All modules for which code is available

• torchref.base.CCTBX_related
• torchref.base.alignment.normalization
• torchref.base.alignment.rotation
• torchref.base.alignment.scoring
• torchref.base.alignment.superposition
• torchref.base.chain_closure.backbone_utils
• torchref.base.chain_closure.closure
• torchref.base.coordinates.periodic_boundary
• torchref.base.coordinates.transforms_numpy
• torchref.base.coordinates.transforms_torch
• torchref.base.direct_summation.anisotropic
• torchref.base.direct_summation.corrections
• torchref.base.direct_summation.isotropic
• torchref.base.electron_density.main
• torchref.base.electron_density.map_building
• torchref.base.electron_density.solvent_mask
• torchref.base.electron_density.voxel_utils
• torchref.base.fourier.fft
• torchref.base.fourier.grid
• torchref.base.french_wilson
• torchref.base.get_scattering_factor_torch
• torchref.base.kernels.cpu_scatter
• torchref.base.kernels.jit_kernel_vectorized_add_to_map
• torchref.base.kernels.optimized_ops
• torchref.base.kernels.separable_triton_kernel
• torchref.base.kernels.triton_kernel
• torchref.base.math_numpy
• torchref.base.math_torch
• torchref.base.metrics.loss
• torchref.base.metrics.rfactor
• torchref.base.reciprocal.basis
• torchref.base.reciprocal.grid_operations
• torchref.base.reciprocal.hkl
• torchref.base.reciprocal.interpolation
• torchref.base.reciprocal.symmetry
• torchref.base.scattering.anomalous_table
• torchref.base.scattering.itc92
• torchref.base.scattering.scattering_table
• torchref.base.targets.adp
• torchref.base.targets.angle
• torchref.base.targets.bond
• torchref.base.targets.chiral
• torchref.base.targets.nonbonded
• torchref.base.targets.planarity
• torchref.base.targets.ramachandran
• torchref.base.targets.torsion
• torchref.base.targets.triton.adp_simu
• torchref.base.targets.triton.angle
• torchref.base.targets.triton.bond
• torchref.base.targets.triton.chiral
• torchref.base.targets.triton.nonbonded
• torchref.base.targets.triton.place_hydrogens
• torchref.base.targets.triton.planarity
• torchref.base.targets.triton.ramachandran
• torchref.base.targets.triton.torsion
• torchref.base.targets.triton.xray_bhattacharyya
• torchref.base.targets.triton.xray_gaussian
• torchref.base.targets.triton.xray_ls
• torchref.base.targets.triton.xray_ml
• torchref.base.targets.xray_bhattacharyya
• torchref.base.targets.xray_gaussian
• torchref.base.targets.xray_ls
• torchref.base.targets.xray_ml
• torchref.cli.add_metadata
• torchref.cli.collection_difference_refine
• torchref.cli.mtz2map
• torchref.cli.phased_difference_map
• torchref.cli.refine
• torchref.cli.strip_altlocs
• torchref.cli.validate_ded
• torchref.config
• torchref.io.cif
• torchref.io.cif_readers
• torchref.io.data_router
• torchref.io.datasets.base
• torchref.io.datasets.collection
• torchref.io.datasets.fcalc_data
• torchref.io.datasets.reflection_data
• torchref.io.ihm
• torchref.io.ihm_mapping
• torchref.io.metadata
• torchref.io.mtz
• torchref.io.pdb
• torchref.kinetic.kinetics
• torchref.kinetic.occupancies
• torchref.kinetic.refinement
• torchref.kinetic.targets
• torchref.maps.difference_map
• torchref.maps.map
• torchref.model.closed_segmented_internal_coordinates
• torchref.model.internal_coordinates
• torchref.model.mixed_model
• torchref.model.model
• torchref.model.model_collection
• torchref.model.model_ft
• torchref.model.parameter_wrappers
• torchref.model.segmented_internal_coordinates
• torchref.model.sf_ds
• torchref.model.sf_fft
• torchref.refinement.base_refinement
• torchref.refinement.lbfgs_refinement
• torchref.refinement.logger
• torchref.refinement.loss_state
• torchref.refinement.optimizers.adam_noise
• torchref.refinement.optimizers.exploratory_lbfgs
• torchref.refinement.optimizers.internal_coord_sa
• torchref.refinement.optimizers.langevin_sa
• torchref.refinement.optimizers.momentum_sa
• torchref.refinement.optimizers.simulated_annealing
• torchref.refinement.targets.adp.base
• torchref.refinement.targets.adp.entropy
• torchref.refinement.targets.adp.locality
• torchref.refinement.targets.adp.rigid_bond
• torchref.refinement.targets.adp.scaler_log_scale
• torchref.refinement.targets.adp.scaler_u
• torchref.refinement.targets.adp.similarity
• torchref.refinement.targets.amber_target
• torchref.refinement.targets.base
• torchref.refinement.targets.combined
• torchref.refinement.targets.difference
• torchref.refinement.targets.forcefield_target
• torchref.refinement.targets.geometry.angles
• torchref.refinement.targets.geometry.base
• torchref.refinement.targets.geometry.bonds
• torchref.refinement.targets.geometry.chiral
• torchref.refinement.targets.geometry.non_bonded
• torchref.refinement.targets.geometry.non_bonded_h
• torchref.refinement.targets.geometry.planarity
• torchref.refinement.targets.geometry.ramachandran
• torchref.refinement.targets.geometry.torsions
• torchref.refinement.targets.occupancy_floor_diagnostic
• torchref.refinement.targets.realspace
• torchref.refinement.targets.sampled_ml_phase_target
• torchref.refinement.targets.similarity
• torchref.refinement.targets.xray.base
• torchref.refinement.targets.xray.bhattacharyya
• torchref.refinement.targets.xray.gaussian
• torchref.refinement.targets.xray.least_squares
• torchref.refinement.targets.xray.maximum_likelihood
• torchref.refinement.weighting.base_weighting
• torchref.refinement.weighting.component_weighting
• torchref.refinement.weighting.es_policy_training
• torchref.refinement.weighting.policy_weighting
• torchref.refinement.weighting.random_weighting
• torchref.restraints.builders
• torchref.restraints.builders_fast
• torchref.restraints.builders_numba
• torchref.restraints.hydrogen_topology
• torchref.restraints.library
• torchref.restraints.neighbor_search
• torchref.restraints.ramachandran
• torchref.restraints.restraints
• torchref.restraints.restraints_helper
• torchref.scaling.collection_scaler
• torchref.scaling.scaler
• torchref.scaling.scaler_base
• torchref.scaling.solvent
• torchref.scripts.generate_scattering_table
• torchref.symmetry.cell
• torchref.symmetry.grid_utils
• torchref.symmetry.map_symmetry
• torchref.symmetry.map_symmetry_interpolation
• torchref.symmetry.reciprocal_symmetry
• torchref.symmetry.spacegroup
• torchref.utils.autograd_introspection
• torchref.utils.autograd_ops
• torchref.utils.caching
• torchref.utils.debug_utils
• torchref.utils.device_mixin
• torchref.utils.device_resolution
• torchref.utils.gradnorm
• torchref.utils.hyperparameters
• torchref.utils.loss_validation
• torchref.utils.serialization
• torchref.utils.stats
• torchref.utils.timing
• torchref.utils.utils