--- /content/alphafold_ori/common/protein.py	2021-08-10 10:03:26.580274340 +0000
+++ /content/alphafold/alphafold/common/protein.py	2021-08-10 10:04:47.660884323 +0000
@@ -19,6 +19,9 @@
 from alphafold.common import residue_constants
 from Bio.PDB import PDBParser
 import numpy as np
+from string import ascii_uppercase,ascii_lowercase
+
+CHAIN_IDs = ascii_uppercase+ascii_lowercase
 
 FeatureDict = Mapping[str, np.ndarray]
 ModelOutput = Mapping[str, Any]  # Is a nested dict.
@@ -75,14 +78,15 @@
 
   if chain_id is not None:
     chain = model[chain_id]
+    chains = [chain]
   else:
     chains = list(model.get_chains())
-    if len(chains) != 1:
-      raise ValueError(
-          'Only single chain PDBs are supported when chain_id not specified. '
-          f'Found {len(chains)} chains.')
-    else:
-      chain = chains[0]
+  #  if len(chains) != 1:
+  #    raise ValueError(
+  #        'Only single chain PDBs are supported when chain_id not specified. '
+  #        f'Found {len(chains)} chains.')
+  #  else:
+  #    chain = chains[0]
 
   atom_positions = []
   aatype = []
@@ -90,31 +94,35 @@
   residue_index = []
   b_factors = []
 
-  for res in chain:
-    if res.id[2] != ' ':
-      raise ValueError(
-          f'PDB contains an insertion code at chain {chain.id} and residue '
-          f'index {res.id[1]}. These are not supported.')
-    res_shortname = residue_constants.restype_3to1.get(res.resname, 'X')
-    restype_idx = residue_constants.restype_order.get(
-        res_shortname, residue_constants.restype_num)
-    pos = np.zeros((residue_constants.atom_type_num, 3))
-    mask = np.zeros((residue_constants.atom_type_num,))
-    res_b_factors = np.zeros((residue_constants.atom_type_num,))
-    for atom in res:
-      if atom.name not in residue_constants.atom_types:
+  PARAM_CHAIN_BREAK = 100
+  residue_index_prev = 0
+  for k,chain in enumerate(chains):
+    for res in chain:
+      if res.id[2] != ' ':
+        raise ValueError(
+            f'PDB contains an insertion code at chain {chain.id} and residue '
+            f'index {res.id[1]}. These are not supported.')
+      res_shortname = residue_constants.restype_3to1.get(res.resname, 'X')
+      restype_idx = residue_constants.restype_order.get(
+          res_shortname, residue_constants.restype_num)
+      pos = np.zeros((residue_constants.atom_type_num, 3))
+      mask = np.zeros((residue_constants.atom_type_num,))
+      res_b_factors = np.zeros((residue_constants.atom_type_num,))
+      for atom in res:
+        if atom.name not in residue_constants.atom_types:
+          continue
+        pos[residue_constants.atom_order[atom.name]] = atom.coord
+        mask[residue_constants.atom_order[atom.name]] = 1.
+        res_b_factors[residue_constants.atom_order[atom.name]] = atom.bfactor
+      if np.sum(mask) < 0.5:
+        # If no known atom positions are reported for the residue then skip it.
         continue
-      pos[residue_constants.atom_order[atom.name]] = atom.coord
-      mask[residue_constants.atom_order[atom.name]] = 1.
-      res_b_factors[residue_constants.atom_order[atom.name]] = atom.bfactor
-    if np.sum(mask) < 0.5:
-      # If no known atom positions are reported for the residue then skip it.
-      continue
-    aatype.append(restype_idx)
-    atom_positions.append(pos)
-    atom_mask.append(mask)
-    residue_index.append(res.id[1])
-    b_factors.append(res_b_factors)
+      aatype.append(restype_idx)
+      atom_positions.append(pos)
+      atom_mask.append(mask)
+      residue_index.append(res.id[1] + residue_index_prev + PARAM_CHAIN_BREAK*k)
+      b_factors.append(res_b_factors)
+    residue_index_prev = residue_index[-1]
 
   return Protein(
       atom_positions=np.array(atom_positions),
@@ -150,10 +158,21 @@
 
   pdb_lines.append('MODEL     1')
   atom_index = 1
-  chain_id = 'A'
+  chain_index = -1
+  residue_index_prev = residue_index[0]-100
   # Add all atom sites.
   for i in range(aatype.shape[0]):
+    if residue_index[i] - residue_index_prev > 1:   # chain break
+      chain_index += 1
+      res_num = 1
+      if chain_index > 0:
+        pdb_lines.append("TER")
+    elif residue_index[i] != residue_index_prev:
+      res_num += 1
+    residue_index_prev = residue_index[i]
+    chain_id = CHAIN_IDs[chain_index]
     res_name_3 = res_1to3(aatype[i])
+    #
     for atom_name, pos, mask, b_factor in zip(
         atom_types, atom_positions[i], atom_mask[i], b_factors[i]):
       if mask < 0.5:
@@ -169,7 +188,7 @@
       # PDB is a columnar format, every space matters here!
       atom_line = (f'{record_type:<6}{atom_index:>5} {name:<4}{alt_loc:>1}'
                    f'{res_name_3:>3} {chain_id:>1}'
-                   f'{residue_index[i]:>4}{insertion_code:>1}   '
+                   f'{res_num:>4}{insertion_code:>1}   '
                    f'{pos[0]:>8.3f}{pos[1]:>8.3f}{pos[2]:>8.3f}'
                    f'{occupancy:>6.2f}{b_factor:>6.2f}          '
                    f'{element:>2}{charge:>2}')