LICENSE
README.md
pyproject.toml
torchref/__init__.py
torchref/_bootstrap.py
torchref/config.py
torchref.egg-info/PKG-INFO
torchref.egg-info/SOURCES.txt
torchref.egg-info/dependency_links.txt
torchref.egg-info/entry_points.txt
torchref.egg-info/requires.txt
torchref.egg-info/top_level.txt
torchref/alignment/__init__.py
torchref/alignment/ball_transform.py
torchref/alignment/clashscore.py
torchref/alignment/distributions.py
torchref/alignment/jax_subpixel_peaks.py
torchref/alignment/pipeline.py
torchref/alignment/rigid_body.py
torchref/alignment/sampling.py
torchref/alignment/transform.py
torchref/alignment/translation.py
torchref/base/CCTBX_related.py
torchref/base/__init__.py
torchref/base/french_wilson.py
torchref/base/get_scattering_factor_torch.py
torchref/base/math_numpy.py
torchref/base/math_torch.py
torchref/base/alignment/__init__.py
torchref/base/alignment/normalization.py
torchref/base/alignment/rotation.py
torchref/base/alignment/scoring.py
torchref/base/alignment/superposition.py
torchref/base/chain_closure/__init__.py
torchref/base/chain_closure/backbone_utils.py
torchref/base/chain_closure/closure.py
torchref/base/coordinates/__init__.py
torchref/base/coordinates/periodic_boundary.py
torchref/base/coordinates/transforms_numpy.py
torchref/base/coordinates/transforms_torch.py
torchref/base/direct_summation/__init__.py
torchref/base/direct_summation/anisotropic.py
torchref/base/direct_summation/corrections.py
torchref/base/direct_summation/isotropic.py
torchref/base/electron_density/__init__.py
torchref/base/electron_density/main.py
torchref/base/electron_density/map_building.py
torchref/base/electron_density/solvent_mask.py
torchref/base/electron_density/voxel_utils.py
torchref/base/fourier/__init__.py
torchref/base/fourier/fft.py
torchref/base/fourier/grid.py
torchref/base/kernels/__init__.py
torchref/base/kernels/cpu_scatter.py
torchref/base/kernels/jit_kernel_vectorized_add_to_map.py
torchref/base/kernels/optimized_ops.py
torchref/base/kernels/separable_triton_kernel.py
torchref/base/kernels/triton_kernel.py
torchref/base/metrics/__init__.py
torchref/base/metrics/loss.py
torchref/base/metrics/rfactor.py
torchref/base/reciprocal/__init__.py
torchref/base/reciprocal/basis.py
torchref/base/reciprocal/grid_operations.py
torchref/base/reciprocal/hkl.py
torchref/base/reciprocal/interpolation.py
torchref/base/reciprocal/symmetry.py
torchref/base/scattering/__init__.py
torchref/base/scattering/anomalous_table.py
torchref/base/scattering/itc92.py
torchref/base/scattering/scattering_table.py
torchref/cli/__init__.py
torchref/cli/difference_refine.py
torchref/cli/mtz2map.py
torchref/cli/phased_difference_map.py
torchref/cli/refine.py
torchref/cli/refine_everything_hyperparameters.py
torchref/cli/refine_everything_policy.py
torchref/cli/refine_everything_random_weights.py
torchref/cli/refine_everything_static.py
torchref/cli/validate_ded.py
torchref/data/atomic_vdw_radii.csv
torchref/data/default_hyperparameters.json
torchref/data/itc92_scattering_factors.pt
torchref/data/policy_latest.pt
torchref/data/rama_nll_surfaces.pt
torchref/data/monomer_library/a/A.cif
torchref/data/monomer_library/a/ALA.cif
torchref/data/monomer_library/a/ARG.cif
torchref/data/monomer_library/a/ASN.cif
torchref/data/monomer_library/a/ASP.cif
torchref/data/monomer_library/c/C.cif
torchref/data/monomer_library/c/CYS.cif
torchref/data/monomer_library/d/DA.cif
torchref/data/monomer_library/d/DC.cif
torchref/data/monomer_library/d/DG.cif
torchref/data/monomer_library/d/DT.cif
torchref/data/monomer_library/g/G.cif
torchref/data/monomer_library/g/GLN.cif
torchref/data/monomer_library/g/GLU.cif
torchref/data/monomer_library/g/GLY.cif
torchref/data/monomer_library/h/HIS.cif
torchref/data/monomer_library/h/HOH.cif
torchref/data/monomer_library/h/HYP.cif
torchref/data/monomer_library/i/ILE.cif
torchref/data/monomer_library/l/LEU.cif
torchref/data/monomer_library/l/LYS.cif
torchref/data/monomer_library/list/mon_lib_list.cif
torchref/data/monomer_library/m/MET.cif
torchref/data/monomer_library/m/MSE.cif
torchref/data/monomer_library/p/PHE.cif
torchref/data/monomer_library/p/PRO.cif
torchref/data/monomer_library/p/PTR.cif
torchref/data/monomer_library/s/SEP.cif
