bug fix (#64)

fastfold/common/residue_constants.py

@@ -1314,3 +1314,179 @@ def aatype_to_str_sequence(aatype):
         restypes_with_x[aatype[i]] 
         for i in range(len(aatype))
     ])
+    
+
+### ALPHAFOLD MULTIMER STUFF ###    
+def _make_chi_atom_indices():
+  """Returns atom indices needed to compute chi angles for all residue types.
+
+  Returns:
+    A tensor of shape [residue_types=21, chis=4, atoms=4]. The residue types are
+    in the order specified in residue_constants.restypes + unknown residue type
+    at the end. For chi angles which are not defined on the residue, the
+    positions indices are by default set to 0.
+  """
+  chi_atom_indices = []
+  for residue_name in restypes:
+    residue_name = restype_1to3[residue_name]
+    residue_chi_angles = chi_angles_atoms[residue_name]
+    atom_indices = []
+    for chi_angle in residue_chi_angles:
+      atom_indices.append(
+          [atom_order[atom] for atom in chi_angle])
+    for _ in range(4 - len(atom_indices)):
+      atom_indices.append([0, 0, 0, 0])  # For chi angles not defined on the AA.
+    chi_atom_indices.append(atom_indices)
+
+  chi_atom_indices.append([[0, 0, 0, 0]] * 4)  # For UNKNOWN residue.
+
+  return np.array(chi_atom_indices)
+
+
+def _make_renaming_matrices():
+  """Matrices to map atoms to symmetry partners in ambiguous case."""
+  # As the atom naming is ambiguous for 7 of the 20 amino acids, provide
+  # alternative groundtruth coordinates where the naming is swapped
+  restype_3 = [
+      restype_1to3[res] for res in restypes
+  ]
+  restype_3 += ['UNK']
+  # Matrices for renaming ambiguous atoms.
+  all_matrices = {res: np.eye(14, dtype=np.float32) for res in restype_3}
+  for resname, swap in residue_atom_renaming_swaps.items():
+    correspondences = np.arange(14)
+    for source_atom_swap, target_atom_swap in swap.items():
+      source_index = restype_name_to_atom14_names[
+          resname].index(source_atom_swap)
+      target_index = restype_name_to_atom14_names[
+          resname].index(target_atom_swap)
+      correspondences[source_index] = target_index
+      correspondences[target_index] = source_index
+      renaming_matrix = np.zeros((14, 14), dtype=np.float32)
+      for index, correspondence in enumerate(correspondences):
+        renaming_matrix[index, correspondence] = 1.
+    all_matrices[resname] = renaming_matrix.astype(np.float32)
+  renaming_matrices = np.stack([all_matrices[restype] for restype in restype_3])
+  return renaming_matrices
+
+
+def _make_restype_atom37_mask():
+  """Mask of which atoms are present for which residue type in atom37."""
+  # create the corresponding mask
+  restype_atom37_mask = np.zeros([21, 37], dtype=np.float32)
+  for restype, restype_letter in enumerate(restypes):
+    restype_name = restype_1to3[restype_letter]
+    atom_names = residue_atoms[restype_name]
+    for atom_name in atom_names:
+      atom_type = atom_order[atom_name]
+      restype_atom37_mask[restype, atom_type] = 1
+  return restype_atom37_mask
+
+
+def _make_restype_atom14_mask():
+  """Mask of which atoms are present for which residue type in atom14."""
+  restype_atom14_mask = []
+
+  for rt in restypes:
+    atom_names = restype_name_to_atom14_names[
+        restype_1to3[rt]]
+    restype_atom14_mask.append([(1. if name else 0.) for name in atom_names])
+
+  restype_atom14_mask.append([0.] * 14)
+  restype_atom14_mask = np.array(restype_atom14_mask, dtype=np.float32)
+  return restype_atom14_mask
+
+
+def _make_restype_atom37_to_atom14():
+  """Map from atom37 to atom14 per residue type."""
+  restype_atom37_to_atom14 = []  # mapping (restype, atom37) --> atom14
+  for rt in restypes:
+    atom_names = restype_name_to_atom14_names[
