add inference pipeline from openfold/alphafold

fastfold/relax/amber_minimize.py

+# Copyright 2021 AlQuraishi Laboratory
+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# 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.
+"""Restrained Amber Minimization of a structure."""
+
+import io
+import time
+from typing import Collection, Optional, Sequence, Dict
+
+from absl import logging
+from fastfold.common import (
+    protein,
+    residue_constants,
+)
+import fastfold.model.loss as loss
+from fastfold.relax import cleanup, utils
+import ml_collections
+import numpy as np
+from simtk import openmm
+from simtk import unit
+from simtk.openmm import app as openmm_app
+from simtk.openmm.app.internal.pdbstructure import PdbStructure
+
+ENERGY = unit.kilocalories_per_mole
+LENGTH = unit.angstroms
+
+
+def will_restrain(atom: openmm_app.Atom, rset: str) -> bool:
+    """Returns True if the atom will be restrained by the given restraint set."""
+
+    if rset == "non_hydrogen":
+        return atom.element.name != "hydrogen"
+    elif rset == "c_alpha":
+        return atom.name == "CA"
+
+
+def _add_restraints(
+    system: openmm.System,
+    reference_pdb: openmm_app.PDBFile,
+    stiffness: unit.Unit,
+    rset: str,
+    exclude_residues: Sequence[int],
+):
+    """Adds a harmonic potential that restrains the system to a structure."""
+    assert rset in ["non_hydrogen", "c_alpha"]
+
+    force = openmm.CustomExternalForce("0.5 * k * ((x-x0)^2 + (y-y0)^2 + (z-z0)^2)")
+    force.addGlobalParameter("k", stiffness)
+    for p in ["x0", "y0", "z0"]:
+        force.addPerParticleParameter(p)
+
+    for i, atom in enumerate(reference_pdb.topology.atoms()):
+        if atom.residue.index in exclude_residues:
+            continue
+        if will_restrain(atom, rset):
+            force.addParticle(i, reference_pdb.positions[i])
+    logging.info(
+        "Restraining %d / %d particles.",
+        force.getNumParticles(),
+        system.getNumParticles(),
+    )
+    system.addForce(force)
+
+
+def _openmm_minimize(
+    pdb_str: str,
+    max_iterations: int,
+    tolerance: unit.Unit,
+    stiffness: unit.Unit,
+    restraint_set: str,
+    exclude_residues: Sequence[int],
+    use_gpu: bool,
+):
+    """Minimize energy via openmm."""
+
+    pdb_file = io.StringIO(pdb_str)
+    pdb = openmm_app.PDBFile(pdb_file)
+
+    force_field = openmm_app.ForceField("amber99sb.xml")
+    constraints = openmm_app.HBonds
+    system = force_field.createSystem(pdb.topology, constraints=constraints)
+    if stiffness > 0 * ENERGY / (LENGTH**2):
+        _add_restraints(system, pdb, stiffness, restraint_set, exclude_residues)
+
+    integrator = openmm.LangevinIntegrator(0, 0.01, 0.0)
+    platform = openmm.Platform.getPlatformByName("CUDA" if use_gpu else "CPU")
+    simulation = openmm_app.Simulation(pdb.topology, system, integrator, platform)
+    simulation.context.setPositions(pdb.positions)
+
+    ret = {}
+    state = simulation.context.getState(getEnergy=True, getPositions=True)
+    ret["einit"] = state.getPotentialEnergy().value_in_unit(ENERGY)
+    ret["posinit"] = state.getPositions(asNumpy=True).value_in_unit(LENGTH)
+    simulation.minimizeEnergy(maxIterations=max_iterations, tolerance=tolerance)
+    state = simulation.context.getState(getEnergy=True, getPositions=True)
+    ret["efinal"] = state.getPotentialEnergy().value_in_unit(ENERGY)
+    ret["pos"] = state.getPositions(asNumpy=True).value_in_unit(LENGTH)
+    ret["min_pdb"] = _get_pdb_string(simulation.topology, state.getPositions())
+    return ret
+
+
+def _get_pdb_string(topology: openmm_app.Topology, positions: unit.Quantity):
+    """Returns a pdb string provided OpenMM topology and positions."""
+    with io.StringIO() as f:
+        openmm_app.PDBFile.writeFile(topology, positions, f)
+        return f.getvalue()
+
+
+def _check_cleaned_atoms(pdb_cleaned_string: str, pdb_ref_string: str):
+    """Checks that no atom positions have been altered by cleaning."""
+    cleaned = openmm_app.PDBFile(io.StringIO(pdb_cleaned_string))
+    reference = openmm_app.PDBFile(io.StringIO(pdb_ref_string))
+
+    cl_xyz = np.array(cleaned.getPositions().value_in_unit(LENGTH))
+    ref_xyz = np.array(reference.getPositions().value_in_unit(LENGTH))
+
+    for ref_res, cl_res in zip(reference.topology.residues(), cleaned.topology.residues()):
+        assert ref_res.name == cl_res.name
+        for rat in ref_res.atoms():
+            for cat in cl_res.atoms():
+                if cat.name == rat.name:
+                    if not np.array_equal(cl_xyz[cat.index], ref_xyz[rat.index]):
+                        raise ValueError(f"Coordinates of cleaned atom {cat} do not match "
+                                         f"coordinates of reference atom {rat}.")
+
+
+def _check_residues_are_well_defined(prot: protein.Protein):
+    """Checks that all residues contain non-empty atom sets."""
+    if (prot.atom_mask.sum(axis=-1) == 0).any():
+        raise ValueError("Amber minimization can only be performed on proteins with"
+                         " well-defined residues. This protein contains at least"
+                         " one residue with no atoms.")
+
+
+def _check_atom_mask_is_ideal(prot):
+    """Sanity-check the atom mask is ideal, up to a possible OXT."""
+    atom_mask = prot.atom_mask
+    ideal_atom_mask = protein.ideal_atom_mask(prot)
+    utils.assert_equal_nonterminal_atom_types(atom_mask, ideal_atom_mask)
+
+
+def clean_protein(prot: protein.Protein, checks: bool = True):
+    """Adds missing atoms to Protein instance.
+
+    Args:
+      prot: A `protein.Protein` instance.
+      checks: A `bool` specifying whether to add additional checks to the cleaning
+        process.
+
+    Returns:
+      pdb_string: A string of the cleaned protein.
+    """
+    _check_atom_mask_is_ideal(prot)
+
+    # Clean pdb.
+    prot_pdb_string = protein.to_pdb(prot)
+    pdb_file = io.StringIO(prot_pdb_string)
+    alterations_info = {}
+    fixed_pdb = cleanup.fix_pdb(pdb_file, alterations_info)
+    fixed_pdb_file = io.StringIO(fixed_pdb)
+    pdb_structure = PdbStructure(fixed_pdb_file)
+    cleanup.clean_structure(pdb_structure, alterations_info)
+
+    logging.info("alterations info: %s", alterations_info)
+
+    # Write pdb file of cleaned structure.
+    as_file = openmm_app.PDBFile(pdb_structure)
+    pdb_string = _get_pdb_string(as_file.getTopology(), as_file.getPositions())
+    if checks:
+        _check_cleaned_atoms(pdb_string, prot_pdb_string)
+    return pdb_string
+
+
+def make_atom14_positions(prot):
+    """Constructs denser atom positions (14 dimensions instead of 37)."""
+    restype_atom14_to_atom37 = []  # mapping (restype, atom14) --> atom37
+    restype_atom37_to_atom14 = []  # mapping (restype, atom37) --> atom14
+    restype_atom14_mask = []
+
+    for rt in residue_constants.restypes:
+        atom_names = residue_constants.restype_name_to_atom14_names[
+            residue_constants.restype_1to3[rt]]
+
+        restype_atom14_to_atom37.append([
+            (residue_constants.atom_order[name] if name else 0) for name in atom_names
+        ])
+
+        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 residue_constants.atom_types
+        ])
+
+        restype_atom14_mask.append([(1.0 if name else 0.0) for name in atom_names])
+
+    # Add dummy mapping for restype 'UNK'.
+    restype_atom14_to_atom37.append([0] * 14)
+    restype_atom37_to_atom14.append([0] * 37)
+    restype_atom14_mask.append([0.0] * 14)
+
+    restype_atom14_to_atom37 = np.array(restype_atom14_to_atom37, dtype=np.int32)
+    restype_atom37_to_atom14 = np.array(restype_atom37_to_atom14, dtype=np.int32)
+    restype_atom14_mask = np.array(restype_atom14_mask, dtype=np.float32)
+
+    # Create the mapping for (residx, atom14) --> atom37, i.e. an array
+    # with shape (num_res, 14) containing the atom37 indices for this protein.
+    residx_atom14_to_atom37 = restype_atom14_to_atom37[prot["aatype"]]
+    residx_atom14_mask = restype_atom14_mask[prot["aatype"]]
+
+    # Create a mask for known ground truth positions.
+    residx_atom14_gt_mask = residx_atom14_mask * np.take_along_axis(
+        prot["all_atom_mask"], residx_atom14_to_atom37, axis=1).astype(np.float32)
+
+    # Gather the ground truth positions.
+    residx_atom14_gt_positions = residx_atom14_gt_mask[:, :, None] * (np.take_along_axis(
+        prot["all_atom_positions"],
+        residx_atom14_to_atom37[..., None],
+        axis=1,
+    ))
+
+    prot["atom14_atom_exists"] = residx_atom14_mask
+    prot["atom14_gt_exists"] = residx_atom14_gt_mask
+    prot["atom14_gt_positions"] = residx_atom14_gt_positions
+
+    prot["residx_atom14_to_atom37"] = residx_atom14_to_atom37.astype(np.int64)
+
+    # Create the gather indices for mapping back.
+    residx_atom37_to_atom14 = restype_atom37_to_atom14[prot["aatype"]]
+    prot["residx_atom37_to_atom14"] = residx_atom37_to_atom14.astype(np.int64)
+
+    # Create the corresponding mask.
+    restype_atom37_mask = np.zeros([21, 37], dtype=np.float32)
+    for restype, restype_letter in enumerate(residue_constants.restypes):
+        restype_name = residue_constants.restype_1to3[restype_letter]
+        atom_names = residue_constants.residue_atoms[restype_name]
+        for atom_name in atom_names:
+            atom_type = residue_constants.atom_order[atom_name]
+            restype_atom37_mask[restype, atom_type] = 1
+
+    residx_atom37_mask = restype_atom37_mask[prot["aatype"]]
+    prot["atom37_atom_exists"] = residx_atom37_mask
+
+    # As the atom naming is ambiguous for 7 of the 20 amino acids, provide
+    # alternative ground truth coordinates where the naming is swapped
+    restype_3 = [residue_constants.restype_1to3[res] for res in residue_constants.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_constants.residue_atom_renaming_swaps.items():
+        correspondences = np.arange(14)
+        for source_atom_swap, target_atom_swap in swap.items():
+            source_index = residue_constants.restype_name_to_atom14_names[resname].index(
+                source_atom_swap)
+            target_index = residue_constants.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] = 1.0
+        all_matrices[resname] = renaming_matrix.astype(np.float32)
+    renaming_matrices = np.stack([all_matrices[restype] for restype in restype_3])
+
+    # Pick the transformation matrices for the given residue sequence
+    # shape (num_res, 14, 14).
+    renaming_transform = renaming_matrices[prot["aatype"]]
+
+    # Apply it to the ground truth positions. shape (num_res, 14, 3).
+    alternative_gt_positions = np.einsum("rac,rab->rbc", residx_atom14_gt_positions,
+                                         renaming_transform)
+    prot["atom14_alt_gt_positions"] = alternative_gt_positions
+
+    # Create the mask for the alternative ground truth (differs from the
+    # ground truth mask, if only one of the atoms in an ambiguous pair has a
+    # ground truth position).
+    alternative_gt_mask = np.einsum("ra,rab->rb", residx_atom14_gt_mask, renaming_transform)
+
+    prot["atom14_alt_gt_exists"] = alternative_gt_mask
+
+    # Create an ambiguous atoms mask.  shape: (21, 14).
+    restype_atom14_is_ambiguous = np.zeros((21, 14), dtype=np.float32)
+    for resname, swap in residue_constants.residue_atom_renaming_swaps.items():
+        for atom_name1, atom_name2 in swap.items():
+            restype = residue_constants.restype_order[residue_constants.restype_3to1[resname]]
+            atom_idx1 = residue_constants.restype_name_to_atom14_names[resname].index(atom_name1)
+            atom_idx2 = residue_constants.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
+
+    # From this create an ambiguous_mask for the given sequence.
+    prot["atom14_atom_is_ambiguous"] = restype_atom14_is_ambiguous[prot["aatype"]]
+
+    return prot
+
+
+def find_violations(prot_np: protein.Protein):
+    """Analyzes a protein and returns structural violation information.
+
+    Args:
+      prot_np: A protein.
+
+    Returns:
+      violations: A `dict` of structure components with structural violations.
+      violation_metrics: A `dict` of violation metrics.
+    """
+    batch = {
+        "aatype": prot_np.aatype,
+        "all_atom_positions": prot_np.atom_positions.astype(np.float32),
+        "all_atom_mask": prot_np.atom_mask.astype(np.float32),
+        "residue_index": prot_np.residue_index,
+    }
+
+    batch["seq_mask"] = np.ones_like(batch["aatype"], np.float32)
+    batch = make_atom14_positions(batch)
+
+    violations = loss.find_structural_violations_np(
+        batch=batch,
+        atom14_pred_positions=batch["atom14_gt_positions"],
+        config=ml_collections.ConfigDict({
+            "violation_tolerance_factor": 12,  # Taken from model config.
+            "clash_overlap_tolerance": 1.5,  # Taken from model config.
+        }),
+    )
+    violation_metrics = loss.compute_violation_metrics_np(
+        batch=batch,
+        atom14_pred_positions=batch["atom14_gt_positions"],
+        violations=violations,
+    )
+
+    return violations, violation_metrics
+
+
+def get_violation_metrics(prot: protein.Protein):
+    """Computes violation and alignment metrics."""
+    structural_violations, struct_metrics = find_violations(prot)
+    violation_idx = np.flatnonzero(structural_violations["total_per_residue_violations_mask"])
+
+    struct_metrics["residue_violations"] = violation_idx
+    struct_metrics["num_residue_violations"] = len(violation_idx)
+    struct_metrics["structural_violations"] = structural_violations
+    return struct_metrics
+
+
+def _run_one_iteration(
+    *,
+    pdb_string: str,
+    max_iterations: int,
+    tolerance: float,
+    stiffness: float,
+    restraint_set: str,
+    max_attempts: int,
+    exclude_residues: Optional[Collection[int]] = None,
+    use_gpu: bool,
+):
+    """Runs the minimization pipeline.
+
+    Args:
+      pdb_string: A pdb string.
+      max_iterations: An `int` specifying the maximum number of L-BFGS iterations.
+      A value of 0 specifies no limit.
+      tolerance: kcal/mol, the energy tolerance of L-BFGS.
+      stiffness: kcal/mol A**2, spring constant of heavy atom restraining
+        potential.
+      restraint_set: The set of atoms to restrain.
+      max_attempts: The maximum number of minimization attempts.
+      exclude_residues: An optional list of zero-indexed residues to exclude from
+          restraints.
+      use_gpu: Whether to run relaxation on GPU
+    Returns:
+      A `dict` of minimization info.
+    """
+    exclude_residues = exclude_residues or []
+
+    # Assign physical dimensions.
+    tolerance = tolerance * ENERGY
+    stiffness = stiffness * ENERGY / (LENGTH**2)
+
+    start = time.perf_counter()
+    minimized = False
+    attempts = 0
+    while not minimized and attempts < max_attempts:
+        attempts += 1
+        try:
+            logging.info("Minimizing protein, attempt %d of %d.", attempts, max_attempts)
+            ret = _openmm_minimize(
+                pdb_string,
+                max_iterations=max_iterations,
+                tolerance=tolerance,
+                stiffness=stiffness,
+                restraint_set=restraint_set,
+                exclude_residues=exclude_residues,
+                use_gpu=use_gpu,
+            )
+            minimized = True
+        except Exception as e:  # pylint: disable=broad-except
+            print(e)
+            logging.info(e)
+    if not minimized:
+        raise ValueError(f"Minimization failed after {max_attempts} attempts.")
+    ret["opt_time"] = time.perf_counter() - start
+    ret["min_attempts"] = attempts
+    return ret
+
+
+def run_pipeline(
+    prot: protein.Protein,
+    stiffness: float,
+    use_gpu: bool,
+    max_outer_iterations: int = 1,
+    place_hydrogens_every_iteration: bool = True,
+    max_iterations: int = 0,
+    tolerance: float = 2.39,
+    restraint_set: str = "non_hydrogen",
+    max_attempts: int = 100,
+    checks: bool = True,
+    exclude_residues: Optional[Sequence[int]] = None,
+):
+    """Run iterative amber relax.
+
+    Successive relax iterations are performed until all violations have been
+    resolved. Each iteration involves a restrained Amber minimization, with
+    restraint exclusions determined by violation-participating residues.
+
+    Args:
+      prot: A protein to be relaxed.
+      stiffness: kcal/mol A**2, the restraint stiffness.
+      use_gpu: Whether to run on GPU
+      max_outer_iterations: The maximum number of iterative minimization.
+      place_hydrogens_every_iteration: Whether hydrogens are re-initialized
+          prior to every minimization.
+      max_iterations: An `int` specifying the maximum number of L-BFGS steps
+          per relax iteration. A value of 0 specifies no limit.
+      tolerance: kcal/mol, the energy tolerance of L-BFGS.
+          The default value is the OpenMM default.
+      restraint_set: The set of atoms to restrain.
+      max_attempts: The maximum number of minimization attempts per iteration.
+      checks: Whether to perform cleaning checks.
+      exclude_residues: An optional list of zero-indexed residues to exclude from
+          restraints.
+
+    Returns:
+      out: A dictionary of output values.
+    """
+
+    # `protein.to_pdb` will strip any poorly-defined residues so we need to
+    # perform this check before `clean_protein`.
+    _check_residues_are_well_defined(prot)
+    pdb_string = clean_protein(prot, checks=checks)
+
+    exclude_residues = exclude_residues or []
+    exclude_residues = set(exclude_residues)
+    violations = np.inf
+    iteration = 0
+
+    while violations > 0 and iteration < max_outer_iterations:
+        ret = _run_one_iteration(
+            pdb_string=pdb_string,
+            exclude_residues=exclude_residues,
+            max_iterations=max_iterations,
+            tolerance=tolerance,
+            stiffness=stiffness,
+            restraint_set=restraint_set,
+            max_attempts=max_attempts,
+            use_gpu=use_gpu,
+        )
+        prot = protein.from_pdb_string(ret["min_pdb"])
+        if place_hydrogens_every_iteration:
+            pdb_string = clean_protein(prot, checks=True)
+        else:
+            pdb_string = ret["min_pdb"]
+        ret.update(get_violation_metrics(prot))
+        ret.update({
+            "num_exclusions": len(exclude_residues),
+            "iteration": iteration,
+        })
+        violations = ret["violations_per_residue"]
+        exclude_residues = exclude_residues.union(ret["residue_violations"])
+
+        logging.info(
+            "Iteration completed: Einit %.2f Efinal %.2f Time %.2f s "
+            "num residue violations %d num residue exclusions %d ",
+            ret["einit"],
+            ret["efinal"],
+            ret["opt_time"],
+            ret["num_residue_violations"],
+            ret["num_exclusions"],
+        )
+        iteration += 1
+    return ret
+
+
+def get_initial_energies(
+    pdb_strs: Sequence[str],
+    stiffness: float = 0.0,
+    restraint_set: str = "non_hydrogen",
+    exclude_residues: Optional[Sequence[int]] = None,
+):
+    """Returns initial potential energies for a sequence of PDBs.
+
+    Assumes the input PDBs are ready for minimization, and all have the same
+    topology.
+    Allows time to be saved by not pdbfixing / rebuilding the system.
+
+    Args:
+      pdb_strs: List of PDB strings.
+      stiffness: kcal/mol A**2, spring constant of heavy atom restraining
+          potential.
+      restraint_set: Which atom types to restrain.
+      exclude_residues: An optional list of zero-indexed residues to exclude from
+          restraints.
+
+    Returns:
+      A list of initial energies in the same order as pdb_strs.
+    """
+    exclude_residues = exclude_residues or []
+
+    openmm_pdbs = [openmm_app.PDBFile(PdbStructure(io.StringIO(p))) for p in pdb_strs]
+    force_field = openmm_app.ForceField("amber99sb.xml")
+    system = force_field.createSystem(openmm_pdbs[0].topology, constraints=openmm_app.HBonds)
+    stiffness = stiffness * ENERGY / (LENGTH**2)
+    if stiffness > 0 * ENERGY / (LENGTH**2):
+        _add_restraints(system, openmm_pdbs[0], stiffness, restraint_set, exclude_residues)
+    simulation = openmm_app.Simulation(
+        openmm_pdbs[0].topology,
+        system,
+        openmm.LangevinIntegrator(0, 0.01, 0.0),
+        openmm.Platform.getPlatformByName("CPU"),
+    )
+    energies = []
+    for pdb in openmm_pdbs:
+        try:
+            simulation.context.setPositions(pdb.positions)
+            state = simulation.context.getState(getEnergy=True)
+            energies.append(state.getPotentialEnergy().value_in_unit(ENERGY))
+        except Exception as e:  # pylint: disable=broad-except
+            logging.error("Error getting initial energy, returning large value %s", e)
+            energies.append(unit.Quantity(1e20, ENERGY))
+    return energies

