDatum.from_atom_array(
             aa2,
             header=dict(
-                idcode=None,
+                idcode=protein,
                 resolution=None,
             ),
         )
+
         p2 = self.pad.transform(p2)
         return [p1, p2]
 
@@ -552,7 +561,6 @@ class ShardedFastFoldingDataset:
     def __init__(
         self, 
         base = "/mas/projects/molecularmachines/db/FastFoldingProteins/web/",
-        num_shards=240,
         proteins=None, 
         tau=0,
         padded=True,
@@ -566,6 +574,8 @@ def __init__(
             for protein in proteins:
                 assert protein in FAST_FOLDING_PROTEINS.keys(), f'{protein} is not a valid option'
 
+        num_shards = len(list(filter(lambda x: 'shards-' in x, os.listdir(base))))
+
         self.base_path = base 
         self.proteins = proteins 
         self.tau = tau