torchref/data/monomer_library/s/SER.cif
torchref/data/monomer_library/t/THR.cif
torchref/data/monomer_library/t/TPO.cif
torchref/data/monomer_library/t/TRP.cif
torchref/data/monomer_library/t/TYR.cif
torchref/data/monomer_library/u/U.cif
torchref/data/monomer_library/v/VAL.cif
torchref/io/__init__.py
torchref/io/cif.py
torchref/io/cif_readers.py
torchref/io/data_router.py
torchref/io/mtz.py
torchref/io/pdb.py
torchref/io/datasets/__init__.py
torchref/io/datasets/base.py
torchref/io/datasets/collection.py
torchref/io/datasets/fcalc_data.py
torchref/io/datasets/reflection_data.py
torchref/maps/__init__.py
torchref/maps/difference_map.py
torchref/maps/map.py
torchref/model/__init__.py
torchref/model/closed_segmented_internal_coordinates.py
torchref/model/internal_coordinates.py
torchref/model/mixed_model.py
torchref/model/model.py
torchref/model/model_ft.py
torchref/model/parameter_wrappers.py
torchref/model/segmented_internal_coordinates.py
torchref/model/sf_ds.py
torchref/model/sf_fft.py
torchref/refinement/__init__.py
torchref/refinement/base_refinement.py
torchref/refinement/lbfgs_refinement.py
torchref/refinement/logger.py
torchref/refinement/loss_state.py
torchref/refinement/optimizers/__init__.py
torchref/refinement/optimizers/adam_noise.py
torchref/refinement/optimizers/exploratory_lbfgs.py
torchref/refinement/optimizers/internal_coord_sa.py
torchref/refinement/optimizers/langevin_sa.py
torchref/refinement/optimizers/momentum_sa.py
torchref/refinement/optimizers/simulated_annealing.py
torchref/refinement/targets/__init__.py
torchref/refinement/targets/amber_target.py
torchref/refinement/targets/base.py
torchref/refinement/targets/combined.py
torchref/refinement/targets/difference.py
torchref/refinement/targets/forcefield_target.py
torchref/refinement/targets/occupancy_floor_diagnostic.py
torchref/refinement/targets/realspace.py
torchref/refinement/targets/sampled_ml_phase_target.py
torchref/refinement/targets/adp/__init__.py
torchref/refinement/targets/adp/base.py
torchref/refinement/targets/adp/entropy.py
torchref/refinement/targets/adp/locality.py
torchref/refinement/targets/adp/rigid_bond.py
torchref/refinement/targets/adp/similarity.py
torchref/refinement/targets/geometry/__init__.py
torchref/refinement/targets/geometry/angles.py
torchref/refinement/targets/geometry/base.py
torchref/refinement/targets/geometry/bonds.py
torchref/refinement/targets/geometry/chiral.py
torchref/refinement/targets/geometry/non_bonded.py
torchref/refinement/targets/geometry/planarity.py
torchref/refinement/targets/geometry/ramachandran.py
torchref/refinement/targets/geometry/torsions.py
torchref/refinement/targets/xray/__init__.py
torchref/refinement/targets/xray/base.py
torchref/refinement/targets/xray/gaussian.py
torchref/refinement/targets/xray/least_squares.py
torchref/refinement/targets/xray/maximum_likelihood.py
torchref/refinement/weighting/__init__.py
torchref/refinement/weighting/base_weighting.py
torchref/refinement/weighting/component_weighting.py
torchref/refinement/weighting/es_policy_training.py
torchref/refinement/weighting/policy_weighting.py
torchref/refinement/weighting/random_weighting.py
torchref/restraints/__init__.py
torchref/restraints/builders.py
torchref/restraints/builders_fast.py
torchref/restraints/builders_numba.py
torchref/restraints/library.py
torchref/restraints/ramachandran.py
torchref/restraints/restraints.py
torchref/restraints/restraints_helper.py
torchref/scaling/__init__.py
torchref/scaling/scaler.py
torchref/scaling/scaler_base.py
torchref/scaling/solvent.py
torchref/scripts/__init__.py
torchref/scripts/generate_scattering_table.py
torchref/symmetry/__init__.py
torchref/symmetry/cell.py
torchref/symmetry/grid_utils.py
torchref/symmetry/map_symmetry.py
torchref/symmetry/map_symmetry_interpolation.py
torchref/symmetry/reciprocal_symmetry.py
torchref/symmetry/spacegroup.py
torchref/symmetry/symmetry.py
torchref/utils/__init__.py
torchref/utils/caching.py
torchref/utils/debug_utils.py
torchref/utils/device_mixin.py
torchref/utils/gradnorm.py
torchref/utils/hyperparameters.py
torchref/utils/pse.py
torchref/utils/serialization.py
torchref/utils/stats.py
torchref/utils/timing.py
torchref/utils/utils.py