fastfold/relax/cleanup.py

+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# 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.
+
+"""Cleans up a PDB file using pdbfixer in preparation for OpenMM simulations.
+
+fix_pdb uses a third-party tool. We also support fixing some additional edge
+cases like removing chains of length one (see clean_structure).
+"""
+import io
+
+import pdbfixer
+from simtk.openmm import app
+from simtk.openmm.app import element
+
+
+def fix_pdb(pdbfile, alterations_info):
+  """Apply pdbfixer to the contents of a PDB file; return a PDB string result.
+
+  1) Replaces nonstandard residues.
+  2) Removes heterogens (non protein residues) including water.
+  3) Adds missing residues and missing atoms within existing residues.
+  4) Adds hydrogens assuming pH=7.0.
+  5) KeepIds is currently true, so the fixer must keep the existing chain and
+     residue identifiers. This will fail for some files in wider PDB that have
+     invalid IDs.
+
+  Args:
+    pdbfile: Input PDB file handle.
+    alterations_info: A dict that will store details of changes made.
+
+  Returns:
+    A PDB string representing the fixed structure.
+  """
+  fixer = pdbfixer.PDBFixer(pdbfile=pdbfile)
+  fixer.findNonstandardResidues()
+  alterations_info['nonstandard_residues'] = fixer.nonstandardResidues
+  fixer.replaceNonstandardResidues()
+  _remove_heterogens(fixer, alterations_info, keep_water=False)
+  fixer.findMissingResidues()
+  alterations_info['missing_residues'] = fixer.missingResidues
+  fixer.findMissingAtoms()
+  alterations_info['missing_heavy_atoms'] = fixer.missingAtoms
+  alterations_info['missing_terminals'] = fixer.missingTerminals
+  fixer.addMissingAtoms(seed=0)
+  fixer.addMissingHydrogens()
+  out_handle = io.StringIO()
+  app.PDBFile.writeFile(fixer.topology, fixer.positions, out_handle,
+                        keepIds=True)
+  return out_handle.getvalue()
+
+
+def clean_structure(pdb_structure, alterations_info):
+  """Applies additional fixes to an OpenMM structure, to handle edge cases.
+
+  Args:
+    pdb_structure: An OpenMM structure to modify and fix.
+    alterations_info: A dict that will store details of changes made.
+  """
+  _replace_met_se(pdb_structure, alterations_info)
+  _remove_chains_of_length_one(pdb_structure, alterations_info)
+
+
+def _remove_heterogens(fixer, alterations_info, keep_water):
+  """Removes the residues that Pdbfixer considers to be heterogens.
+
+  Args:
+    fixer: A Pdbfixer instance.
+    alterations_info: A dict that will store details of changes made.
+    keep_water: If True, water (HOH) is not considered to be a heterogen.
+  """
+  initial_resnames = set()
+  for chain in fixer.topology.chains():
+    for residue in chain.residues():
+      initial_resnames.add(residue.name)
+  fixer.removeHeterogens(keepWater=keep_water)
+  final_resnames = set()
+  for chain in fixer.topology.chains():
+    for residue in chain.residues():
+      final_resnames.add(residue.name)
+  alterations_info['removed_heterogens'] = (
+      initial_resnames.difference(final_resnames))
+
+
+def _replace_met_se(pdb_structure, alterations_info):
+  """Replace the Se in any MET residues that were not marked as modified."""
+  modified_met_residues = []
+  for res in pdb_structure.iter_residues():
+    name = res.get_name_with_spaces().strip()
+    if name == 'MET':
+      s_atom = res.get_atom('SD')
+      if s_atom.element_symbol == 'Se':
+        s_atom.element_symbol = 'S'
+        s_atom.element = element.get_by_symbol('S')
+        modified_met_residues.append(s_atom.residue_number)
+  alterations_info['Se_in_MET'] = modified_met_residues
+
+
+def _remove_chains_of_length_one(pdb_structure, alterations_info):
+  """Removes chains that correspond to a single amino acid.
+
+  A single amino acid in a chain is both N and C terminus. There is no force
+  template for this case.
+
+  Args:
+    pdb_structure: An OpenMM pdb_structure to modify and fix.
+    alterations_info: A dict that will store details of changes made.
+  """
+  removed_chains = {}
+  for model in pdb_structure.iter_models():
+    valid_chains = [c for c in model.iter_chains() if len(c) > 1]
+    invalid_chain_ids = [c.chain_id for c in model.iter_chains() if len(c) <= 1]
+    model.chains = valid_chains
+    for chain_id in invalid_chain_ids:
+      model.chains_by_id.pop(chain_id)
+    removed_chains[model.number] = invalid_chain_ids
+  alterations_info['removed_chains'] = removed_chains
\ No newline at end of file

fastfold/relax/relax.py

+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# 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.
+"""Amber relaxation."""
+from typing import Any, Dict, Sequence, Tuple
+from fastfold.common import protein
+from fastfold.relax import amber_minimize
+from fastfold.relax import utils
+import numpy as np
+
+
+class AmberRelaxation(object):
+    """Amber relaxation."""
+    def __init__(
+        self,
+        *,
+        max_iterations: int,
+        tolerance: float,
+        stiffness: float,
+        exclude_residues: Sequence[int],
+        max_outer_iterations: int,
+        use_gpu: bool,
+    ):
+        """Initialize Amber Relaxer.
+
+        Args:
+          max_iterations: Maximum number of L-BFGS iterations. 0 means no max.
+          tolerance: kcal/mol, the energy tolerance of L-BFGS.
+          stiffness: kcal/mol A**2, spring constant of heavy atom restraining
+            potential.
+          exclude_residues: Residues to exclude from per-atom restraining.
+            Zero-indexed.
+          max_outer_iterations: Maximum number of violation-informed relax
+           iterations. A value of 1 will run the non-iterative procedure used in
+           CASP14. Use 20 so that >95% of the bad cases are relaxed. Relax finishes
+           as soon as there are no violations, hence in most cases this causes no
+           slowdown. In the worst case we do 20 outer iterations.
+          use_gpu: Whether to run on GPU
+        """
+
+        self._max_iterations = max_iterations
+        self._tolerance = tolerance
+        self._stiffness = stiffness
+        self._exclude_residues = exclude_residues
+        self._max_outer_iterations = max_outer_iterations
+        self._use_gpu = use_gpu
+
+    def process(
+        self, *, prot: protein.Protein
+    ) -> Tuple[str, Dict[str, Any], np.ndarray]:
+        """Runs Amber relax on a prediction, adds hydrogens, returns PDB string."""
+        out = amber_minimize.run_pipeline(
+            prot=prot,
+            max_iterations=self._max_iterations,
+            tolerance=self._tolerance,
+            stiffness=self._stiffness,
+            exclude_residues=self._exclude_residues,
+            max_outer_iterations=self._max_outer_iterations,
+            use_gpu=self._use_gpu,
+        )
+        min_pos = out["pos"]
+        start_pos = out["posinit"]
+        rmsd = np.sqrt(np.sum((start_pos - min_pos) ** 2) / start_pos.shape[0])
+        debug_data = {
+            "initial_energy": out["einit"],
+            "final_energy": out["efinal"],
+            "attempts": out["min_attempts"],
+            "rmsd": rmsd,
+        }
+        pdb_str = amber_minimize.clean_protein(prot)
+        min_pdb = utils.overwrite_pdb_coordinates(pdb_str, min_pos)
+        min_pdb = utils.overwrite_b_factors(min_pdb, prot.b_factors)
+        utils.assert_equal_nonterminal_atom_types(
+            protein.from_pdb_string(min_pdb).atom_mask, prot.atom_mask
+        )
+        violations = out["structural_violations"][
+            "total_per_residue_violations_mask"
+        ]
+        return min_pdb, debug_data, violations
\ No newline at end of file

fastfold/relax/utils.py

+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# 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."""
+import io
+import numbers
+import collections
+from fastfold.common import residue_constants
+from Bio import PDB
+import numpy as np
+from simtk.openmm import app as openmm_app
+from simtk.openmm.app.internal.pdbstructure import PdbStructure
+
+
+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:
+        raise ValueError(f'Invalid final dimension size for bfactors: {bfactors.shape[-1]}.')
+
+    parser = PDB.PDBParser(QUIET=True)
+    handle = io.StringIO(pdb_str)
+    structure = parser.get_structure('', handle)
+
+    curr_resid = ('', '', '')
+    idx = -1
+    for atom in structure.get_atoms():
+        atom_resid = atom.parent.get_id()
+        if atom_resid != curr_resid:
+            idx += 1
+            if idx >= bfactors.shape[0]:
+                raise ValueError('Index into bfactors exceeds number of residues. '
+                                 'B-factors shape: {shape}, idx: {idx}.')
+        curr_resid = atom_resid
+        atom.bfactor = bfactors[idx, residue_constants.atom_order['CA']]
+
+    new_pdb = io.StringIO()
+    pdb_io = PDB.PDBIO()
+    pdb_io.set_structure(structure)
+    pdb_io.save(new_pdb)
+    return new_pdb.getvalue()
+
+
+def assert_equal_nonterminal_atom_types(atom_mask: np.ndarray, ref_atom_mask: np.ndarray):
+    """Checks that pre- and post-minimized proteins have same atom set."""
+    # Ignore any terminal OXT atoms which may have been added by minimization.
+    oxt = residue_constants.atom_order['OXT']
+    no_oxt_mask = np.ones(shape=atom_mask.shape, dtype=np.bool)
+    no_oxt_mask[..., oxt] = False
+    np.testing.assert_almost_equal(ref_atom_mask[no_oxt_mask], atom_mask[no_oxt_mask])
+
+
+def mask_mean_np(mask, value, axis=None, drop_mask_channel=False, eps=1e-10):
+    """Masked mean with numpy."""
+    if drop_mask_channel:
+        mask = mask[..., 0]
+
+    mask_shape = mask.shape
+    value_shape = value.shape
+
+    assert len(mask_shape) == len(value_shape)
+
+    if isinstance(axis, numbers.Integral):
+        axis = [axis]
+    elif axis is None:
+        axis = list(range(len(mask_shape)))
+    assert isinstance(
+        axis, collections.Iterable), ('axis needs to be either an iterable, integer or "None"')
+
+    broadcast_factor = 1.
+    for axis_ in axis:
+        value_size = value_shape[axis_]
+        mask_size = mask_shape[axis_]
+        if mask_size == 1:
+            broadcast_factor *= value_size
+        else:
+            assert mask_size == value_size
+
+    axis = tuple(axis)
+    return (np.sum(mask * value, axis=axis) / (np.sum(mask, axis=axis) * broadcast_factor + eps))

fastfold/utils/__init__.py

-from .inject_openfold import inject_openfold
+from .inject_fastnn import inject_fastnn
 
