# Path: alphafold/common/residue_constants.py
# def load_stereo_chemical_props() -> Tuple[Mapping[str, List[Bond]],
#   def make_bond_key(atom1_name, atom2_name):
# def sequence_to_onehot(
#     sequence: str,
#     mapping: Mapping[str, int],
#     map_unknown_to_x: bool = False) -> np.ndarray:
# def _make_standard_atom_mask() -> np.ndarray:
# def chi_angle_atom(atom_index: int) -> np.ndarray:
# def _make_rigid_transformation_4x4(ex, ey, translation):
# def _make_rigid_group_constants():
# def make_atom14_dists_bounds(overlap_tolerance=1.5,
#                              bond_length_tolerance_factor=15):
# HHBLITS_AA_TO_ID = {
#     'A': 0,
#     'B': 2,
#     'C': 1,
#     'D': 2,
#     'E': 3,
#     'F': 4,
#     'G': 5,
#     'H': 6,
#     'I': 7,
#     'J': 20,
#     'K': 8,
#     'L': 9,
#     'M': 10,
#     'N': 11,
#     'O': 20,
#     'P': 12,
#     'Q': 13,
#     'R': 14,
#     'S': 15,
#     'T': 16,
#     'U': 1,
#     'V': 17,
#     'W': 18,
#     'X': 20,
#     'Y': 19,
#     'Z': 3,
#     '-': 21,
# }
# ID_TO_HHBLITS_AA = {
#     0: 'A',
#     1: 'C',  # Also U.
#     2: 'D',  # Also B.
#     3: 'E',  # Also Z.
#     4: 'F',
#     5: 'G',
#     6: 'H',
#     7: 'I',
#     8: 'K',
#     9: 'L',
#     10: 'M',
#     11: 'N',
#     12: 'P',
#     13: 'Q',
#     14: 'R',
#     15: 'S',
#     16: 'T',
#     17: 'V',
#     18: 'W',
#     19: 'Y',
#     20: 'X',  # Includes J and O.
#     21: '-',
# }
# MAP_HHBLITS_AATYPE_TO_OUR_AATYPE = tuple(
#     restypes_with_x_and_gap.index(ID_TO_HHBLITS_AA[i])
#     for i in range(len(restypes_with_x_and_gap)))
# STANDARD_ATOM_MASK = _make_standard_atom_mask()


import io
import numpy as np
from alphafold.common import residue_constants
from Bio import PDB
from simtk.openmm import app as openmm_app
from simtk.openmm.app.internal.pdbstructure import PdbStructure
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

"""Utils for minimization."""


def overwrite_pdb_coordinates(pdb_str: str, pos) -> str:
  pdb_file = io.StringIO(pdb_str)
  structure = PdbStructure(pdb_file)
  topology = openmm_app.PDBFile(structure).getTopology()
  with io.StringIO() as f:
    openmm_app.PDBFile.writeFile(topology, pos, f)
    return f.getvalue()


def overwrite_b_factors(pdb_str: str, bfactors: np.ndarray) -> str:
  """Overwrites the B-factors in pdb_str with contents of bfactors array.

  Args:
    pdb_str: An input PDB string.
    bfactors: A numpy array with shape [1, n_residues, 37]. We assume that the
      B-factors are per residue; i.e. that the nonzero entries are identical in
      [0, i, :].

  Returns:
    A new PDB string with the B-factors replaced.
  """

# Path: alphafold/common/residue_constants.py
# def load_stereo_chemical_props() -> Tuple[Mapping[str, List[Bond]],
#   def make_bond_key(atom1_name, atom2_name):
# def sequence_to_onehot(
#     sequence: str,
#     mapping: Mapping[str, int],
#     map_unknown_to_x: bool = False) -> np.ndarray:
# def _make_standard_atom_mask() -> np.ndarray:
# def chi_angle_atom(atom_index: int) -> np.ndarray:
# def _make_rigid_transformation_4x4(ex, ey, translation):
# def _make_rigid_group_constants():
# def make_atom14_dists_bounds(overlap_tolerance=1.5,
#                              bond_length_tolerance_factor=15):
# HHBLITS_AA_TO_ID = {
#     'A': 0,
#     'B': 2,
#     'C': 1,
#     'D': 2,
#     'E': 3,
#     'F': 4,
#     'G': 5,
#     'H': 6,
#     'I': 7,
#     'J': 20,
#     'K': 8,
#     'L': 9,
#     'M': 10,
#     'N': 11,
#     'O': 20,
#     'P': 12,
#     'Q': 13,
#     'R': 14,
#     'S': 15,
#     'T': 16,
#     'U': 1,
#     'V': 17,
#     'W': 18,
#     'X': 20,
#     'Y': 19,
#     'Z': 3,
#     '-': 21,
# }
# ID_TO_HHBLITS_AA = {
#     0: 'A',
#     1: 'C',  # Also U.
#     2: 'D',  # Also B.
#     3: 'E',  # Also Z.
#     4: 'F',
#     5: 'G',
#     6: 'H',
#     7: 'I',
#     8: 'K',
#     9: 'L',
#     10: 'M',
#     11: 'N',
#     12: 'P',
#     13: 'Q',
#     14: 'R',
#     15: 'S',
#     16: 'T',
#     17: 'V',
#     18: 'W',
#     19: 'Y',
#     20: 'X',  # Includes J and O.
#     21: '-',
# }
# MAP_HHBLITS_AATYPE_TO_OUR_AATYPE = tuple(
#     restypes_with_x_and_gap.index(ID_TO_HHBLITS_AA[i])
#     for i in range(len(restypes_with_x_and_gap)))
# STANDARD_ATOM_MASK = _make_standard_atom_mask()


# Path: alphafold/relax/utils.py
import io
import numpy as np
from alphafold.common import residue_constants
from Bio import PDB
from simtk.openmm import app as openmm_app
from simtk.openmm.app.internal.pdbstructure import PdbStructure

# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

"""Utils for minimization."""


def overwrite_pdb_coordinates(pdb_str: str, pos) -> str:
  pdb_file = io.StringIO(pdb_str)
  structure = PdbStructure(pdb_file)
  topology = openmm_app.PDBFile(structure).getTopology()
  with io.StringIO() as f:
    openmm_app.PDBFile.writeFile(topology, pos, f)
    return f.getvalue()


def overwrite_b_factors(pdb_str: str, bfactors: np.ndarray) -> str:
  """Overwrites the B-factors in pdb_str with contents of bfactors array.

  Args:
    pdb_str: An input PDB string.
    bfactors: A numpy array with shape [1, n_residues, 37]. We assume that the
      B-factors are per residue; i.e. that the nonzero entries are identical in
      [0, i, :].

  Returns:
    A new PDB string with the B-factors replaced.
  """

  if bfactors.shape[-1] != residue_constants.atom_type_num: