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Fix unit mismatch issue in Amber relax

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Fixes:
* https://github.com/google-deepmind/alphafold/issues/1091
* https://github.com/google-deepmind/alphafold/issues/923

Thanks Alex! :)

PiperOrigin-RevId: 802200540
Change-Id: Ic6e2aeaf67403ef88cafc07c8532f0cd2e7cb3ce
This commit is contained in:
Augustin Zidek
2025-09-02 10:32:55 -07:00
committed by Copybara-Service
parent c095a657ad
commit c77d8b52d3
1 changed files with 15 additions and 13 deletions
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28
alphafold/relax/amber_minimize.py
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@@ -374,21 +374,22 @@ def _run_one_iteration(
restraint_set: str,
max_attempts: int,
use_gpu: bool,
exclude_residues: Optional[Collection[int]] = None):
exclude_residues: Optional[Collection[int]] = None,
):
"""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.
A value of 0 specifies no limit.
tolerance: kcal/(mol * nm), the force 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.
use_gpu: Whether to run on GPU.
exclude_residues: An optional list of zero-indexed residues to exclude from
restraints.
restraints.
Returns:
A `dict` of minimization info.
@@ -396,7 +397,7 @@ def _run_one_iteration(
exclude_residues = exclude_residues or []
# Assign physical dimensions.
tolerance = tolerance * ENERGY
tolerance = tolerance * ENERGY / unit.nanometer
stiffness = stiffness * ENERGY / (LENGTH**2)
start = time.time()
@@ -434,7 +435,8 @@ def run_pipeline(
restraint_set: str = "non_hydrogen",
max_attempts: int = 100,
checks: bool = True,
exclude_residues: Optional[Sequence[int]] = None):
exclude_residues: Optional[Sequence[int]] = None,
):
"""Run iterative amber relax.
Successive relax iterations are performed until all violations have been
@@ -446,17 +448,17 @@ def run_pipeline(
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.
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 * nm), the force 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.
restraints.
Returns:
out: A dictionary of output values.