-__all__ = ['inject_openfold']
\ No newline at end of file
+__all__ = ['inject_fastnn']
\ No newline at end of file

fastfold/utils/checkpointing.py

+# Copyright 2021 AlQuraishi Laboratory
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# 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.
+
+import torch
+import torch.utils.checkpoint
+from typing import Any, Tuple, List, Callable, Optional
+
+
+BLOCK_ARG = Any
+BLOCK_ARGS = List[BLOCK_ARG]
+
+
+def get_checkpoint_fn():
+    checkpoint = torch.utils.checkpoint.checkpoint
+
+    return checkpoint
+
+
+@torch.jit.ignore
+def checkpoint_blocks(
+    blocks: List[Callable],
+    args: BLOCK_ARGS,
+    blocks_per_ckpt: Optional[int],
+) -> BLOCK_ARGS:
+    """
+    Chunk a list of blocks and run each chunk with activation
+    checkpointing. We define a "block" as a callable whose only inputs are
+    the outputs of the previous block.
+
+    Implements Subsection 1.11.8
+
+    Args:
+        blocks:
+            List of blocks
+        args:
+            Tuple of arguments for the first block.
+        blocks_per_ckpt:
+            Size of each chunk. A higher value corresponds to fewer 
+            checkpoints, and trades memory for speed. If None, no checkpointing 
+            is performed.
+    Returns:
+        The output of the final block
+    """
+    def wrap(a):
+        return (a,) if type(a) is not tuple else a
+
+    def exec(b, a):
+        for block in b:
+            a = wrap(block(*a))
+        return a
+
+    def chunker(s, e):
+        def exec_sliced(*a):
+            return exec(blocks[s:e], a)
+
+        return exec_sliced
+
+    # Avoids mishaps when the blocks take just one argument
+    args = wrap(args)
+
+    if blocks_per_ckpt is None:
+        return exec(blocks, args)
+    elif blocks_per_ckpt < 1 or blocks_per_ckpt > len(blocks):
+        raise ValueError("blocks_per_ckpt must be between 1 and len(blocks)")
+
+    checkpoint = get_checkpoint_fn() 
+
+    for s in range(0, len(blocks), blocks_per_ckpt):
+        e = s + blocks_per_ckpt
+        args = checkpoint(chunker(s, e), *args)
+        args = wrap(args)
+
+    return args

fastfold/utils/feats.py

+# Copyright 2021 AlQuraishi Laboratory
+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# 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.
+
+import math
+
+import numpy as np
+import torch
+import torch.nn as nn
+from typing import Dict
+
+from fastfold.common import protein
+import fastfold.common.residue_constants as rc
+from fastfold.utils.rigid_utils import Rotation, Rigid
+from fastfold.utils.tensor_utils import (
+    batched_gather,
+    one_hot,
+    tree_map,
+    tensor_tree_map,
+)
+
+
+def pseudo_beta_fn(aatype, all_atom_positions, all_atom_masks):
+    is_gly = aatype == rc.restype_order["G"]
+    ca_idx = rc.atom_order["CA"]
+    cb_idx = rc.atom_order["CB"]
+    pseudo_beta = torch.where(
+        is_gly[..., None].expand(*((-1,) * len(is_gly.shape)), 3),
+        all_atom_positions[..., ca_idx, :],
+        all_atom_positions[..., cb_idx, :],
+    )
+
+    if all_atom_masks is not None:
+        pseudo_beta_mask = torch.where(
+            is_gly,
+            all_atom_masks[..., ca_idx],
+            all_atom_masks[..., cb_idx],
+        )
+        return pseudo_beta, pseudo_beta_mask
+    else:
+        return pseudo_beta
+
+
+def atom14_to_atom37(atom14, batch):
+    atom37_data = batched_gather(
+        atom14,
+        batch["residx_atom37_to_atom14"],
+        dim=-2,
+        no_batch_dims=len(atom14.shape[:-2]),
+    )
+
+    atom37_data = atom37_data * batch["atom37_atom_exists"][..., None]
+
+    return atom37_data
+
+
+def build_template_angle_feat(template_feats):
+    template_aatype = template_feats["template_aatype"]
+    torsion_angles_sin_cos = template_feats["template_torsion_angles_sin_cos"]
+    alt_torsion_angles_sin_cos = template_feats[
+        "template_alt_torsion_angles_sin_cos"
+    ]
+    torsion_angles_mask = template_feats["template_torsion_angles_mask"]
+    template_angle_feat = torch.cat(
+        [
+            nn.functional.one_hot(template_aatype, 22),
+            torsion_angles_sin_cos.reshape(
+                *torsion_angles_sin_cos.shape[:-2], 14
+            ),
+            alt_torsion_angles_sin_cos.reshape(
+                *alt_torsion_angles_sin_cos.shape[:-2], 14
+            ),
+            torsion_angles_mask,
+        ],
+        dim=-1,
+    )
+
+    return template_angle_feat
+
+
+def build_template_pair_feat(
+    batch, min_bin, max_bin, no_bins, eps=1e-20, inf=1e8
+):
+    template_mask = batch["template_pseudo_beta_mask"]
+    template_mask_2d = template_mask[..., None] * template_mask[..., None, :]
+
+    # Compute distogram (this seems to differ slightly from Alg. 5)
+    tpb = batch["template_pseudo_beta"]
+    dgram = torch.sum(
+        (tpb[..., None, :] - tpb[..., None, :, :]) ** 2, dim=-1, keepdim=True
+    )
+    lower = torch.linspace(min_bin, max_bin, no_bins, device=tpb.device) ** 2
+    upper = torch.cat([lower[:-1], lower.new_tensor([inf])], dim=-1)
+    dgram = ((dgram > lower) * (dgram < upper)).type(dgram.dtype)
+
+    to_concat = [dgram, template_mask_2d[..., None]]
+
+    aatype_one_hot = nn.functional.one_hot(
+        batch["template_aatype"],
+        rc.restype_num + 2,
+    )
+
+    n_res = batch["template_aatype"].shape[-1]
+    to_concat.append(
+        aatype_one_hot[..., None, :, :].expand(
+            *aatype_one_hot.shape[:-2], n_res, -1, -1
+        )
+    )
+    to_concat.append(
+        aatype_one_hot[..., None, :].expand(
+            *aatype_one_hot.shape[:-2], -1, n_res, -1
+        )
+    )
+
+    n, ca, c = [rc.atom_order[a] for a in ["N", "CA", "C"]]
+    rigids = Rigid.make_transform_from_reference(
+        n_xyz=batch["template_all_atom_positions"][..., n, :],
+        ca_xyz=batch["template_all_atom_positions"][..., ca, :],
+        c_xyz=batch["template_all_atom_positions"][..., c, :],
+        eps=eps,
+    )
+    points = rigids.get_trans()[..., None, :, :]
+    rigid_vec = rigids[..., None].invert_apply(points)
+
+    inv_distance_scalar = torch.rsqrt(eps + torch.sum(rigid_vec ** 2, dim=-1))
+
+    t_aa_masks = batch["template_all_atom_mask"]
+    template_mask = (
+        t_aa_masks[..., n] * t_aa_masks[..., ca] * t_aa_masks[..., c]
+    )
+    template_mask_2d = template_mask[..., None] * template_mask[..., None, :]
+
+    inv_distance_scalar = inv_distance_scalar * template_mask_2d
+    unit_vector = rigid_vec * inv_distance_scalar[..., None]
+    to_concat.extend(torch.unbind(unit_vector[..., None, :], dim=-1))
+    to_concat.append(template_mask_2d[..., None])
+
+    act = torch.cat(to_concat, dim=-1)
+    act = act * template_mask_2d[..., None]
+
+    return act
+
+
+def build_extra_msa_feat(batch):
+    msa_1hot = nn.functional.one_hot(batch["extra_msa"], 23)
+    msa_feat = [
+        msa_1hot,
+        batch["extra_has_deletion"].unsqueeze(-1),
+        batch["extra_deletion_value"].unsqueeze(-1),
+    ]
+    return torch.cat(msa_feat, dim=-1)
+
+
+def torsion_angles_to_frames(
+    r: Rigid,
+    alpha: torch.Tensor,
+    aatype: torch.Tensor,
+    rrgdf: torch.Tensor,
+):
+    # [*, N, 8, 4, 4]
+    default_4x4 = rrgdf[aatype, ...]
+
+    # [*, N, 8] transformations, i.e.
+    #   One [*, N, 8, 3, 3] rotation matrix and
+    #   One [*, N, 8, 3]    translation matrix
+    default_r = r.from_tensor_4x4(default_4x4)
+
+    bb_rot = alpha.new_zeros((*((1,) * len(alpha.shape[:-1])), 2))
+    bb_rot[..., 1] = 1
+
+    # [*, N, 8, 2]
+    alpha = torch.cat(
+        [bb_rot.expand(*alpha.shape[:-2], -1, -1), alpha], dim=-2
+    )
+
+    # [*, N, 8, 3, 3]
+    # Produces rotation matrices of the form:
+    # [
+    #   [1, 0  , 0  ],
+    #   [0, a_2,-a_1],
+    #   [0, a_1, a_2]
+    # ]
+    # This follows the original code rather than the supplement, which uses
+    # different indices.
+
+    all_rots = alpha.new_zeros(default_r.get_rots().get_rot_mats().shape)
+    all_rots[..., 0, 0] = 1
+    all_rots[..., 1, 1] = alpha[..., 1]
+    all_rots[..., 1, 2] = -alpha[..., 0]
+    all_rots[..., 2, 1:] = alpha
+
+    all_rots = Rigid(Rotation(rot_mats=all_rots), None)
+
+    all_frames = default_r.compose(all_rots)
+
+    chi2_frame_to_frame = all_frames[..., 5]
+    chi3_frame_to_frame = all_frames[..., 6]
+    chi4_frame_to_frame = all_frames[..., 7]
+
+    chi1_frame_to_bb = all_frames[..., 4]
+    chi2_frame_to_bb = chi1_frame_to_bb.compose(chi2_frame_to_frame)
+    chi3_frame_to_bb = chi2_frame_to_bb.compose(chi3_frame_to_frame)
+    chi4_frame_to_bb = chi3_frame_to_bb.compose(chi4_frame_to_frame)
+
+    all_frames_to_bb = Rigid.cat(
+        [
+            all_frames[..., :5],
+            chi2_frame_to_bb.unsqueeze(-1),
+            chi3_frame_to_bb.unsqueeze(-1),
+            chi4_frame_to_bb.unsqueeze(-1),
+        ],
+        dim=-1,
+    )
+
+    all_frames_to_global = r[..., None].compose(all_frames_to_bb)
+
+    return all_frames_to_global
+
+
+def frames_and_literature_positions_to_atom14_pos(
+    r: Rigid,
+    aatype: torch.Tensor,
+    default_frames,
+    group_idx,
+    atom_mask,
+    lit_positions,
+):
+    # [*, N, 14, 4, 4]
+    default_4x4 = default_frames[aatype, ...]
+
+    # [*, N, 14]
+    group_mask = group_idx[aatype, ...]
+
+    # [*, N, 14, 8]
+    group_mask = nn.functional.one_hot(
+        group_mask,
+        num_classes=default_frames.shape[-3],
+    )
+
+    # [*, N, 14, 8]
+    t_atoms_to_global = r[..., None, :] * group_mask
+
+    # [*, N, 14]
+    t_atoms_to_global = t_atoms_to_global.map_tensor_fn(
+        lambda x: torch.sum(x, dim=-1)
+    )
+
+    # [*, N, 14, 1]
+    atom_mask = atom_mask[aatype, ...].unsqueeze(-1)
+
+    # [*, N, 14, 3]
+    lit_positions = lit_positions[aatype, ...]
+    pred_positions = t_atoms_to_global.apply(lit_positions)
+    pred_positions = pred_positions * atom_mask
+
+    return pred_positions

