"""TMol: GPU-accelerated molecular modeling with PyTorch."""
# flake8: noqa
# Load precompiled native operators.
# This must happen early so that torch.ops.tmol_* namespaces are available
# before any compiled module is imported.
import contextlib
from importlib import import_module as _import_module
from importlib.metadata import PackageNotFoundError, version
[docs]
def include_paths():
"""C++/CUDA include paths for tmol components.
Defined before other imports because JIT extension loading
(tmol.utility._cpp_extension) imports this during module init.
"""
import os.path
return [os.path.abspath(os.path.dirname(__file__) + "/..")]
from tmol._cpp_lib import has_cuda
from tmol._load_ext import ensure_compiled_or_jit as _ensure_compiled_or_jit
# Extensions may not be built yet (e.g. during sdist creation).
# Individual compiled.py modules will raise a clear error if needed.
with contextlib.suppress(Exception):
_ensure_compiled_or_jit()
try:
__version__ = version("tmol")
except PackageNotFoundError:
__version__ = "unknown version"
__all__ = [
"CanonicalOrdering",
"CartesianMinimizer",
"CartesianMoveMap",
"ConstraintEnergyTerm",
"ConstraintSet",
"EdgeType",
"FoldForest",
"KinematicModuleData",
"MoveMap",
"PackedBlockTypes",
"ParameterDatabase",
"PoseStack",
"ScoreFunction",
"ScoreType",
"atom_label",
"atom_array_from_file",
"atom_array_from_pose_stack",
"file_from_atom_array",
"file_from_pose_stack",
"pose_stack_from_atom_array",
"pose_stack_from_file",
"beta2016_score_function",
"block_for_residue_label",
"blocks_for_residue_labels",
"build_kinforest_network",
"create_mainchain_coordinate_constraints",
"default_canonical_ordering",
"default_packed_block_types",
"extended_pose_stack_from_sequences",
"fast_relax",
"get_ligand_mask",
"get_named_torsions",
"get_polymer_type_mask",
"get_sequence",
"get_torsion_names",
"include_paths",
"has_cuda",
"metal_blocks",
"mutate_residue",
"mutate_to_sequence",
"one2three",
"overlay_view",
"pose_stack_from_canonical_form",
"residue_label",
"run_cart_min",
"run_kin_min",
"run_min",
"selection_gallery",
"set_named_torsions",
"switchable_view",
"three2one",
"torsion_labels",
"view",
]
_LAZY_ATTRS = {}
for _module, _names in (
("tmol.chemical", ("one2three", "three2one")),
("tmol.database", ("ParameterDatabase",)),
(
"tmol.io",
(
"CanonicalOrdering",
"atom_array_from_file",
"atom_array_from_pose_stack",
"file_from_atom_array",
"file_from_pose_stack",
"pose_stack_from_atom_array",
"pose_stack_from_file",
"default_canonical_ordering",
"default_packed_block_types",
"extended_pose_stack_from_sequences",
"overlay_view",
"pose_stack_from_canonical_form",
"selection_gallery",
"switchable_view",
"view",
),
),
(
"tmol.kinematics",
(
"CartesianMoveMap",
"EdgeType",
"FoldForest",
"KinematicModuleData",
"MoveMap",
"set_named_torsions",
"torsion_labels",
),
),
(
"tmol.optimization",
(
"CartesianMinimizer",
"build_kinforest_network",
"run_cart_min",
"run_kin_min",
"run_min",
),
),
(
"tmol.pose",
(
"ConstraintSet",
"PackedBlockTypes",
"PoseStack",
"atom_label",
"block_for_residue_label",
"blocks_for_residue_labels",
"get_ligand_mask",
"get_named_torsions",
"get_polymer_type_mask",
"get_sequence",
"get_torsion_names",
"metal_blocks",
"residue_label",
),
),
(
"tmol.pack",
("mutate_residue", "mutate_to_sequence"),
),
(
"tmol.score",
("ScoreFunction", "ScoreType", "beta2016_score_function"),
),
(
"tmol.score.constraint",
("ConstraintEnergyTerm", "create_mainchain_coordinate_constraints"),
),
("tmol.relax", ("fast_relax",)),
):
_LAZY_ATTRS.update(dict.fromkeys(_names, _module))
del _module, _names
def __getattr__(name):
module_name = _LAZY_ATTRS.get(name)
if module_name is None:
raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
value = getattr(_import_module(module_name), name)
globals()[name] = value
return value
def __dir__():
return sorted(set(globals()) | set(__all__))
