update data_transforms_multimer to the latest version of multimer branch

openfold/data/data_transforms_multimer.py

@@ -347,7 +347,7 @@ def get_spatial_crop_idx(protein, crop_size, interface_threshold, generator):
         return get_contiguous_crop_idx(protein, crop_size, generator)
 
     target_res_idx = randint(lower=0,
-                             upper=interface_residues.shape[-1],
+                             upper=interface_residues.shape[-1] - 1,
                              generator=generator,
                              device=positions.device)
 
@@ -374,43 +374,45 @@ def get_spatial_crop_idx(protein, crop_size, interface_threshold, generator):
 
 
 def get_contiguous_crop_idx(protein, crop_size, generator):
-    unique_asym_ids, chain_lens = protein["asym_id"].unique(return_counts=True)
+    unique_asym_ids, chain_idxs, chain_lens = protein["asym_id"].unique(dim=-1,
+                                                                        return_inverse=True,
+                                                                        return_counts=True)
+
     shuffle_idx = torch.randperm(chain_lens.shape[-1], device=chain_lens.device, generator=generator)
-    num_remaining = int(chain_lens.sum())
+
+    _, idx_sorted = torch.sort(chain_idxs, stable=True)
+    cum_sum = chain_lens.cumsum(dim=0)
+    cum_sum = torch.cat((torch.tensor([0]), cum_sum[:-1]), dim=0)
+    asym_offsets = idx_sorted[cum_sum]
+
     num_budget = crop_size
+    num_remaining = int(protein["seq_length"])
+
     crop_idxs = []
+    for idx in shuffle_idx:
+        chain_len = int(chain_lens[idx])
+        num_remaining -= chain_len
 
-    per_asym_residue_index = {}
-    for cur_asym_id in unique_asym_ids:
-        asym_mask = (protein["asym_id"]== cur_asym_id).bool()
-        per_asym_residue_index[int(cur_asym_id)] = torch.masked_select(protein["asym_id"], asym_mask)[0]
-
-    for j, idx in enumerate(shuffle_idx):
-        this_len = int(chain_lens[idx])
-        num_remaining -= this_len
-        # num res at most we can keep in this ent
-        crop_size_max = min(num_budget, this_len)
-        # num res at least we shall keep in this ent
-        crop_size_min = min(this_len, max(0, num_budget - num_remaining))
+        crop_size_max = min(num_budget, chain_len)
+        crop_size_min = min(chain_len, max(0, num_budget - num_remaining))
         chain_crop_size = randint(lower=crop_size_min,
-                                  upper=crop_size_max + 1,
+                                  upper=crop_size_max,
                                   generator=generator,
                                   device=chain_lens.device)
 
+        num_budget -= chain_crop_size
+
         chain_start = randint(lower=0,
-                              upper=this_len - chain_crop_size + 1,
+                              upper=chain_len - chain_crop_size,
                               generator=generator,
                               device=chain_lens.device)
-        cur_asym_id = unique_asym_ids[int(idx)].item()
-        asym_offset = per_asym_residue_index[int(cur_asym_id)]
+
+        asym_offset = asym_offsets[idx]
         crop_idxs.append(
             torch.arange(asym_offset + chain_start, asym_offset + chain_start + chain_crop_size)
         )
-        asym_offset += this_len
-
-        num_budget -= chain_crop_size
 
-    return torch.concat(crop_idxs)
+    return torch.concat(crop_idxs).sort().values
 
 
 @curry1
@@ -453,7 +455,7 @@ def random_crop_to_size(
 
     if subsample_templates:
         templates_crop_start = randint(lower=0,
-                                       upper=num_templates + 1,
+                                       upper=num_templates,
                                        generator=g,
                                        device=protein["seq_length"].device)
         templates_select_indices = torch.randperm(
@@ -480,8 +482,7 @@ def random_crop_to_size(
         for i, (dim_size, dim) in enumerate(zip(shape_schema[k], v.shape)):
             is_num_res = dim_size == NUM_RES
             if i == 0 and k.startswith("template"):
-                crop_start = templates_crop_start
-                v = v[slice(crop_start, crop_start + num_templates_crop_size)]
+                v = v[slice(templates_crop_start, templates_crop_start + num_templates_crop_size)]
             elif is_num_res:
                 v = torch.index_select(v, i, crop_idxs)