fastfold/utils/import_weights.py

+# Copyright 2021 AlQuraishi Laboratory
+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# 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.
+
+from enum import Enum
+from dataclasses import dataclass
+from functools import partial
+import numpy as np
+import torch
+from typing import Union, List
+
+
+_NPZ_KEY_PREFIX = "alphafold/alphafold_iteration/"
+
+
+# With Param, a poor man's enum with attributes (Rust-style)
+class ParamType(Enum):
+    LinearWeight = partial(  # hack: partial prevents fns from becoming methods
+        lambda w: w.transpose(-1, -2)
+    )
+    LinearWeightMHA = partial(
+        lambda w: w.reshape(*w.shape[:-2], -1).transpose(-1, -2)
+    )
+    LinearMHAOutputWeight = partial(
+        lambda w: w.reshape(*w.shape[:-3], -1, w.shape[-1]).transpose(-1, -2)
+    )
+    LinearBiasMHA = partial(lambda w: w.reshape(*w.shape[:-2], -1))
+    LinearWeightOPM = partial(
+        lambda w: w.reshape(*w.shape[:-3], -1, w.shape[-1]).transpose(-1, -2)
+    )
+    Other = partial(lambda w: w)
+
+    def __init__(self, fn):
+        self.transformation = fn
+
+
+@dataclass
+class Param:
+    param: Union[torch.Tensor, List[torch.Tensor]]
+    param_type: ParamType = ParamType.Other
+    stacked: bool = False
+
+
+def _process_translations_dict(d, top_layer=True):
+    flat = {}
+    for k, v in d.items():
+        if type(v) == dict:
+            prefix = _NPZ_KEY_PREFIX if top_layer else ""
+            sub_flat = {
+                (prefix + "/".join([k, k_prime])): v_prime
+                for k_prime, v_prime in _process_translations_dict(
+                    v, top_layer=False
+                ).items()
+            }
+            flat.update(sub_flat)
+        else:
+            k = "/" + k if not top_layer else k
+            flat[k] = v
+
+    return flat
+
+
+def stacked(param_dict_list, out=None):
+    """
+    Args:
+        param_dict_list:
+            A list of (nested) Param dicts to stack. The structure of
+            each dict must be the identical (down to the ParamTypes of
+            "parallel" Params). There must be at least one dict
+            in the list.
+    """
+    if out is None:
+        out = {}
+    template = param_dict_list[0]
+    for k, _ in template.items():
+        v = [d[k] for d in param_dict_list]
+        if type(v[0]) is dict:
+            out[k] = {}
+            stacked(v, out=out[k])
+        elif type(v[0]) is Param:
+            stacked_param = Param(
+                param=[param.param for param in v],
+                param_type=v[0].param_type,
+                stacked=True,
+            )
+
+            out[k] = stacked_param
+
+    return out
+
+
+def assign(translation_dict, orig_weights):
+    for k, param in translation_dict.items():
+        with torch.no_grad():
+            weights = torch.as_tensor(orig_weights[k])
+            ref, param_type = param.param, param.param_type
+            if param.stacked:
+                weights = torch.unbind(weights, 0)
+            else:
+                weights = [weights]
+                ref = [ref]
+
+            try:
+                weights = list(map(param_type.transformation, weights))
+                for p, w in zip(ref, weights):
+                    p.copy_(w)
+            except:
+                print(k)
+                print(ref[0].shape)
+                print(weights[0].shape)
+                raise
+
+
+def import_jax_weights_(model, npz_path, version="model_1"):
+    data = np.load(npz_path)
+
+    #######################
+    # Some templates
+    #######################
+
+    LinearWeight = lambda l: (Param(l, param_type=ParamType.LinearWeight))
+
+    LinearBias = lambda l: (Param(l))
+
+    LinearWeightMHA = lambda l: (Param(l, param_type=ParamType.LinearWeightMHA))
+
+    LinearBiasMHA = lambda b: (Param(b, param_type=ParamType.LinearBiasMHA))
+
+    LinearWeightOPM = lambda l: (Param(l, param_type=ParamType.LinearWeightOPM))
+
+    LinearParams = lambda l: {
+        "weights": LinearWeight(l.weight),
+        "bias": LinearBias(l.bias),
+    }
+
+    LayerNormParams = lambda l: {
+        "scale": Param(l.weight),
+        "offset": Param(l.bias),
+    }
+
+    AttentionParams = lambda att: {
+        "query_w": LinearWeightMHA(att.linear_q.weight),
+        "key_w": LinearWeightMHA(att.linear_k.weight),
+        "value_w": LinearWeightMHA(att.linear_v.weight),
+        "output_w": Param(
+            att.linear_o.weight,
+            param_type=ParamType.LinearMHAOutputWeight,
+        ),
+        "output_b": LinearBias(att.linear_o.bias),
+    }
+
+    AttentionGatedParams = lambda att: dict(
+        **AttentionParams(att),
+        **{
+            "gating_w": LinearWeightMHA(att.linear_g.weight),
+            "gating_b": LinearBiasMHA(att.linear_g.bias),
+        },
+    )
+
+    GlobalAttentionParams = lambda att: dict(
+        AttentionGatedParams(att),
+        key_w=LinearWeight(att.linear_k.weight),
+        value_w=LinearWeight(att.linear_v.weight),
+    )
+
+    TriAttParams = lambda tri_att: {
+        "query_norm": LayerNormParams(tri_att.layer_norm),
+        "feat_2d_weights": LinearWeight(tri_att.linear.weight),
+        "attention": AttentionGatedParams(tri_att.mha),
+    }
+
+    TriMulOutParams = lambda tri_mul: {
+        "layer_norm_input": LayerNormParams(tri_mul.layer_norm_in),
+        "left_projection": LinearParams(tri_mul.linear_a_p),
+        "right_projection": LinearParams(tri_mul.linear_b_p),
+        "left_gate": LinearParams(tri_mul.linear_a_g),
+        "right_gate": LinearParams(tri_mul.linear_b_g),
+        "center_layer_norm": LayerNormParams(tri_mul.layer_norm_out),
+        "output_projection": LinearParams(tri_mul.linear_z),
+        "gating_linear": LinearParams(tri_mul.linear_g),
+    }
+
+    # see commit b88f8da on the Alphafold repo
+    # Alphafold swaps the pseudocode's a and b between the incoming/outcoming
+    # iterations of triangle multiplication, which is confusing and not
+    # reproduced in our implementation.
+    TriMulInParams = lambda tri_mul: {
+        "layer_norm_input": LayerNormParams(tri_mul.layer_norm_in),
+        "left_projection": LinearParams(tri_mul.linear_b_p),
+        "right_projection": LinearParams(tri_mul.linear_a_p),
+        "left_gate": LinearParams(tri_mul.linear_b_g),
+        "right_gate": LinearParams(tri_mul.linear_a_g),
+        "center_layer_norm": LayerNormParams(tri_mul.layer_norm_out),
+        "output_projection": LinearParams(tri_mul.linear_z),
+        "gating_linear": LinearParams(tri_mul.linear_g),
+    }
+
+    PairTransitionParams = lambda pt: {
+        "input_layer_norm": LayerNormParams(pt.layer_norm),
+        "transition1": LinearParams(pt.linear_1),
+        "transition2": LinearParams(pt.linear_2),
+    }
+
+    MSAAttParams = lambda matt: {
+        "query_norm": LayerNormParams(matt.layer_norm_m),
+        "attention": AttentionGatedParams(matt.mha),
+    }
+
+    MSAColAttParams = lambda matt: {
+        "query_norm": LayerNormParams(matt._msa_att.layer_norm_m),
+        "attention": AttentionGatedParams(matt._msa_att.mha),
+    }
+
+    MSAGlobalAttParams = lambda matt: {
+        "query_norm": LayerNormParams(matt.layer_norm_m),
+        "attention": GlobalAttentionParams(matt.global_attention),
+    }
+
+    MSAAttPairBiasParams = lambda matt: dict(
+        **MSAAttParams(matt),
+        **{
+            "feat_2d_norm": LayerNormParams(matt.layer_norm_z),
+            "feat_2d_weights": LinearWeight(matt.linear_z.weight),
+        },
+    )
+
+    IPAParams = lambda ipa: {
+        "q_scalar": LinearParams(ipa.linear_q),
+        "kv_scalar": LinearParams(ipa.linear_kv),
+        "q_point_local": LinearParams(ipa.linear_q_points),
+        "kv_point_local": LinearParams(ipa.linear_kv_points),
+        "trainable_point_weights": Param(
+            param=ipa.head_weights, param_type=ParamType.Other
+        ),
+        "attention_2d": LinearParams(ipa.linear_b),
+        "output_projection": LinearParams(ipa.linear_out),
+    }
+
+    TemplatePairBlockParams = lambda b: {
+        "triangle_attention_starting_node": TriAttParams(b.tri_att_start),
+        "triangle_attention_ending_node": TriAttParams(b.tri_att_end),
+        "triangle_multiplication_outgoing": TriMulOutParams(b.tri_mul_out),
+        "triangle_multiplication_incoming": TriMulInParams(b.tri_mul_in),
+        "pair_transition": PairTransitionParams(b.pair_transition),
+    }
+
+    MSATransitionParams = lambda m: {
+        "input_layer_norm": LayerNormParams(m.layer_norm),
+        "transition1": LinearParams(m.linear_1),
+        "transition2": LinearParams(m.linear_2),
+    }
+
+    OuterProductMeanParams = lambda o: {
+        "layer_norm_input": LayerNormParams(o.layer_norm),
+        "left_projection": LinearParams(o.linear_1),
+        "right_projection": LinearParams(o.linear_2),
+        "output_w": LinearWeightOPM(o.linear_out.weight),
+        "output_b": LinearBias(o.linear_out.bias),
+    }
+
+    def EvoformerBlockParams(b, is_extra_msa=False):
+        if is_extra_msa:
+            col_att_name = "msa_column_global_attention"
+            msa_col_att_params = MSAGlobalAttParams(b.msa_att_col)
+        else:
+            col_att_name = "msa_column_attention"
+            msa_col_att_params = MSAColAttParams(b.msa_att_col)
+
+        d = {
+            "msa_row_attention_with_pair_bias": MSAAttPairBiasParams(
+                b.msa_att_row
+            ),
+            col_att_name: msa_col_att_params,
+            "msa_transition": MSATransitionParams(b.core.msa_transition),
+            "outer_product_mean": 
+                OuterProductMeanParams(b.core.outer_product_mean),
+            "triangle_multiplication_outgoing": 
+                TriMulOutParams(b.core.tri_mul_out),
+            "triangle_multiplication_incoming": 
+                TriMulInParams(b.core.tri_mul_in),
+            "triangle_attention_starting_node": 
+                TriAttParams(b.core.tri_att_start),
+            "triangle_attention_ending_node": 
+                TriAttParams(b.core.tri_att_end),
+            "pair_transition": 
+                PairTransitionParams(b.core.pair_transition),
+        }
+
+        return d
+
+    ExtraMSABlockParams = partial(EvoformerBlockParams, is_extra_msa=True)
+
+    FoldIterationParams = lambda sm: {
+        "invariant_point_attention": IPAParams(sm.ipa),
+        "attention_layer_norm": LayerNormParams(sm.layer_norm_ipa),
+        "transition": LinearParams(sm.transition.layers[0].linear_1),
+        "transition_1": LinearParams(sm.transition.layers[0].linear_2),
+        "transition_2": LinearParams(sm.transition.layers[0].linear_3),
+        "transition_layer_norm": LayerNormParams(sm.transition.layer_norm),
+        "affine_update": LinearParams(sm.bb_update.linear),
+        "rigid_sidechain": {
+            "input_projection": LinearParams(sm.angle_resnet.linear_in),
+            "input_projection_1": LinearParams(sm.angle_resnet.linear_initial),
+            "resblock1": LinearParams(sm.angle_resnet.layers[0].linear_1),
+            "resblock2": LinearParams(sm.angle_resnet.layers[0].linear_2),
+            "resblock1_1": LinearParams(sm.angle_resnet.layers[1].linear_1),
+            "resblock2_1": LinearParams(sm.angle_resnet.layers[1].linear_2),
+            "unnormalized_angles": LinearParams(sm.angle_resnet.linear_out),
+        },
+    }
+
+    ############################
+    # translations dict overflow
+    ############################
+
+    tps_blocks = model.template_pair_stack.blocks
+    tps_blocks_params = stacked(
+        [TemplatePairBlockParams(b) for b in tps_blocks]
+    )
+
+    ems_blocks = model.extra_msa_stack.blocks
+    ems_blocks_params = stacked([ExtraMSABlockParams(b) for b in ems_blocks])
+
+    evo_blocks = model.evoformer.blocks
+    evo_blocks_params = stacked([EvoformerBlockParams(b) for b in evo_blocks])
+
+    translations = {
+        "evoformer": {
+            "preprocess_1d": LinearParams(model.input_embedder.linear_tf_m),
+            "preprocess_msa": LinearParams(model.input_embedder.linear_msa_m),
+            "left_single": LinearParams(model.input_embedder.linear_tf_z_i),
+            "right_single": LinearParams(model.input_embedder.linear_tf_z_j),
+            "prev_pos_linear": LinearParams(model.recycling_embedder.linear),
+            "prev_msa_first_row_norm": LayerNormParams(
+                model.recycling_embedder.layer_norm_m
+            ),
+            "prev_pair_norm": LayerNormParams(
+                model.recycling_embedder.layer_norm_z
+            ),
+            "pair_activiations": LinearParams(
+                model.input_embedder.linear_relpos
+            ),
+            "template_embedding": {
+                "single_template_embedding": {
+                    "embedding2d": LinearParams(
+                        model.template_pair_embedder.linear
+                    ),
+                    "template_pair_stack": {
+                        "__layer_stack_no_state": tps_blocks_params,
+                    },
+                    "output_layer_norm": LayerNormParams(
+                        model.template_pair_stack.layer_norm
+                    ),
+                },
+                "attention": AttentionParams(model.template_pointwise_att.mha),
+            },
+            "extra_msa_activations": LinearParams(
+                model.extra_msa_embedder.linear
+            ),
+            "extra_msa_stack": ems_blocks_params,
+            "template_single_embedding": LinearParams(
+                model.template_angle_embedder.linear_1
+            ),
+            "template_projection": LinearParams(
+                model.template_angle_embedder.linear_2
+            ),
+            "evoformer_iteration": evo_blocks_params,
+            "single_activations": LinearParams(model.evoformer.linear),
+        },
+        "structure_module": {
+            "single_layer_norm": LayerNormParams(
+                model.structure_module.layer_norm_s
+            ),
+            "initial_projection": LinearParams(
+                model.structure_module.linear_in
+            ),
+            "pair_layer_norm": LayerNormParams(
+                model.structure_module.layer_norm_z
+            ),
+            "fold_iteration": FoldIterationParams(model.structure_module),
+        },
+        "predicted_lddt_head": {
+            "input_layer_norm": LayerNormParams(
+                model.aux_heads.plddt.layer_norm
+            ),
+            "act_0": LinearParams(model.aux_heads.plddt.linear_1),
+            "act_1": LinearParams(model.aux_heads.plddt.linear_2),
+            "logits": LinearParams(model.aux_heads.plddt.linear_3),
+        },
+        "distogram_head": {
+            "half_logits": LinearParams(model.aux_heads.distogram.linear),
+        },
+        "experimentally_resolved_head": {
+            "logits": LinearParams(
+                model.aux_heads.experimentally_resolved.linear
+            ),
+        },
+        "masked_msa_head": {
+            "logits": LinearParams(model.aux_heads.masked_msa.linear),
+        },
+    }
+
+    no_templ = [
+        "model_3",
+        "model_4",
+        "model_5",
+        "model_3_ptm",
+        "model_4_ptm",
+        "model_5_ptm",
+    ]
+    if version in no_templ:
+        evo_dict = translations["evoformer"]
+        keys = list(evo_dict.keys())
+        for k in keys:
+            if "template_" in k:
+                evo_dict.pop(k)
+
+    if "_ptm" in version:
+        translations["predicted_aligned_error_head"] = {
+            "logits": LinearParams(model.aux_heads.tm.linear)
+        }
+
+    # Flatten keys and insert missing key prefixes
+    flat = _process_translations_dict(translations)
+
+    # Sanity check
+    keys = list(data.keys())
+    flat_keys = list(flat.keys())
+    incorrect = [k for k in flat_keys if k not in keys]
+    missing = [k for k in keys if k not in flat_keys]
+    # print(f"Incorrect: {incorrect}")
+    # print(f"Missing: {missing}")
+
+    assert len(incorrect) == 0
+    # assert(sorted(list(flat.keys())) == sorted(list(data.keys())))
+
+    # Set weights
+    assign(flat, data)

fastfold/utils/inject_openfold.py → fastfold/utils/inject_fastnn.py

@@ -6,7 +6,7 @@ import torch.nn as nn
 from colossalai.context.parallel_mode import ParallelMode
 from colossalai.core import global_context as gpc
 
-from fastfold.model import MSAStack, OutProductMean, PairStack
+from fastfold.model.fastnn import MSAStack, OutProductMean, PairStack
 from fastfold.distributed.comm_async import All_to_All_Async, All_to_All_Async_Opp
 from fastfold.distributed.comm import gather, scatter
 
@@ -179,19 +179,19 @@ def copy_para(block_fast, block_ori):
     copy_transition(block_fast.pair_stack.PairTransition, block_ori.core.pair_transition)
 
 
-def inject_openfold(model):
+def inject_fastnn(model):
     with torch.no_grad():
         fastfold_blocks = nn.ModuleList()
-        for block_id, openfold_block in enumerate(model.evoformer.blocks):
-            c_m = openfold_block.msa_att_row.c_in
-            c_z = openfold_block.msa_att_row.c_z
+        for block_id, ori_block in enumerate(model.evoformer.blocks):
+            c_m = ori_block.msa_att_row.c_in
+            c_z = ori_block.msa_att_row.c_z
             fastfold_block = EvoformerBlock(c_m=c_m,
                                             c_z=c_z,
                                             first_block=(block_id == 0),
                                             last_block=(block_id == len(model.evoformer.blocks) -
                                                         1))
 
-            copy_para(fastfold_block, openfold_block)
+            copy_para(fastfold_block, ori_block)
 
             fastfold_blocks.append(fastfold_block)
 