+        restype_1to3[rt]]
+    atom_name_to_idx14 = {name: i for i, name in enumerate(atom_names)}
+    restype_atom37_to_atom14.append([
+        (atom_name_to_idx14[name] if name in atom_name_to_idx14 else 0)
+        for name in atom_types
+    ])
+
+  restype_atom37_to_atom14.append([0] * 37)
+  restype_atom37_to_atom14 = np.array(restype_atom37_to_atom14, dtype=np.int32)
+  return restype_atom37_to_atom14
+
+
+def _make_restype_atom14_to_atom37():
+  """Map from atom14 to atom37 per residue type."""
+  restype_atom14_to_atom37 = []  # mapping (restype, atom14) --> atom37
+  for rt in restypes:
+    atom_names = restype_name_to_atom14_names[
+        restype_1to3[rt]]
+    restype_atom14_to_atom37.append([
+        (atom_order[name] if name else 0)
+        for name in atom_names
+    ])
+  # Add dummy mapping for restype 'UNK'
+  restype_atom14_to_atom37.append([0] * 14)
+  restype_atom14_to_atom37 = np.array(restype_atom14_to_atom37, dtype=np.int32)
+  return restype_atom14_to_atom37
+
+
+def _make_restype_atom14_is_ambiguous():
+  """Mask which atoms are ambiguous in atom14."""
+  # create an ambiguous atoms mask.  shape: (21, 14)
+  restype_atom14_is_ambiguous = np.zeros((21, 14), dtype=np.float32)
+  for resname, swap in residue_atom_renaming_swaps.items():
+    for atom_name1, atom_name2 in swap.items():
+      restype = restype_order[
+          restype_3to1[resname]]
+      atom_idx1 = restype_name_to_atom14_names[resname].index(
+          atom_name1)
+      atom_idx2 = restype_name_to_atom14_names[resname].index(
+          atom_name2)
+      restype_atom14_is_ambiguous[restype, atom_idx1] = 1
+      restype_atom14_is_ambiguous[restype, atom_idx2] = 1
+
+  return restype_atom14_is_ambiguous
+
+
+def _make_restype_rigidgroup_base_atom37_idx():
+  """Create Map from rigidgroups to atom37 indices."""
+  # Create an array with the atom names.
+  # shape (num_restypes, num_rigidgroups, 3_atoms): (21, 8, 3)
+  base_atom_names = np.full([21, 8, 3], '', dtype=object)
+
+  # 0: backbone frame
+  base_atom_names[:, 0, :] = ['C', 'CA', 'N']
+
+  # 3: 'psi-group'
+  base_atom_names[:, 3, :] = ['CA', 'C', 'O']
+
+  # 4,5,6,7: 'chi1,2,3,4-group'
+  for restype, restype_letter in enumerate(restypes):
+    resname = restype_1to3[restype_letter]
+    for chi_idx in range(4):
+      if chi_angles_mask[restype][chi_idx]:
+        atom_names = chi_angles_atoms[resname][chi_idx]
+        base_atom_names[restype, chi_idx + 4, :] = atom_names[1:]
+
+  # Translate atom names into atom37 indices.
+  lookuptable = atom_order.copy()
+  lookuptable[''] = 0
+  restype_rigidgroup_base_atom37_idx = np.vectorize(lambda x: lookuptable[x])(
+      base_atom_names)
+  return restype_rigidgroup_base_atom37_idx
+
+
+CHI_ATOM_INDICES = _make_chi_atom_indices()
+RENAMING_MATRICES = _make_renaming_matrices()
+RESTYPE_ATOM14_TO_ATOM37 = _make_restype_atom14_to_atom37()
+RESTYPE_ATOM37_TO_ATOM14 = _make_restype_atom37_to_atom14()
+RESTYPE_ATOM37_MASK = _make_restype_atom37_mask()
+RESTYPE_ATOM14_MASK = _make_restype_atom14_mask()
+RESTYPE_ATOM14_IS_AMBIGUOUS = _make_restype_atom14_is_ambiguous()
+RESTYPE_RIGIDGROUP_BASE_ATOM37_IDX = _make_restype_rigidgroup_base_atom37_idx()
+
+# Create mask for existing rigid groups.
+RESTYPE_RIGIDGROUP_MASK = np.zeros([21, 8], dtype=np.float32)
+RESTYPE_RIGIDGROUP_MASK[:, 0] = 1
+RESTYPE_RIGIDGROUP_MASK[:, 3] = 1
+RESTYPE_RIGIDGROUP_MASK[:20, 4:] = chi_angles_mask

fastfold/utils/all_atom_multimer.py

@@ -18,12 +18,7 @@ from typing import Dict, Text, Tuple
 
 import torch
 
-from fastfold.common import residue_const
-
-
-
-
-ants as rc
+from fastfold.common import residue_constants as rc
 from fastfold.utils import geometry, tensor_utils
 import numpy as np