fastfold/utils/rigid_utils.py

+# Copyright 2021 AlQuraishi Laboratory
+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# 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.
+
+from __future__ import annotations
+from typing import Tuple, Any, Sequence, Callable, Optional
+
+import numpy as np
+import torch
+
+
+def rot_matmul(
+    a: torch.Tensor, 
+    b: torch.Tensor
+) -> torch.Tensor:
+    """
+        Performs matrix multiplication of two rotation matrix tensors. Written
+        out by hand to avoid AMP downcasting.
+
+        Args:
+            a: [*, 3, 3] left multiplicand
+            b: [*, 3, 3] right multiplicand
+        Returns:
+            The product ab
+    """
+    row_1 = torch.stack(
+        [
+            a[..., 0, 0] * b[..., 0, 0]
+            + a[..., 0, 1] * b[..., 1, 0]
+            + a[..., 0, 2] * b[..., 2, 0],
+            a[..., 0, 0] * b[..., 0, 1]
+            + a[..., 0, 1] * b[..., 1, 1]
+            + a[..., 0, 2] * b[..., 2, 1],
+            a[..., 0, 0] * b[..., 0, 2]
+            + a[..., 0, 1] * b[..., 1, 2]
+            + a[..., 0, 2] * b[..., 2, 2],
+        ],
+        dim=-1,
+    )
+    row_2 = torch.stack(
+        [
+            a[..., 1, 0] * b[..., 0, 0]
+            + a[..., 1, 1] * b[..., 1, 0]
+            + a[..., 1, 2] * b[..., 2, 0],
+            a[..., 1, 0] * b[..., 0, 1]
+            + a[..., 1, 1] * b[..., 1, 1]
+            + a[..., 1, 2] * b[..., 2, 1],
+            a[..., 1, 0] * b[..., 0, 2]
+            + a[..., 1, 1] * b[..., 1, 2]
+            + a[..., 1, 2] * b[..., 2, 2],
+        ],
+        dim=-1,
+    )
+    row_3 = torch.stack(
+        [
+            a[..., 2, 0] * b[..., 0, 0]
+            + a[..., 2, 1] * b[..., 1, 0]
+            + a[..., 2, 2] * b[..., 2, 0],
+            a[..., 2, 0] * b[..., 0, 1]
+            + a[..., 2, 1] * b[..., 1, 1]
+            + a[..., 2, 2] * b[..., 2, 1],
+            a[..., 2, 0] * b[..., 0, 2]
+            + a[..., 2, 1] * b[..., 1, 2]
+            + a[..., 2, 2] * b[..., 2, 2],
+        ],
+        dim=-1,
+    )
+
+    return torch.stack([row_1, row_2, row_3], dim=-2)
+
+
+def rot_vec_mul(
+    r: torch.Tensor, 
+    t: torch.Tensor
+) -> torch.Tensor:
+    """
+        Applies a rotation to a vector. Written out by hand to avoid transfer
+        to avoid AMP downcasting.
+
+        Args:
+            r: [*, 3, 3] rotation matrices
+            t: [*, 3] coordinate tensors
+        Returns:
+            [*, 3] rotated coordinates
+    """
+    x = t[..., 0]
+    y = t[..., 1]
+    z = t[..., 2]
+    return torch.stack(
+        [
+            r[..., 0, 0] * x + r[..., 0, 1] * y + r[..., 0, 2] * z,
+            r[..., 1, 0] * x + r[..., 1, 1] * y + r[..., 1, 2] * z,
+            r[..., 2, 0] * x + r[..., 2, 1] * y + r[..., 2, 2] * z,
+        ],
+        dim=-1,
+    )
+
+    
+def identity_rot_mats(
+    batch_dims: Tuple[int], 
+    dtype: Optional[torch.dtype] = None, 
+    device: Optional[torch.device] = None, 
+    requires_grad: bool = True,
+) -> torch.Tensor:
+    rots = torch.eye(
+        3, dtype=dtype, device=device, requires_grad=requires_grad
+    )
+    rots = rots.view(*((1,) * len(batch_dims)), 3, 3)
+    rots = rots.expand(*batch_dims, -1, -1)
+
+    return rots
+
+
+def identity_trans(
+    batch_dims: Tuple[int], 
+    dtype: Optional[torch.dtype] = None,
+    device: Optional[torch.device] = None, 
+    requires_grad: bool = True,
+) -> torch.Tensor:
+    trans = torch.zeros(
+        (*batch_dims, 3), 
+        dtype=dtype, 
+        device=device, 
+        requires_grad=requires_grad
+    )
+    return trans
+
+
+def identity_quats(
+    batch_dims: Tuple[int], 
+    dtype: Optional[torch.dtype] = None,
+    device: Optional[torch.device] = None, 
+    requires_grad: bool = True,
+) -> torch.Tensor:
+    quat = torch.zeros(
+        (*batch_dims, 4), 
+        dtype=dtype, 
+        device=device, 
+        requires_grad=requires_grad
+    )
+
+    with torch.no_grad():
+        quat[..., 0] = 1
+
+    return quat
+
+
+_quat_elements = ["a", "b", "c", "d"]
+_qtr_keys = [l1 + l2 for l1 in _quat_elements for l2 in _quat_elements]
+_qtr_ind_dict = {key: ind for ind, key in enumerate(_qtr_keys)}
+
+
+def _to_mat(pairs):
+    mat = np.zeros((4, 4))
+    for pair in pairs:
+        key, value = pair
+        ind = _qtr_ind_dict[key]
+        mat[ind // 4][ind % 4] = value
+
+    return mat
+
+
+_QTR_MAT = np.zeros((4, 4, 3, 3))
+_QTR_MAT[..., 0, 0] = _to_mat([("aa", 1), ("bb", 1), ("cc", -1), ("dd", -1)])
+_QTR_MAT[..., 0, 1] = _to_mat([("bc", 2), ("ad", -2)])
+_QTR_MAT[..., 0, 2] = _to_mat([("bd", 2), ("ac", 2)])
+_QTR_MAT[..., 1, 0] = _to_mat([("bc", 2), ("ad", 2)])
+_QTR_MAT[..., 1, 1] = _to_mat([("aa", 1), ("bb", -1), ("cc", 1), ("dd", -1)])
+_QTR_MAT[..., 1, 2] = _to_mat([("cd", 2), ("ab", -2)])
+_QTR_MAT[..., 2, 0] = _to_mat([("bd", 2), ("ac", -2)])
+_QTR_MAT[..., 2, 1] = _to_mat([("cd", 2), ("ab", 2)])
+_QTR_MAT[..., 2, 2] = _to_mat([("aa", 1), ("bb", -1), ("cc", -1), ("dd", 1)])
+
+
+def quat_to_rot(quat: torch.Tensor) -> torch.Tensor:
+    """
+        Converts a quaternion to a rotation matrix.
+
+        Args:
+            quat: [*, 4] quaternions
+        Returns:
+            [*, 3, 3] rotation matrices
+    """
+    # [*, 4, 4]
+    quat = quat[..., None] * quat[..., None, :]
+
+    # [4, 4, 3, 3]
+    mat = quat.new_tensor(_QTR_MAT, requires_grad=False)
+
+    # [*, 4, 4, 3, 3]
+    shaped_qtr_mat = mat.view((1,) * len(quat.shape[:-2]) + mat.shape)
+    quat = quat[..., None, None] * shaped_qtr_mat
+
+    # [*, 3, 3]
+    return torch.sum(quat, dim=(-3, -4))
+
+
+def rot_to_quat(
+    rot: torch.Tensor,
+):
+    if(rot.shape[-2:] != (3, 3)):
+        raise ValueError("Input rotation is incorrectly shaped")
+
+    rot = [[rot[..., i, j] for j in range(3)] for i in range(3)]
+    [[xx, xy, xz], [yx, yy, yz], [zx, zy, zz]] = rot 
+
+    k = [
+        [ xx + yy + zz,      zy - yz,      xz - zx,      yx - xy,],
+        [      zy - yz, xx - yy - zz,      xy + yx,      xz + zx,],
+        [      xz - zx,      xy + yx, yy - xx - zz,      yz + zy,],
+        [      yx - xy,      xz + zx,      yz + zy, zz - xx - yy,]
+    ]
+
+    k = (1./3.) * torch.stack([torch.stack(t, dim=-1) for t in k], dim=-2)
+
+    _, vectors = torch.linalg.eigh(k)
+    return vectors[..., -1]
+
+
+_QUAT_MULTIPLY = np.zeros((4, 4, 4))
+_QUAT_MULTIPLY[:, :, 0] = [[ 1, 0, 0, 0],
+                          [ 0,-1, 0, 0],
+                          [ 0, 0,-1, 0],
+                          [ 0, 0, 0,-1]]
+
+_QUAT_MULTIPLY[:, :, 1] = [[ 0, 1, 0, 0],
+                          [ 1, 0, 0, 0],
+                          [ 0, 0, 0, 1],
+                          [ 0, 0,-1, 0]]
+
+_QUAT_MULTIPLY[:, :, 2] = [[ 0, 0, 1, 0],
+                          [ 0, 0, 0,-1],
+                          [ 1, 0, 0, 0],
+                          [ 0, 1, 0, 0]]
+
+_QUAT_MULTIPLY[:, :, 3] = [[ 0, 0, 0, 1],
+                          [ 0, 0, 1, 0],
+                          [ 0,-1, 0, 0],
+                          [ 1, 0, 0, 0]]
+
+_QUAT_MULTIPLY_BY_VEC = _QUAT_MULTIPLY[:, 1:, :]
+
+
+def quat_multiply(quat1, quat2):
+    """Multiply a quaternion by another quaternion."""
+    mat = quat1.new_tensor(_QUAT_MULTIPLY)
+    reshaped_mat = mat.view((1,) * len(quat1.shape[:-1]) + mat.shape)
+    return torch.sum(
+        reshaped_mat *
+        quat1[..., :, None, None] *
+        quat2[..., None, :, None],
+        dim=(-3, -2)
+      )
+
+
+def quat_multiply_by_vec(quat, vec):
+    """Multiply a quaternion by a pure-vector quaternion."""
+    mat = quat.new_tensor(_QUAT_MULTIPLY_BY_VEC)
+    reshaped_mat = mat.view((1,) * len(quat.shape[:-1]) + mat.shape)
+    return torch.sum(
+        reshaped_mat *
+        quat[..., :, None, None] *
+        vec[..., None, :, None],
+        dim=(-3, -2)
+    )
+
+
+def invert_rot_mat(rot_mat: torch.Tensor):
+    return rot_mat.transpose(-1, -2)
+
+
+def invert_quat(quat: torch.Tensor):
+    quat_prime = quat.clone()
+    quat_prime[..., 1:] *= -1
+    inv = quat_prime / torch.sum(quat ** 2, dim=-1, keepdim=True)
+    return inv
+
+
+class Rotation:
+    """
+        A 3D rotation. Depending on how the object is initialized, the
+        rotation is represented by either a rotation matrix or a
+        quaternion, though both formats are made available by helper functions.
+        To simplify gradient computation, the underlying format of the
+        rotation cannot be changed in-place. Like Rigid, the class is designed
+        to mimic the behavior of a torch Tensor, almost as if each Rotation
+        object were a tensor of rotations, in one format or another.
+    """
+    def __init__(self,
+        rot_mats: Optional[torch.Tensor] = None,
+        quats: Optional[torch.Tensor] = None,
+        normalize_quats: bool = True,
+    ):
+        """
+            Args:
+                rot_mats:
+                    A [*, 3, 3] rotation matrix tensor. Mutually exclusive with
+                    quats
+                quats:
+                    A [*, 4] quaternion. Mutually exclusive with rot_mats. If
+                    normalize_quats is not True, must be a unit quaternion
+                normalize_quats:
+                    If quats is specified, whether to normalize quats
+        """
+        if((rot_mats is None and quats is None) or 
+            (rot_mats is not None and quats is not None)):
+            raise ValueError("Exactly one input argument must be specified")
+
+        if((rot_mats is not None and rot_mats.shape[-2:] != (3, 3)) or 
+            (quats is not None and quats.shape[-1] != 4)):
+            raise ValueError(
+                "Incorrectly shaped rotation matrix or quaternion"
+            )
+
+        # Force full-precision
+        if(quats is not None):
+            quats = quats.to(dtype=torch.float32)
+        if(rot_mats is not None):
+            rot_mats = rot_mats.to(dtype=torch.float32)
+
+        if(quats is not None and normalize_quats):
+            quats = quats / torch.linalg.norm(quats, dim=-1, keepdim=True)
+
+        self._rot_mats = rot_mats
+        self._quats = quats
+
+    @staticmethod
+    def identity(
+        shape,
+        dtype: Optional[torch.dtype] = None,
+        device: Optional[torch.device] = None,
+        requires_grad: bool = True,
+        fmt: str = "quat",
+    ) -> Rotation:
+        """
+            Returns an identity Rotation.
+
+            Args:
+                shape:
+                    The "shape" of the resulting Rotation object. See documentation
+                    for the shape property
+                dtype:
+                    The torch dtype for the rotation
+                device:
+                    The torch device for the new rotation
+                requires_grad:
+                    Whether the underlying tensors in the new rotation object
+                    should require gradient computation
+                fmt:
+                    One of "quat" or "rot_mat". Determines the underlying format
+                    of the new object's rotation 
+            Returns:
+                A new identity rotation
+        """
+        if(fmt == "rot_mat"):
+            rot_mats = identity_rot_mats(
+                shape, dtype, device, requires_grad,
+            )
+            return Rotation(rot_mats=rot_mats, quats=None)
+        elif(fmt == "quat"):
+            quats = identity_quats(shape, dtype, device, requires_grad)
+            return Rotation(rot_mats=None, quats=quats, normalize_quats=False)
+        else:
+            raise ValueError(f"Invalid format: f{fmt}")
+
+    # Magic methods
+
+    def __getitem__(self, index: Any) -> Rotation:
+        """
+            Allows torch-style indexing over the virtual shape of the rotation
+            object. See documentation for the shape property.
+
+            Args:
+                index:
+                    A torch index. E.g. (1, 3, 2), or (slice(None,))
+            Returns:
+                The indexed rotation
+        """
+        if type(index) != tuple:
+            index = (index,)
+
+        if(self._rot_mats is not None):
+            rot_mats = self._rot_mats[index + (slice(None), slice(None))]
+            return Rotation(rot_mats=rot_mats)
+        elif(self._quats is not None):
+            quats = self._quats[index + (slice(None),)]
+            return Rotation(quats=quats, normalize_quats=False)
+        else:
+            raise ValueError("Both rotations are None")
+
+    def __mul__(self,
+        right: torch.Tensor,
+    ) -> Rotation:
+        """
+            Pointwise left multiplication of the rotation with a tensor. Can be
+            used to e.g. mask the Rotation.
+
+            Args:
+                right:
+                    The tensor multiplicand
+            Returns:
+                The product
+        """
+        if not(isinstance(right, torch.Tensor)):
+            raise TypeError("The other multiplicand must be a Tensor")
+
+        if(self._rot_mats is not None):
+            rot_mats = self._rot_mats * right[..., None, None]
+            return Rotation(rot_mats=rot_mats, quats=None)
+        elif(self._quats is not None):
+            quats = self._quats * right[..., None]
+            return Rotation(rot_mats=None, quats=quats, normalize_quats=False)
+        else:
+            raise ValueError("Both rotations are None")
+
+    def __rmul__(self,
+        left: torch.Tensor,
+    ) -> Rotation:
+        """
+            Reverse pointwise multiplication of the rotation with a tensor.
+
+            Args:
+                left:
+                    The left multiplicand
+            Returns:
+                The product
+        """
+        return self.__mul__(left)
+    
+    # Properties
+
+    @property
+    def shape(self) -> torch.Size:
+        """
+            Returns the virtual shape of the rotation object. This shape is
+            defined as the batch dimensions of the underlying rotation matrix
+            or quaternion. If the Rotation was initialized with a [10, 3, 3]
+            rotation matrix tensor, for example, the resulting shape would be
+            [10].
+        
+            Returns:
+                The virtual shape of the rotation object
+        """
+        s = None
+        if(self._quats is not None):
+            s = self._quats.shape[:-1]
+        else:
+            s = self._rot_mats.shape[:-2]
+
+        return s
+
+    @property
+    def dtype(self) -> torch.dtype:
+        """
+            Returns the dtype of the underlying rotation.
+
+            Returns:
+                The dtype of the underlying rotation
+        """
+        if(self._rot_mats is not None):
+            return self._rot_mats.dtype
+        elif(self._quats is not None):
+            return self._quats.dtype
+        else:
+            raise ValueError("Both rotations are None")
+
+    @property
+    def device(self) -> torch.device:
+        """
+            The device of the underlying rotation
+
+            Returns:
+                The device of the underlying rotation
+        """
+        if(self._rot_mats is not None):
+            return self._rot_mats.device
+        elif(self._quats is not None):
+            return self._quats.device
+        else:
+            raise ValueError("Both rotations are None")
+
+    @property
+    def requires_grad(self) -> bool:
+        """
+            Returns the requires_grad property of the underlying rotation
+
+            Returns:
+                The requires_grad property of the underlying tensor
+        """
+        if(self._rot_mats is not None):
+            return self._rot_mats.requires_grad
+        elif(self._quats is not None):
+            return self._quats.requires_grad
+        else:
+            raise ValueError("Both rotations are None")
+
+    def get_rot_mats(self) -> torch.Tensor:
+        """
+            Returns the underlying rotation as a rotation matrix tensor.
+
+            Returns:
+                The rotation as a rotation matrix tensor
+        """
+        rot_mats = self._rot_mats
+        if(rot_mats is None):
+            if(self._quats is None):
+                raise ValueError("Both rotations are None")
+            else:
+                rot_mats = quat_to_rot(self._quats)
+
+        return rot_mats 
+
+    def get_quats(self) -> torch.Tensor:
+        """
+            Returns the underlying rotation as a quaternion tensor.
+
+            Depending on whether the Rotation was initialized with a
+            quaternion, this function may call torch.linalg.eigh.
+
+            Returns:
+                The rotation as a quaternion tensor.
+        """
+        quats = self._quats
+        if(quats is None):
+            if(self._rot_mats is None):
+                raise ValueError("Both rotations are None")
+            else:
+                quats = rot_to_quat(self._rot_mats)
+
+        return quats
+
+    def get_cur_rot(self) -> torch.Tensor:
+        """
+            Return the underlying rotation in its current form
+
+            Returns:
+                The stored rotation
+        """
+        if(self._rot_mats is not None):
+            return self._rot_mats
+        elif(self._quats is not None):
+            return self._quats
+        else:
+            raise ValueError("Both rotations are None")
+
+    # Rotation functions
+
+    def compose_q_update_vec(self, 
+        q_update_vec: torch.Tensor, 
+        normalize_quats: bool = True
+    ) -> Rotation:
+        """
+            Returns a new quaternion Rotation after updating the current
+            object's underlying rotation with a quaternion update, formatted
+            as a [*, 3] tensor whose final three columns represent x, y, z such 
+            that (1, x, y, z) is the desired (not necessarily unit) quaternion
+            update.
+
+            Args:
+                q_update_vec:
+                    A [*, 3] quaternion update tensor
+                normalize_quats:
+                    Whether to normalize the output quaternion
+            Returns:
+                An updated Rotation
+        """
+        quats = self.get_quats()
+        new_quats = quats + quat_multiply_by_vec(quats, q_update_vec)
+        return Rotation(
+            rot_mats=None, 
+            quats=new_quats, 
+            normalize_quats=normalize_quats,
+        )
+
+    def compose_r(self, r: Rotation) -> Rotation:
+        """
+            Compose the rotation matrices of the current Rotation object with
+            those of another.
+
+            Args:
+                r:
+                    An update rotation object
+            Returns:
+                An updated rotation object
+        """
+        r1 = self.get_rot_mats()
+        r2 = r.get_rot_mats()
+        new_rot_mats = rot_matmul(r1, r2)
+        return Rotation(rot_mats=new_rot_mats, quats=None)
+
+    def compose_q(self, r: Rotation, normalize_quats: bool = True) -> Rotation:
+        """
+            Compose the quaternions of the current Rotation object with those
+            of another.
+
+            Depending on whether either Rotation was initialized with
+            quaternions, this function may call torch.linalg.eigh.
+
+            Args:
+                r:
+                    An update rotation object
+            Returns:
+                An updated rotation object
+        """
+        q1 = self.get_quats()
+        q2 = r.get_quats()
+        new_quats = quat_multiply(q1, q2)
+        return Rotation(
+            rot_mats=None, quats=new_quats, normalize_quats=normalize_quats
+        )
+
+    def apply(self, pts: torch.Tensor) -> torch.Tensor:
+        """
+            Apply the current Rotation as a rotation matrix to a set of 3D
+            coordinates.
+
+            Args:
+                pts:
+                    A [*, 3] set of points
+            Returns:
+                [*, 3] rotated points
+        """
+        rot_mats = self.get_rot_mats()
+        return rot_vec_mul(rot_mats, pts)
+
+    def invert_apply(self, pts: torch.Tensor) -> torch.Tensor:
+        """
+            The inverse of the apply() method.
+
+            Args:
+                pts:
+                    A [*, 3] set of points
+            Returns:
+                [*, 3] inverse-rotated points
+        """
+        rot_mats = self.get_rot_mats()
+        inv_rot_mats = invert_rot_mat(rot_mats) 
+        return rot_vec_mul(inv_rot_mats, pts)
+
+    def invert(self) -> Rotation:
+        """
+            Returns the inverse of the current Rotation.
+
+            Returns:
+                The inverse of the current Rotation
+        """
+        if(self._rot_mats is not None):
+            return Rotation(
+                rot_mats=invert_rot_mat(self._rot_mats), 
+                quats=None
+            )
+        elif(self._quats is not None):
+            return Rotation(
+                rot_mats=None,
+                quats=invert_quat(self._quats),
+                normalize_quats=False,
+            )
+        else:
+            raise ValueError("Both rotations are None")
+
+    # "Tensor" stuff
+
+    def unsqueeze(self, 
+        dim: int,
+    ) -> Rigid:
+        """
+            Analogous to torch.unsqueeze. The dimension is relative to the
+            shape of the Rotation object.
+            
+            Args:
+                dim: A positive or negative dimension index.
+            Returns:
+                The unsqueezed Rotation.
+        """
+        if dim >= len(self.shape):
+            raise ValueError("Invalid dimension")
+
+        if(self._rot_mats is not None):
+            rot_mats = self._rot_mats.unsqueeze(dim if dim >= 0 else dim - 2)
+            return Rotation(rot_mats=rot_mats, quats=None)
+        elif(self._quats is not None):
+            quats = self._quats.unsqueeze(dim if dim >= 0 else dim - 1)
+            return Rotation(rot_mats=None, quats=quats, normalize_quats=False)
+        else:
+            raise ValueError("Both rotations are None")
+
+    @staticmethod
+    def cat(
+        rs: Sequence[Rotation], 
+        dim: int,
+    ) -> Rigid:
+        """
+            Concatenates rotations along one of the batch dimensions. Analogous
+            to torch.cat().
+
+            Note that the output of this operation is always a rotation matrix,
+            regardless of the format of input rotations.
+
+            Args:
+                rs: 
+                    A list of rotation objects
+                dim: 
+                    The dimension along which the rotations should be 
+                    concatenated
+            Returns:
+                A concatenated Rotation object in rotation matrix format
+        """
+        rot_mats = [r.get_rot_mats() for r in rs]
+        rot_mats = torch.cat(rot_mats, dim=dim if dim >= 0 else dim - 2)
+
+        return Rotation(rot_mats=rot_mats, quats=None) 
+
+    def map_tensor_fn(self, 
+        fn: Callable[torch.Tensor, torch.Tensor]
+    ) -> Rotation:
+        """
+            Apply a Tensor -> Tensor function to underlying rotation tensors,
+            mapping over the rotation dimension(s). Can be used e.g. to sum out
+            a one-hot batch dimension.
+
+            Args:
+                fn:
+                    A Tensor -> Tensor function to be mapped over the Rotation 
+            Returns:
+                The transformed Rotation object
+        """ 
+        if(self._rot_mats is not None):
+            rot_mats = self._rot_mats.view(self._rot_mats.shape[:-2] + (9,))
+            rot_mats = torch.stack(
+                list(map(fn, torch.unbind(rot_mats, dim=-1))), dim=-1
+            )
+            rot_mats = rot_mats.view(rot_mats.shape[:-1] + (3, 3))
+            return Rotation(rot_mats=rot_mats, quats=None)
+        elif(self._quats is not None):
+            quats = torch.stack(
+                list(map(fn, torch.unbind(self._quats, dim=-1))), dim=-1
+            )
+            return Rotation(rot_mats=None, quats=quats, normalize_quats=False)
+        else:
+            raise ValueError("Both rotations are None")
+    
+    def cuda(self) -> Rotation:
+        """
+            Analogous to the cuda() method of torch Tensors
+
+            Returns:
+                A copy of the Rotation in CUDA memory
+        """
+        if(self._rot_mats is not None):
+            return Rotation(rot_mats=self._rot_mats.cuda(), quats=None)
+        elif(self._quats is not None):
+            return Rotation(
+                rot_mats=None, 
+                quats=self._quats.cuda(),
+                normalize_quats=False
+            )
+        else:
+            raise ValueError("Both rotations are None")
+
+    def to(self, 
+        device: Optional[torch.device], 
+        dtype: Optional[torch.dtype]
+    ) -> Rotation:
+        """
+            Analogous to the to() method of torch Tensors
+
+            Args:
+                device:
+                    A torch device
+                dtype:
+                    A torch dtype
+            Returns:
+                A copy of the Rotation using the new device and dtype
+        """
+        if(self._rot_mats is not None):
+            return Rotation(
+                rot_mats=self._rot_mats.to(device=device, dtype=dtype), 
+                quats=None,
+            )
+        elif(self._quats is not None):
+            return Rotation(
+                rot_mats=None, 
+                quats=self._quats.to(device=device, dtype=dtype),
+                normalize_quats=False,
+            )
+        else:
+            raise ValueError("Both rotations are None")
+
+    def detach(self) -> Rotation:
+        """
+            Returns a copy of the Rotation whose underlying Tensor has been
+            detached from its torch graph.
+
+            Returns:
+                A copy of the Rotation whose underlying Tensor has been detached
+                from its torch graph
+        """
+        if(self._rot_mats is not None):
+            return Rotation(rot_mats=self._rot_mats.detach(), quats=None)
+        elif(self._quats is not None):
+            return Rotation(
+                rot_mats=None, 
+                quats=self._quats.detach(), 
+                normalize_quats=False,
+            )
+        else:
+            raise ValueError("Both rotations are None")
+
+
+class Rigid:
+    """
+        A class representing a rigid transformation. Little more than a wrapper
+        around two objects: a Rotation object and a [*, 3] translation
+        Designed to behave approximately like a single torch tensor with the 
+        shape of the shared batch dimensions of its component parts.
+    """
+    def __init__(self, 
+        rots: Optional[Rotation],
+        trans: Optional[torch.Tensor],
+    ):
+        """
+            Args:
+                rots: A [*, 3, 3] rotation tensor
+                trans: A corresponding [*, 3] translation tensor
+        """
+        # (we need device, dtype, etc. from at least one input)
+
+        batch_dims, dtype, device, requires_grad = None, None, None, None
+        if(trans is not None):
+            batch_dims = trans.shape[:-1]
+            dtype = trans.dtype
+            device = trans.device
+            requires_grad = trans.requires_grad
+        elif(rots is not None):
+            batch_dims = rots.shape
+            dtype = rots.dtype
+            device = rots.device
+            requires_grad = rots.requires_grad
+        else:
+            raise ValueError("At least one input argument must be specified")
+
+        if(rots is None):
+            rots = Rotation.identity(
+                batch_dims, dtype, device, requires_grad,
+            )
+        elif(trans is None):
+            trans = identity_trans(
+                batch_dims, dtype, device, requires_grad,
+            )
+
+        if((rots.shape != trans.shape[:-1]) or
+           (rots.device != trans.device)):
+            raise ValueError("Rots and trans incompatible")
+
+        # Force full precision. Happens to the rotations automatically.
+        trans = trans.to(dtype=torch.float32)
+
+        self._rots = rots
+        self._trans = trans
+
+    @staticmethod
+    def identity(
+        shape: Tuple[int], 
+        dtype: Optional[torch.dtype] = None,
+        device: Optional[torch.device] = None, 
+        requires_grad: bool = True,
+        fmt: str = "quat",
+    ) -> Rigid:
+        """
+            Constructs an identity transformation.
+
+            Args:
+                shape: 
+                    The desired shape
+                dtype: 
+                    The dtype of both internal tensors
+                device: 
+                    The device of both internal tensors
+                requires_grad: 
+                    Whether grad should be enabled for the internal tensors
+            Returns:
+                The identity transformation
+        """
+        return Rigid(
+            Rotation.identity(shape, dtype, device, requires_grad, fmt=fmt),
+            identity_trans(shape, dtype, device, requires_grad),
+        )
+
+    def __getitem__(self, 
+        index: Any,
+    ) -> Rigid:
+        """ 
+            Indexes the affine transformation with PyTorch-style indices.
+            The index is applied to the shared dimensions of both the rotation
+            and the translation.
+
+            E.g.::
+
+                r = Rotation(rot_mats=torch.rand(10, 10, 3, 3), quats=None)
+                t = Rigid(r, torch.rand(10, 10, 3))
+                indexed = t[3, 4:6]
+                assert(indexed.shape == (2,))
+                assert(indexed.get_rots().shape == (2,))
+                assert(indexed.get_trans().shape == (2, 3))
+
+            Args:
+                index: A standard torch tensor index. E.g. 8, (10, None, 3),
+                or (3, slice(0, 1, None))
+            Returns:
+                The indexed tensor 
+        """
+        if type(index) != tuple:
+            index = (index,)
+        
+        return Rigid(
+            self._rots[index],
+            self._trans[index + (slice(None),)],
+        )
+
+    def __mul__(self,
+        right: torch.Tensor,
+    ) -> Rigid:
+        """
+            Pointwise left multiplication of the transformation with a tensor.
+            Can be used to e.g. mask the Rigid.
+
+            Args:
+                right:
+                    The tensor multiplicand
+            Returns:
+                The product
+        """
+        if not(isinstance(right, torch.Tensor)):
+            raise TypeError("The other multiplicand must be a Tensor")
+
+        new_rots = self._rots * right
+        new_trans = self._trans * right[..., None]
+
+        return Rigid(new_rots, new_trans)
+
+    def __rmul__(self,
+        left: torch.Tensor,
+    ) -> Rigid:
+        """
+            Reverse pointwise multiplication of the transformation with a 
+            tensor.
+
+            Args:
+                left:
+                    The left multiplicand
+            Returns:
+                The product
+        """
+        return self.__mul__(left)
+
+    @property
+    def shape(self) -> torch.Size:
+        """
+            Returns the shape of the shared dimensions of the rotation and
+            the translation.
+            
+            Returns:
+                The shape of the transformation
+        """
+        s = self._trans.shape[:-1]
+        return s
+
+    @property
+    def device(self) -> torch.device:
+        """
+            Returns the device on which the Rigid's tensors are located.
+
+            Returns:
+                The device on which the Rigid's tensors are located
+        """
+        return self._trans.device
+
+    def get_rots(self) -> Rotation:
+        """
+            Getter for the rotation.
+
+            Returns:
+                The rotation object
+        """
+        return self._rots
+
+    def get_trans(self) -> torch.Tensor:
+        """
+            Getter for the translation.
+
+            Returns:
+                The stored translation
+        """
+        return self._trans
+
+    def compose_q_update_vec(self, 
+        q_update_vec: torch.Tensor,
+    ) -> Rigid:
+        """
+            Composes the transformation with a quaternion update vector of
+            shape [*, 6], where the final 6 columns represent the x, y, and
+            z values of a quaternion of form (1, x, y, z) followed by a 3D
+            translation.
+
+            Args:
+                q_vec: The quaternion update vector.
+            Returns:
+                The composed transformation.
+        """
+        q_vec, t_vec = q_update_vec[..., :3], q_update_vec[..., 3:]
+        new_rots = self._rots.compose_q_update_vec(q_vec)
+
+        trans_update = self._rots.apply(t_vec)
+        new_translation = self._trans + trans_update
+
+        return Rigid(new_rots, new_translation)
+
+    def compose(self,
+        r: Rigid,
+    ) -> Rigid:
+        """
+            Composes the current rigid object with another.
+
+            Args:
+                r:
+                    Another Rigid object
+            Returns:
+                The composition of the two transformations
+        """
+        new_rot = self._rots.compose_r(r._rots)
+        new_trans = self._rots.apply(r._trans) + self._trans
+        return Rigid(new_rot, new_trans)
+
+    def apply(self, 
+        pts: torch.Tensor,
+    ) -> torch.Tensor:
+        """
+            Applies the transformation to a coordinate tensor.
+
+            Args:
+                pts: A [*, 3] coordinate tensor.
+            Returns:
+                The transformed points.
+        """
+        rotated = self._rots.apply(pts) 
+        return rotated + self._trans
+
+    def invert_apply(self, 
+        pts: torch.Tensor
+    ) -> torch.Tensor:
+        """
+            Applies the inverse of the transformation to a coordinate tensor.
+
+            Args:
+                pts: A [*, 3] coordinate tensor
+            Returns:
+                The transformed points.
+        """
+        pts = pts - self._trans
+        return self._rots.invert_apply(pts) 
+
+    def invert(self) -> Rigid:
+        """
+            Inverts the transformation.
+
+            Returns:
+                The inverse transformation.
+        """
+        rot_inv = self._rots.invert() 
+        trn_inv = rot_inv.apply(self._trans)
+
+        return Rigid(rot_inv, -1 * trn_inv)
+
+    def map_tensor_fn(self, 
+        fn: Callable[torch.Tensor, torch.Tensor]
+    ) -> Rigid:
+        """
+            Apply a Tensor -> Tensor function to underlying translation and
+            rotation tensors, mapping over the translation/rotation dimensions
+            respectively.
+
+            Args:
+                fn:
+                    A Tensor -> Tensor function to be mapped over the Rigid
+            Returns:
+                The transformed Rigid object
+        """     
+        new_rots = self._rots.map_tensor_fn(fn) 
+        new_trans = torch.stack(
+            list(map(fn, torch.unbind(self._trans, dim=-1))), 
+            dim=-1
+        )
+
+        return Rigid(new_rots, new_trans)
+
+    def to_tensor_4x4(self) -> torch.Tensor:
+        """
+            Converts a transformation to a homogenous transformation tensor.
+
+            Returns:
+                A [*, 4, 4] homogenous transformation tensor
+        """
+        tensor = self._trans.new_zeros((*self.shape, 4, 4))
+        tensor[..., :3, :3] = self._rots.get_rot_mats()
+        tensor[..., :3, 3] = self._trans
+        tensor[..., 3, 3] = 1
+        return tensor
+
+    @staticmethod
+    def from_tensor_4x4(
+        t: torch.Tensor
+    ) -> Rigid:
+        """
+            Constructs a transformation from a homogenous transformation
+            tensor.
+
+            Args:
+                t: [*, 4, 4] homogenous transformation tensor
+            Returns:
+                T object with shape [*]
+        """
+        if(t.shape[-2:] != (4, 4)):
+            raise ValueError("Incorrectly shaped input tensor")
+
+        rots = Rotation(rot_mats=t[..., :3, :3], quats=None)
+        trans = t[..., :3, 3]
+        
+        return Rigid(rots, trans)
+
+    def to_tensor_7(self) -> torch.Tensor:
+        """
+            Converts a transformation to a tensor with 7 final columns, four 
+            for the quaternion followed by three for the translation.
+
+            Returns:
+                A [*, 7] tensor representation of the transformation
+        """
+        tensor = self._trans.new_zeros((*self.shape, 7))
+        tensor[..., :4] = self._rots.get_quats()
+        tensor[..., 4:] = self._trans
+
+        return tensor
+
+    @staticmethod
+    def from_tensor_7(
+        t: torch.Tensor,
+        normalize_quats: bool = False,
+    ) -> Rigid:
+        if(t.shape[-1] != 7):
+            raise ValueError("Incorrectly shaped input tensor")
+
+        quats, trans = t[..., :4], t[..., 4:]
+
+        rots = Rotation(
+            rot_mats=None, 
+            quats=quats, 
+            normalize_quats=normalize_quats
+        )
+
+        return Rigid(rots, trans)
+
+    @staticmethod
+    def from_3_points(
+        p_neg_x_axis: torch.Tensor, 
+        origin: torch.Tensor, 
+        p_xy_plane: torch.Tensor, 
+        eps: float = 1e-8
+    ) -> Rigid:
+        """
+            Implements algorithm 21. Constructs transformations from sets of 3 
+            points using the Gram-Schmidt algorithm.
+
+            Args:
+                p_neg_x_axis: [*, 3] coordinates
+                origin: [*, 3] coordinates used as frame origins
+                p_xy_plane: [*, 3] coordinates
+                eps: Small epsilon value
+            Returns:
+                A transformation object of shape [*]
+        """
+        p_neg_x_axis = torch.unbind(p_neg_x_axis, dim=-1)
+        origin = torch.unbind(origin, dim=-1)
+        p_xy_plane = torch.unbind(p_xy_plane, dim=-1)
+
+        e0 = [c1 - c2 for c1, c2 in zip(origin, p_neg_x_axis)]
+        e1 = [c1 - c2 for c1, c2 in zip(p_xy_plane, origin)]
+
+        denom = torch.sqrt(sum((c * c for c in e0)) + eps)
+        e0 = [c / denom for c in e0]
+        dot = sum((c1 * c2 for c1, c2 in zip(e0, e1)))
+        e1 = [c2 - c1 * dot for c1, c2 in zip(e0, e1)]
+        denom = torch.sqrt(sum((c * c for c in e1)) + eps)
+        e1 = [c / denom for c in e1]
+        e2 = [
+            e0[1] * e1[2] - e0[2] * e1[1],
+            e0[2] * e1[0] - e0[0] * e1[2],
+            e0[0] * e1[1] - e0[1] * e1[0],
+        ]
+
+        rots = torch.stack([c for tup in zip(e0, e1, e2) for c in tup], dim=-1)
+        rots = rots.reshape(rots.shape[:-1] + (3, 3))
+
+        rot_obj = Rotation(rot_mats=rots, quats=None)
+
+        return Rigid(rot_obj, torch.stack(origin, dim=-1))
+
+    def unsqueeze(self, 
+        dim: int,
+    ) -> Rigid:
+        """
+            Analogous to torch.unsqueeze. The dimension is relative to the
+            shared dimensions of the rotation/translation.
+            
+            Args:
+                dim: A positive or negative dimension index.
+            Returns:
+                The unsqueezed transformation.
+        """
+        if dim >= len(self.shape):
+            raise ValueError("Invalid dimension")
+        rots = self._rots.unsqueeze(dim)
+        trans = self._trans.unsqueeze(dim if dim >= 0 else dim - 1)
+
+        return Rigid(rots, trans)
+
+    @staticmethod
+    def cat(
+        ts: Sequence[Rigid], 
+        dim: int,
+    ) -> Rigid:
+        """
+            Concatenates transformations along a new dimension.
+
+            Args:
+                ts: 
+                    A list of T objects
+                dim: 
+                    The dimension along which the transformations should be 
+                    concatenated
+            Returns:
+                A concatenated transformation object
+        """
+        rots = Rotation.cat([t._rots for t in ts], dim) 
+        trans = torch.cat(
+            [t._trans for t in ts], dim=dim if dim >= 0 else dim - 1
+        )
+
+        return Rigid(rots, trans)
+
+    def apply_rot_fn(self, fn: Callable[Rotation, Rotation]) -> Rigid:
+        """
+            Applies a Rotation -> Rotation function to the stored rotation
+            object.
+
+            Args:
+                fn: A function of type Rotation -> Rotation
+            Returns:
+                A transformation object with a transformed rotation.
+        """
+        return Rigid(fn(self._rots), self._trans)
+
+    def apply_trans_fn(self, fn: Callable[torch.Tensor, torch.Tensor]) -> Rigid:
+        """
+            Applies a Tensor -> Tensor function to the stored translation.
+
+            Args:
+                fn: 
+                    A function of type Tensor -> Tensor to be applied to the
+                    translation
+            Returns:
+                A transformation object with a transformed translation.
+        """
+        return Rigid(self._rots, fn(self._trans))
+
+    def scale_translation(self, trans_scale_factor: float) -> Rigid:
+        """
+            Scales the translation by a constant factor.
+
+            Args:
+                trans_scale_factor:
+                    The constant factor
+            Returns:
+                A transformation object with a scaled translation.
+        """
+        fn = lambda t: t * trans_scale_factor
+        return self.apply_trans_fn(fn)
+
+    def stop_rot_gradient(self) -> Rigid:
+        """
+            Detaches the underlying rotation object
+
+            Returns:
+                A transformation object with detached rotations
+        """
+        fn = lambda r: r.detach()
+        return self.apply_rot_fn(fn)
+
+    @staticmethod
+    def make_transform_from_reference(n_xyz, ca_xyz, c_xyz, eps=1e-20):
+        """
+            Returns a transformation object from reference coordinates.
+  
+            Note that this method does not take care of symmetries. If you 
+            provide the atom positions in the non-standard way, the N atom will 
+            end up not at [-0.527250, 1.359329, 0.0] but instead at 
+            [-0.527250, -1.359329, 0.0]. You need to take care of such cases in 
+            your code.
+  
+            Args:
+                n_xyz: A [*, 3] tensor of nitrogen xyz coordinates.
+                ca_xyz: A [*, 3] tensor of carbon alpha xyz coordinates.
+                c_xyz: A [*, 3] tensor of carbon xyz coordinates.
+            Returns:
+                A transformation object. After applying the translation and 
+                rotation to the reference backbone, the coordinates will 
+                approximately equal to the input coordinates.
+        """    
+        translation = -1 * ca_xyz
+        n_xyz = n_xyz + translation
+        c_xyz = c_xyz + translation
+
+        c_x, c_y, c_z = [c_xyz[..., i] for i in range(3)]
+        norm = torch.sqrt(eps + c_x ** 2 + c_y ** 2)
+        sin_c1 = -c_y / norm
+        cos_c1 = c_x / norm
+        zeros = sin_c1.new_zeros(sin_c1.shape)
+        ones = sin_c1.new_ones(sin_c1.shape)
+
+        c1_rots = sin_c1.new_zeros((*sin_c1.shape, 3, 3))
+        c1_rots[..., 0, 0] = cos_c1
+        c1_rots[..., 0, 1] = -1 * sin_c1
+        c1_rots[..., 1, 0] = sin_c1
+        c1_rots[..., 1, 1] = cos_c1
+        c1_rots[..., 2, 2] = 1
+
+        norm = torch.sqrt(eps + c_x ** 2 + c_y ** 2 + c_z ** 2)
+        sin_c2 = c_z / norm
+        cos_c2 = torch.sqrt(c_x ** 2 + c_y ** 2) / norm
+
+        c2_rots = sin_c2.new_zeros((*sin_c2.shape, 3, 3))
+        c2_rots[..., 0, 0] = cos_c2
+        c2_rots[..., 0, 2] = sin_c2
+        c2_rots[..., 1, 1] = 1
+        c1_rots[..., 2, 0] = -1 * sin_c2
+        c1_rots[..., 2, 2] = cos_c2
+
+        c_rots = rot_matmul(c2_rots, c1_rots)
+        n_xyz = rot_vec_mul(c_rots, n_xyz)
+
+        _, n_y, n_z = [n_xyz[..., i] for i in range(3)]
+        norm = torch.sqrt(eps + n_y ** 2 + n_z ** 2)
+        sin_n = -n_z / norm
+        cos_n = n_y / norm
+
+        n_rots = sin_c2.new_zeros((*sin_c2.shape, 3, 3))
+        n_rots[..., 0, 0] = 1
+        n_rots[..., 1, 1] = cos_n
+        n_rots[..., 1, 2] = -1 * sin_n
+        n_rots[..., 2, 1] = sin_n
+        n_rots[..., 2, 2] = cos_n
+
+        rots = rot_matmul(n_rots, c_rots)
+
+        rots = rots.transpose(-1, -2)
+        translation = -1 * translation
+
+        rot_obj = Rotation(rot_mats=rots, quats=None)
+
+        return Rigid(rot_obj, translation)
+
+    def cuda(self) -> Rigid:
+        """
+            Moves the transformation object to GPU memory
+            
+            Returns:
+                A version of the transformation on GPU
+        """
+        return Rigid(self._rots.cuda(), self._trans.cuda())

fastfold/utils/tensor_utils.py

+# Copyright 2021 AlQuraishi Laboratory
+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# 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.
+
+from functools import partial
+import torch
+import torch.nn as nn
+from typing import Tuple, List, Callable, Any, Dict, Sequence, Optional
+
+
+def permute_final_dims(tensor: torch.Tensor, inds: List[int]):
+    zero_index = -1 * len(inds)
+    first_inds = list(range(len(tensor.shape[:zero_index])))
+    return tensor.permute(first_inds + [zero_index + i for i in inds])
+
+
+def flatten_final_dims(t: torch.Tensor, no_dims: int):
+    return t.reshape(t.shape[:-no_dims] + (-1,))
+
+
+def masked_mean(mask, value, dim, eps=1e-4):
+    mask = mask.expand(*value.shape)
+    return torch.sum(mask * value, dim=dim) / (eps + torch.sum(mask, dim=dim))
+
+
+def pts_to_distogram(pts, min_bin=2.3125, max_bin=21.6875, no_bins=64):
+    boundaries = torch.linspace(
+        min_bin, max_bin, no_bins - 1, device=pts.device
+    )
+    dists = torch.sqrt(
+        torch.sum((pts.unsqueeze(-2) - pts.unsqueeze(-3)) ** 2, dim=-1)
+    )
+    return torch.bucketize(dists, boundaries)
+
+
+def dict_multimap(fn, dicts):
+    first = dicts[0]
+    new_dict = {}
+    for k, v in first.items():
+        all_v = [d[k] for d in dicts]
+        if type(v) is dict:
+            new_dict[k] = dict_multimap(fn, all_v)
+        else:
+            new_dict[k] = fn(all_v)
+
+    return new_dict
+
+
+def one_hot(x, v_bins):
+    reshaped_bins = v_bins.view(((1,) * len(x.shape)) + (len(v_bins),))
+    diffs = x[..., None] - reshaped_bins
+    am = torch.argmin(torch.abs(diffs), dim=-1)
+    return nn.functional.one_hot(am, num_classes=len(v_bins)).float()
+
+
+def batched_gather(data, inds, dim=0, no_batch_dims=0):
+    ranges = []
+    for i, s in enumerate(data.shape[:no_batch_dims]):
+        r = torch.arange(s)
+        r = r.view(*(*((1,) * i), -1, *((1,) * (len(inds.shape) - i - 1))))
+        ranges.append(r)
+
+    remaining_dims = [
+        slice(None) for _ in range(len(data.shape) - no_batch_dims)
+    ]
+    remaining_dims[dim - no_batch_dims if dim >= 0 else dim] = inds
+    ranges.extend(remaining_dims)
+    return data[ranges]
+
+
+# With tree_map, a poor man's JAX tree_map
+def dict_map(fn, dic, leaf_type):
+    new_dict = {}
+    for k, v in dic.items():
+        if type(v) is dict:
+            new_dict[k] = dict_map(fn, v, leaf_type)
+        else:
+            new_dict[k] = tree_map(fn, v, leaf_type)
+
+    return new_dict
+
+
+def tree_map(fn, tree, leaf_type):
+    if isinstance(tree, dict):
+        return dict_map(fn, tree, leaf_type)
+    elif isinstance(tree, list):
+        return [tree_map(fn, x, leaf_type) for x in tree]
+    elif isinstance(tree, tuple):
+        return tuple([tree_map(fn, x, leaf_type) for x in tree])
+    elif isinstance(tree, leaf_type):
+        return fn(tree)
+    else:
+        print(type(tree))
+        raise ValueError("Not supported")
+
+
+tensor_tree_map = partial(tree_map, leaf_type=torch.Tensor)
+
+def _fetch_dims(tree):
+    shapes = []
+    tree_type = type(tree)
+    if tree_type is dict:
+        for v in tree.values():
+            shapes.extend(_fetch_dims(v))
+    elif tree_type is list or tree_type is tuple:
+        for t in tree:
+            shapes.extend(_fetch_dims(t))
+    elif tree_type is torch.Tensor:
+        shapes.append(tree.shape)
+    else:
+        raise ValueError("Not supported")
+
+    return shapes
+
+
+@torch.jit.ignore
+def _flat_idx_to_idx(
+    flat_idx: int,
+    dims: Tuple[int],
+) -> Tuple[int]:
+    idx = []
+    for d in reversed(dims):
+        idx.append(flat_idx % d)
+        flat_idx = flat_idx // d
+
+    return tuple(reversed(idx))
+
+
+@torch.jit.ignore
+def _get_minimal_slice_set(
+    start: Sequence[int],
+    end: Sequence[int],
+    dims: int,
+    start_edges: Optional[Sequence[bool]] = None,
+    end_edges: Optional[Sequence[bool]] = None,
+) -> Sequence[Tuple[int]]:
+    """ 
+        Produces an ordered sequence of tensor slices that, when used in
+        sequence on a tensor with shape dims, yields tensors that contain every
+        leaf in the contiguous range [start, end]. Care is taken to yield a 
+        short sequence of slices, and perhaps even the shortest possible (I'm 
+        pretty sure it's the latter).
+         
+        end is INCLUSIVE. 
+    """
+    # start_edges and end_edges both indicate whether, starting from any given
+    # dimension, the start/end index is at the top/bottom edge of the
+    # corresponding tensor, modeled as a tree
+    def reduce_edge_list(l):
+        tally = 1
+        for i in range(len(l)):
+            reversed_idx = -1 * (i + 1)
+            l[reversed_idx] *= tally
+            tally = l[reversed_idx]
+
+    if(start_edges is None):
+        start_edges = [s == 0 for s in start]
+        reduce_edge_list(start_edges)
+    if(end_edges is None):
+        end_edges = [e == (d - 1) for e,d in zip(end, dims)]
+        reduce_edge_list(end_edges)        
+
+    # Base cases. Either start/end are empty and we're done, or the final,
+    # one-dimensional tensor can be simply sliced
+    if(len(start) == 0):
+        return [tuple()]
+    elif(len(start) == 1):
+        return [(slice(start[0], end[0] + 1),)]
+
+    slices = []
+    path = []
+ 
+    # Dimensions common to start and end can be selected directly
+    for s,e in zip(start, end):
+        if(s == e):
+            path.append(slice(s, s + 1))
+        else:
+            break
+
+    path = tuple(path)
+    divergence_idx = len(path)
+
+    # start == end, and we're done
+    if(divergence_idx == len(dims)):
+        return [tuple(path)]
+
+    def upper():
+        sdi = start[divergence_idx]
+        return [
+            path + (slice(sdi, sdi + 1),) + s for s in 
+            _get_minimal_slice_set(
+                start[divergence_idx + 1:],
+                [d - 1 for d in dims[divergence_idx + 1:]],
+                dims[divergence_idx + 1:],
+                start_edges=start_edges[divergence_idx + 1:],
+                end_edges=[1 for _ in end_edges[divergence_idx + 1:]]
+            )
+        ]
+
+    def lower():
+        edi = end[divergence_idx]
+        return [
+            path + (slice(edi, edi + 1),) + s for s in 
+            _get_minimal_slice_set(
+                [0 for _ in start[divergence_idx + 1:]],
+                end[divergence_idx + 1:],
+                dims[divergence_idx + 1:],
+                start_edges=[1 for _ in start_edges[divergence_idx + 1:]],
+                end_edges=end_edges[divergence_idx + 1:],
+            )
+        ]
+
+    # If both start and end are at the edges of the subtree rooted at
+    # divergence_idx, we can just select the whole subtree at once
+    if(start_edges[divergence_idx] and end_edges[divergence_idx]):
+        slices.append(
+            path + (slice(start[divergence_idx], end[divergence_idx] + 1),)
+        )
+    # If just start is at the edge, we can grab almost all of the subtree, 
+    # treating only the ragged bottom edge as an edge case
+    elif(start_edges[divergence_idx]):
+        slices.append(
+            path + (slice(start[divergence_idx], end[divergence_idx]),)
+        )
+        slices.extend(lower())
+    # Analogous to the previous case, but the top is ragged this time
+    elif(end_edges[divergence_idx]):
+        slices.extend(upper())
+        slices.append(
+            path + (slice(start[divergence_idx] + 1, end[divergence_idx] + 1),)
+        )
+    # If both sides of the range are ragged, we need to handle both sides
+    # separately. If there's contiguous meat in between them, we can index it
+    # in one big chunk
+    else:
+        slices.extend(upper())
+        middle_ground = end[divergence_idx] - start[divergence_idx]
+        if(middle_ground > 1):
+            slices.append(
+                path + (slice(start[divergence_idx] + 1, end[divergence_idx]),)
+            )
+        slices.extend(lower())
+
+    return [tuple(s) for s in slices]
+
+
+@torch.jit.ignore
+def _chunk_slice(
+    t: torch.Tensor,
+    flat_start: int,
+    flat_end: int,
+    no_batch_dims: int,
+) -> torch.Tensor:
+    """
+        Equivalent to
+        
+            t.reshape((-1,) + t.shape[no_batch_dims:])[flat_start:flat_end]
+
+        but without the need for the initial reshape call, which can be 
+        memory-intensive in certain situations. The only reshape operations
+        in this function are performed on sub-tensors that scale with
+        (flat_end - flat_start), the chunk size.
+    """
+
+    batch_dims = t.shape[:no_batch_dims]
+    start_idx = list(_flat_idx_to_idx(flat_start, batch_dims))
+    # _get_minimal_slice_set is inclusive
+    end_idx = list(_flat_idx_to_idx(flat_end - 1, batch_dims))
+
+    # Get an ordered list of slices to perform
+    slices = _get_minimal_slice_set(
+        start_idx,
+        end_idx,
+        batch_dims,
+    )
+
+    sliced_tensors = [t[s] for s in slices]
+
+    return torch.cat(
+        [s.view((-1,) + t.shape[no_batch_dims:]) for s in sliced_tensors]
+    )
+
+
+def chunk_layer(
+    layer: Callable,
+    inputs: Dict[str, Any],
+    chunk_size: int,
+    no_batch_dims: int,
+    low_mem: bool = False, 
+) -> Any:
+    """
+    Implements the "chunking" procedure described in section 1.11.8.
+
+    Layer outputs and inputs are assumed to be simple "pytrees,"
+    consisting only of (arbitrarily nested) lists, tuples, and dicts with
+    torch.Tensor leaves.
+
+    Args:
+        layer:
+            The layer to be applied chunk-wise
+        inputs:
+            A (non-nested) dictionary of keyworded inputs. All leaves must
+            be tensors and must share the same batch dimensions.
+        chunk_size:
+            The number of sub-batches per chunk. If multiple batch
+            dimensions are specified, a "sub-batch" is defined as a single
+            indexing of all batch dimensions simultaneously (s.t. the
+            number of sub-batches is the product of the batch dimensions).
+        no_batch_dims:
+            How many of the initial dimensions of each input tensor can
+            be considered batch dimensions.
+        low_mem:
+            Avoids flattening potentially large input tensors. Unnecessary
+            in most cases, and is ever so slightly slower than the default
+            setting.
+    Returns:
+        The reassembled output of the layer on the inputs.
+    """
+    if not (len(inputs) > 0):
+        raise ValueError("Must provide at least one input")
+
+    initial_dims = [shape[:no_batch_dims] for shape in _fetch_dims(inputs)]
+    orig_batch_dims = tuple([max(s) for s in zip(*initial_dims)])
+
+    def _prep_inputs(t):
+        # TODO: make this more memory efficient. This sucks
+        if(not low_mem):
+            if not sum(t.shape[:no_batch_dims]) == no_batch_dims:
+                t = t.expand(orig_batch_dims + t.shape[no_batch_dims:])
+            t = t.reshape(-1, *t.shape[no_batch_dims:])
+        else:
+            t = t.expand(orig_batch_dims + t.shape[no_batch_dims:])
+        return t
+
+    prepped_inputs = tensor_tree_map(_prep_inputs, inputs)
+
+    flat_batch_dim = 1
+    for d in orig_batch_dims:
+        flat_batch_dim *= d
+
+    no_chunks = flat_batch_dim // chunk_size + (
+        flat_batch_dim % chunk_size != 0
+    )
+
+    i = 0
+    out = None
+    for _ in range(no_chunks):
+        # Chunk the input
+        if(not low_mem):
+            select_chunk = (
+                lambda t: t[i : i + chunk_size] if t.shape[0] != 1 else t
+            )
+        else:
+            select_chunk = (
+                partial(
+                    _chunk_slice, 
+                    flat_start=i, 
+                    flat_end=min(flat_batch_dim, i + chunk_size), 
+                    no_batch_dims=len(orig_batch_dims)
+                )
+            )
+
+        chunks = tensor_tree_map(select_chunk, prepped_inputs)
+
+        # Run the layer on the chunk
+        output_chunk = layer(**chunks)
+
+        # Allocate space for the output
+        if out is None:
+            allocate = lambda t: t.new_zeros((flat_batch_dim,) + t.shape[1:])
+            out = tensor_tree_map(allocate, output_chunk)
+
+        # Put the chunk in its pre-allocated space
+        out_type = type(output_chunk)
+        if out_type is dict:
+            def assign(d1, d2):
+                for k, v in d1.items():
+                    if type(v) is dict:
+                        assign(v, d2[k])
+                    else:
+                        v[i : i + chunk_size] = d2[k]
+
+            assign(out, output_chunk)
+        elif out_type is tuple:
+            for x1, x2 in zip(out, output_chunk):
+                x1[i : i + chunk_size] = x2
+        elif out_type is torch.Tensor:
+            out[i : i + chunk_size] = output_chunk
+        else:
+            raise ValueError("Not supported")
+
+        i += chunk_size
+
+    reshape = lambda t: t.view(orig_batch_dims + t.shape[1:])
+    out = tensor_tree_map(reshape, out)
+
+    return out

inference.py

@@ -18,38 +18,70 @@ import os
 import random
 import sys
 import time
+from datetime import date
 
 import numpy as np
 import torch
+from fastfold.model.hub import AlphaFold
 
 import fastfold
-import openfold.np.relax.relax as relax
-from fastfold.utils import inject_openfold
-from openfold.config import model_config
-from openfold.data import data_pipeline, feature_pipeline, templates
-from openfold.model.model import AlphaFold
-from openfold.model.torchscript import script_preset_
-from openfold.np import protein, residue_constants
-from openfold.utils.import_weights import import_jax_weights_
-from openfold.utils.tensor_utils import tensor_tree_map
-from scripts.utils import add_data_args
+import fastfold.relax.relax as relax
+from fastfold.common import protein, residue_constants
+from fastfold.config import model_config
+from fastfold.data import data_pipeline, feature_pipeline, templates
+from fastfold.utils import inject_fastnn
+from fastfold.utils.import_weights import import_jax_weights_
+from fastfold.utils.tensor_utils import tensor_tree_map
+
+
+def add_data_args(parser: argparse.ArgumentParser):
+    parser.add_argument(
+        '--uniref90_database_path',
+        type=str,
+        default=None,
+    )
+    parser.add_argument(
+        '--mgnify_database_path',
+        type=str,
+        default=None,
+    )
+    parser.add_argument(
+        '--pdb70_database_path',
+        type=str,
+        default=None,
+    )
+    parser.add_argument(
+        '--uniclust30_database_path',
+        type=str,
+        default=None,
+    )
+    parser.add_argument(
+        '--bfd_database_path',
+        type=str,
+        default=None,
+    )
+    parser.add_argument('--jackhmmer_binary_path', type=str, default='/usr/bin/jackhmmer')
+    parser.add_argument('--hhblits_binary_path', type=str, default='/usr/bin/hhblits')
+    parser.add_argument('--hhsearch_binary_path', type=str, default='/usr/bin/hhsearch')
+    parser.add_argument('--kalign_binary_path', type=str, default='/usr/bin/kalign')
+    parser.add_argument(
+        '--max_template_date',
+        type=str,
+        default=date.today().strftime("%Y-%m-%d"),
+    )
+    parser.add_argument('--obsolete_pdbs_path', type=str, default=None)
+    parser.add_argument('--release_dates_path', type=str, default=None)
 
 
 def main(args):
     # init distributed for Dynamic Axial Parallelism
-    local_rank = int(os.getenv('LOCAL_RANK', -1))
-
-    if local_rank != -1:
-        distributed_inference_ = True
-        fastfold.distributed.init_dap()
-    else:
-        distributed_inference_ = False
+    fastfold.distributed.init_dap()
 
     config = model_config(args.model_name)
     model = AlphaFold(config)
     import_jax_weights_(model, args.param_path, version=args.model_name)
 
-    model = inject_openfold(model)
+    model = inject_fastnn(model)
     model = model.eval()
     #script_preset_(model)
     model = model.cuda()
@@ -62,7 +94,12 @@ def main(args):
         release_dates_path=args.release_dates_path,
         obsolete_pdbs_path=args.obsolete_pdbs_path)
 
-    use_small_bfd = (args.bfd_database_path is None)
+    use_small_bfd = args.preset == 'reduced_dbs'  # (args.bfd_database_path is None)
+    if use_small_bfd:
+        assert args.bfd_database_path is not None
+    else:
+        assert args.bfd_database_path is not None
+        assert args.uniclust30_database_path is not None
 
     data_processor = data_pipeline.DataPipeline(template_featurizer=template_featurizer,)
 
@@ -87,7 +124,7 @@ def main(args):
 
     for tag, seq in zip(tags, seqs):
         batch = [None]
-        if (not distributed_inference_) or (torch.distributed.get_rank() == 0):
+        if torch.distributed.get_rank() == 0:
             fasta_path = os.path.join(args.output_dir, "tmp.fasta")
             with open(fasta_path, "w") as fp:
                 fp.write(f">{tag}\n{seq}")
@@ -125,8 +162,8 @@ def main(args):
 
             batch = [processed_feature_dict]
 
-        if distributed_inference_:
-            torch.distributed.broadcast_object_list(batch, src=0)
+
+        torch.distributed.broadcast_object_list(batch, src=0)
         batch = batch[0]
 
         print("Executing model...")
@@ -138,10 +175,9 @@ def main(args):
             out = model(batch)
             print(f"Inference time: {time.perf_counter() - t}")
 
-        if distributed_inference_:
-            torch.distributed.barrier()
+        torch.distributed.barrier()
 
-        if (not distributed_inference_) or (torch.distributed.get_rank() == 0):
+        if torch.distributed.get_rank() == 0:
             # Toss out the recycling dimensions --- we don't need them anymore
             batch = tensor_tree_map(lambda x: np.array(x[..., -1].cpu()), batch)
             out = tensor_tree_map(lambda x: np.array(x.cpu()), out)
@@ -177,8 +213,7 @@ def main(args):
             with open(relaxed_output_path, 'w') as f:
                 f.write(relaxed_pdb_str)
 
-        if distributed_inference_:
-            torch.distributed.barrier()
+        torch.distributed.barrier()
 
 
 if __name__ == "__main__":
@@ -212,21 +247,20 @@ if __name__ == "__main__":
                         default=None,
                         help="""Path to model parameters. If None, parameters are selected
              automatically according to the model name from 
-             openfold/resources/params""")
+             ./data/params""")
     parser.add_argument("--cpus",
                         type=int,
                         default=12,
                         help="""Number of CPUs with which to run alignment tools""")
     parser.add_argument('--preset',
                         type=str,
-                        default='reduced_dbs',
+                        default='full_dbs',
                         choices=('reduced_dbs', 'full_dbs'))
     parser.add_argument('--data_random_seed', type=str, default=None)
     add_data_args(parser)
     args = parser.parse_args()
 
     if (args.param_path is None):
-        args.param_path = os.path.join("openfold", "resources", "params",
-                                       "params_" + args.model_name + ".npz")
+        args.param_path = os.path.join("data", "params", "params_" + args.model_name + ".npz")
 
     main(args)

scripts/download_all_data.sh

+#!/bin/bash
+#
+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# 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.
+#
+# Downloads and unzips all required data for AlphaFold.
+#
+# Usage: bash download_all_data.sh /path/to/download/directory
+set -e
+
+if [[ $# -eq 0 ]]; then
+  echo "Error: download directory must be provided as an input argument."
+  exit 1
+fi
+
+if ! command -v aria2c &> /dev/null ; then
+  echo "Error: aria2c could not be found. Please install aria2c (sudo apt install aria2)."
+  exit 1
+fi
+
+DOWNLOAD_DIR="$1"
+DOWNLOAD_MODE="${2:-full_dbs}"  # Default mode to full_dbs.
+if [[ "${DOWNLOAD_MODE}" != full_dbs && "${DOWNLOAD_MODE}" != reduced_dbs ]]
+then
+  echo "DOWNLOAD_MODE ${DOWNLOAD_MODE} not recognized."
+  exit 1
+fi
+
+SCRIPT_DIR="$(dirname "$(realpath "$0")")"
+
+echo "Downloading AlphaFold parameters..."
+bash "${SCRIPT_DIR}/download_alphafold_params.sh" "${DOWNLOAD_DIR}"
+
+if [[ "${DOWNLOAD_MODE}" = reduced_dbs ]] ; then
+  echo "Downloading Small BFD..."
+  bash "${SCRIPT_DIR}/download_small_bfd.sh" "${DOWNLOAD_DIR}"
+else
+  echo "Downloading BFD..."
+  bash "${SCRIPT_DIR}/download_bfd.sh" "${DOWNLOAD_DIR}"
+fi
+
+echo "Downloading MGnify..."
+bash "${SCRIPT_DIR}/download_mgnify.sh" "${DOWNLOAD_DIR}"
+
+echo "Downloading PDB70..."
+bash "${SCRIPT_DIR}/download_pdb70.sh" "${DOWNLOAD_DIR}"
+
+echo "Downloading PDB mmCIF files..."
+bash "${SCRIPT_DIR}/download_pdb_mmcif.sh" "${DOWNLOAD_DIR}"
+
+echo "Downloading Uniclust30..."
+bash "${SCRIPT_DIR}/download_uniclust30.sh" "${DOWNLOAD_DIR}"
+
+echo "Downloading Uniref90..."
+bash "${SCRIPT_DIR}/download_uniref90.sh" "${DOWNLOAD_DIR}"
+
+# UniProt and PDB SeqRes for multimer version
+# echo "Downloading UniProt..."
+# bash "${SCRIPT_DIR}/download_uniprot.sh" "${DOWNLOAD_DIR}"
+
+# echo "Downloading PDB SeqRes..."
+# bash "${SCRIPT_DIR}/download_pdb_seqres.sh" "${DOWNLOAD_DIR}"
+
+echo "All data downloaded."

scripts/download_alphafold_params.sh

+#!/bin/bash
+#
+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# 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.
+#
+# Downloads and unzips the AlphaFold parameters.
+#
+# Usage: bash download_alphafold_params.sh /path/to/download/directory
+set -e
+
+if [[ $# -eq 0 ]]; then
+    echo "Error: download directory must be provided as an input argument."
+    exit 1
+fi
+
+if ! command -v aria2c &> /dev/null ; then
+    echo "Error: aria2c could not be found. Please install aria2c (sudo apt install aria2)."
+    exit 1
+fi
+
+DOWNLOAD_DIR="$1"
+ROOT_DIR="${DOWNLOAD_DIR}/params"
+SOURCE_URL="https://storage.googleapis.com/alphafold/alphafold_params_2022-03-02.tar"
+BASENAME=$(basename "${SOURCE_URL}")
+
+mkdir --parents "${ROOT_DIR}"
+aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
+tar --extract --verbose --file="${ROOT_DIR}/${BASENAME}" \
+  --directory="${ROOT_DIR}" --preserve-permissions
+rm "${ROOT_DIR}/${BASENAME}"

scripts/download_bfd.sh

+#!/bin/bash
+#
+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# 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.
+#
+# Downloads and unzips the BFD database for AlphaFold.
+#
+# Usage: bash download_bfd.sh /path/to/download/directory
+set -e
+
+if [[ $# -eq 0 ]]; then
+    echo "Error: download directory must be provided as an input argument."
+    exit 1
+fi
+
+if ! command -v aria2c &> /dev/null ; then
+    echo "Error: aria2c could not be found. Please install aria2c (sudo apt install aria2)."
+    exit 1
+fi
+
+DOWNLOAD_DIR="$1"
+ROOT_DIR="${DOWNLOAD_DIR}/bfd"
+# Mirror of:
+# https://bfd.mmseqs.com/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz.
+SOURCE_URL="https://storage.googleapis.com/alphafold-databases/casp14_versions/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz"
+BASENAME=$(basename "${SOURCE_URL}")
+
+mkdir --parents "${ROOT_DIR}"
+aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
+tar --extract --verbose --file="${ROOT_DIR}/${BASENAME}" \
+  --directory="${ROOT_DIR}"
+rm "${ROOT_DIR}/${BASENAME}"

scripts/download_mgnify.sh

+#!/bin/bash
+#
+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# 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.
+#
+# Downloads and unzips the MGnify database for AlphaFold.
+#
+# Usage: bash download_mgnify.sh /path/to/download/directory
+set -e
+
+if [[ $# -eq 0 ]]; then
+    echo "Error: download directory must be provided as an input argument."
+    exit 1
+fi
+
+if ! command -v aria2c &> /dev/null ; then
+    echo "Error: aria2c could not be found. Please install aria2c (sudo apt install aria2)."
+    exit 1
+fi
+
+DOWNLOAD_DIR="$1"
+ROOT_DIR="${DOWNLOAD_DIR}/mgnify"
+# Mirror of:
+# ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/peptide_database/2018_12/mgy_clusters.fa.gz
+SOURCE_URL="https://storage.googleapis.com/alphafold-databases/casp14_versions/mgy_clusters_2018_12.fa.gz"
+BASENAME=$(basename "${SOURCE_URL}")
+
+mkdir --parents "${ROOT_DIR}"
+aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
+pushd "${ROOT_DIR}"
+gunzip "${ROOT_DIR}/${BASENAME}"
+popd

scripts/download_pdb70.sh

+#!/bin/bash
+#
+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# 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.
+#
+# Downloads and unzips the PDB70 database for AlphaFold.
+#
+# Usage: bash download_pdb70.sh /path/to/download/directory
+set -e
+
+if [[ $# -eq 0 ]]; then
+    echo "Error: download directory must be provided as an input argument."
+    exit 1
+fi
+
+if ! command -v aria2c &> /dev/null ; then
+    echo "Error: aria2c could not be found. Please install aria2c (sudo apt install aria2)."
+    exit 1
+fi
+
+DOWNLOAD_DIR="$1"
+ROOT_DIR="${DOWNLOAD_DIR}/pdb70"
+SOURCE_URL="http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/pdb70_from_mmcif_200401.tar.gz"
+BASENAME=$(basename "${SOURCE_URL}")
+
+mkdir --parents "${ROOT_DIR}"
+aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
+tar --extract --verbose --file="${ROOT_DIR}/${BASENAME}" \
+  --directory="${ROOT_DIR}"
+rm "${ROOT_DIR}/${BASENAME}"

scripts/download_pdb_mmcif.sh

+#!/bin/bash
+#
+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# 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.
+#
+# Downloads, unzips and flattens the PDB database for AlphaFold.
+#
+# Usage: bash download_pdb_mmcif.sh /path/to/download/directory
+set -e
+
+if [[ $# -eq 0 ]]; then
+    echo "Error: download directory must be provided as an input argument."
+    exit 1
+fi
+
+if ! command -v aria2c &> /dev/null ; then
+    echo "Error: aria2c could not be found. Please install aria2c (sudo apt install aria2)."
+    exit 1
+fi
+
+if ! command -v rsync &> /dev/null ; then
+    echo "Error: rsync could not be found. Please install rsync."
+    exit 1
+fi
+
+DOWNLOAD_DIR="$1"
+ROOT_DIR="${DOWNLOAD_DIR}/pdb_mmcif"
+RAW_DIR="${ROOT_DIR}/raw"
+MMCIF_DIR="${ROOT_DIR}/mmcif_files"
+
+echo "Running rsync to fetch all mmCIF files (note that the rsync progress estimate might be inaccurate)..."
+echo "If the download speed is too slow, try changing the mirror to:"
+echo "  * rsync.ebi.ac.uk::pub/databases/pdb/data/structures/divided/mmCIF/ (Europe)"
+echo "  * ftp.pdbj.org::ftp_data/structures/divided/mmCIF/ (Asia)"
+echo "or see https://www.wwpdb.org/ftp/pdb-ftp-sites for more download options."
+mkdir --parents "${RAW_DIR}"
+rsync --recursive --links --perms --times --compress --info=progress2 --delete --port=33444 \
+  rsync.rcsb.org::ftp_data/structures/divided/mmCIF/ \
+  "${RAW_DIR}"
+
+echo "Unzipping all mmCIF files..."
+find "${RAW_DIR}/" -type f -iname "*.gz" -exec gunzip {} +
+
+echo "Flattening all mmCIF files..."
+mkdir --parents "${MMCIF_DIR}"
+find "${RAW_DIR}" -type d -empty -delete  # Delete empty directories.
+for subdir in "${RAW_DIR}"/*; do
+  mv "${subdir}/"*.cif "${MMCIF_DIR}"
+done
+
+# Delete empty download directory structure.
+find "${RAW_DIR}" -type d -empty -delete
+
+aria2c "ftp://ftp.wwpdb.org/pub/pdb/data/status/obsolete.dat" --dir="${ROOT_DIR}"

scripts/download_pdb_seqres.sh

+#!/bin/bash
+#
+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# 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.
+#
+# Downloads and unzips the PDB SeqRes database for AlphaFold.
+#
+# Usage: bash download_pdb_seqres.sh /path/to/download/directory
+set -e
+
+if [[ $# -eq 0 ]]; then
+    echo "Error: download directory must be provided as an input argument."
+    exit 1
+fi
+
+if ! command -v aria2c &> /dev/null ; then
+    echo "Error: aria2c could not be found. Please install aria2c (sudo apt install aria2)."
+    exit 1
+fi
+
+DOWNLOAD_DIR="$1"
+ROOT_DIR="${DOWNLOAD_DIR}/pdb_seqres"
+SOURCE_URL="ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt"
+BASENAME=$(basename "${SOURCE_URL}")
+
+mkdir --parents "${ROOT_DIR}"
+aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"

scripts/download_small_bfd.sh

+#!/bin/bash
+#
+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# 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.
+#
+# Downloads and unzips the Small BFD database for AlphaFold.
+#
+# Usage: bash download_small_bfd.sh /path/to/download/directory
+set -e
+
+if [[ $# -eq 0 ]]; then
+    echo "Error: download directory must be provided as an input argument."
+    exit 1
+fi
+
+if ! command -v aria2c &> /dev/null ; then
+    echo "Error: aria2c could not be found. Please install aria2c (sudo apt install aria2)."
+    exit 1
+fi
+
+DOWNLOAD_DIR="$1"
+ROOT_DIR="${DOWNLOAD_DIR}/small_bfd"
+SOURCE_URL="https://storage.googleapis.com/alphafold-databases/reduced_dbs/bfd-first_non_consensus_sequences.fasta.gz"
+BASENAME=$(basename "${SOURCE_URL}")
+
+mkdir --parents "${ROOT_DIR}"
+trickle -s  -u 1024 -d 10240 aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
+pushd "${ROOT_DIR}"
+gunzip "${ROOT_DIR}/${BASENAME}"
+popd