Getting Started
User Guide
torchref.refine
torchref.difference-refine
torchref.mtz2map
torchref.validate-ded
torchref.phased-difference-map
API Reference
main()
setup_model_collection()
setup_dataset_collection()
setup_scaler()
compute_rfactors()
setup_loss_state()
compute_bayes_extrapolated_amplitudes()
write_results_mtz()
optimize_lbfgs()
strip_altlocs()
build_atom_mask()
compute_correlation()
compute_map_from_coefficients()
generate_plots()
setup_ded_context()
compute_ded_maps()
run_validation()
CrystalDataset
CrystalDataset.hkl
CrystalDataset.F
CrystalDataset.F_sigma
CrystalDataset.I
CrystalDataset.I_sigma
CrystalDataset.rfree_flags
CrystalDataset.resolution
CrystalDataset.bin_indices
CrystalDataset.outlier_flags
CrystalDataset.phase
CrystalDataset.fom
CrystalDataset.E
CrystalDataset.E_squared
CrystalDataset.F_squared_corrected
CrystalDataset.U_aniso
CrystalDataset.radial_shell_indices
CrystalDataset.cell
CrystalDataset.spacegroup
CrystalDataset.device
CrystalDataset.verbose
CrystalDataset.rfree_source
CrystalDataset.amplitude_source
CrystalDataset.intensity_source
CrystalDataset.phase_source
CrystalDataset.wilson_b
CrystalDataset.wilson_b_structure
CrystalDataset.wilson_b_solvent
CrystalDataset.wilson_k_sol
CrystalDataset.outlier_detection_params
CrystalDataset.__post_init__()
CrystalDataset.save_state()
CrystalDataset.load_state()
CrystalDataset.__len__()
CrystalDataset.__repr__()
CrystalDataset.spacegroup_name
CrystalDataset.spacegroup_hm
CrystalDataset.spacegroup_number
CrystalDataset.__init__()
ReflectionData
ReflectionData.hkl
ReflectionData.F
ReflectionData.F_sigma
ReflectionData.I
ReflectionData.I_sigma
ReflectionData.rfree_flags
ReflectionData.cell
ReflectionData.spacegroup
ReflectionData.resolution
ReflectionData.wilson_b
ReflectionData.source
ReflectionData.dataset
ReflectionData.last_op
ReflectionData.reader
ReflectionData.__post_init__()
ReflectionData.load()
ReflectionData.from_tensors()
ReflectionData.load_mtz()
ReflectionData.load_cif()
ReflectionData.list_cif_data_blocks()
ReflectionData.get_bins()
ReflectionData.mean_res_per_bin()
ReflectionData.mean_F_per_bin()
ReflectionData.mean_sigma_per_bin()
ReflectionData.regenerate_rfree_flags()
ReflectionData.get_structure_factors()
ReflectionData.get_structure_factors_with_sigma()
ReflectionData.get_hkl()
ReflectionData.filter_by_resolution()
ReflectionData.get_mask()
ReflectionData.cut_res()
ReflectionData.get_rfree_masks()
ReflectionData.get_work_set()
ReflectionData.get_test_set()
ReflectionData.get_max_res()
ReflectionData.get_min_res()
ReflectionData.__len__()
ReflectionData.d_min
ReflectionData.__repr__()
ReflectionData.get_valid_mask()
ReflectionData.data_indexed()
ReflectionData.__call__()
ReflectionData.data_fill_masked()
ReflectionData.__getitem__()
ReflectionData.__select__()
ReflectionData.sanitize_F()
ReflectionData.check_all_data_types()
ReflectionData.validate_hkl()
ReflectionData.find_outliers()
ReflectionData.get_log_ratio()
ReflectionData.get_outlier_statistics()
ReflectionData.unpack_one()
ReflectionData.flag_suspicious_sigma()
ReflectionData.dump()
ReflectionData.write_mtz()
ReflectionData.centric
ReflectionData.calc_patterson()
ReflectionData.possible_hkl()
ReflectionData.remap()
ReflectionData.fill()
ReflectionData.expand_to_p1()
ReflectionData.reduce_to_spacegroup()
ReflectionData.canonicalize()
ReflectionData.get_scattering_vectors()
ReflectionData.get_radial_shells()
ReflectionData.fit_anisotropy()
ReflectionData.setup_anisotropy()
ReflectionData.apply_anisotropy_correction()
ReflectionData.compute_e_values()
ReflectionData.setup_scale()
ReflectionData.get_corrected_data()
ReflectionData.parameters()
ReflectionData.__init__()
DatasetCollection
DatasetCollection.hkl
DatasetCollection.n_datasets
DatasetCollection.add_dataset()
DatasetCollection.datasets
DatasetCollection.reference_dataset
DatasetCollection.spacegroup
DatasetCollection.__getitem__()
DatasetCollection.__iter__()
DatasetCollection.__len__()
DatasetCollection.__contains__()
DatasetCollection.__call__()
DatasetCollection.scale()
DatasetCollection.keys()
DatasetCollection.values()
DatasetCollection.items()
DatasetCollection.__init__()
DatasetCollection.get()
DatasetCollection.__repr__()
FcalcDataset
FcalcDataset.spacegroup
FcalcDataset.fcalc
FcalcDataset.fcalc_amp
FcalcDataset.fcalc_phase
FcalcDataset.from_cell_and_resolution()
FcalcDataset.set_fcalc()
FcalcDataset.write_mtz()
FcalcDataset.write_mtz_as_fobs()
FcalcDataset.__repr__()
FcalcDataset.spacegroup_name
FcalcDataset.spacegroup_hm
FcalcDataset.spacegroup_number
FcalcDataset.__init__()
MTZReader
MTZReader.verbose
MTZReader.data
MTZReader.cell
MTZReader.spacegroup
MTZReader.AMPLITUDE_PRIORITY
MTZReader.INTENSITY_PRIORITY
MTZReader.RFREE_FLAG_NAMES
MTZReader.__init__()
MTZReader.read()
MTZReader.__call__()
PDBReader
PDBReader.verbose
PDBReader.dataframe
PDBReader.cell
PDBReader.spacegroup
PDBReader.__init__()
PDBReader.read()
PDBReader.__call__()
CIFReader
CIFReader.data
CIFReader.filepath
CIFReader.available_blocks
CIFReader.__init__()
CIFReader.from_string()
CIFReader.load()
CIFReader.write()
CIFReader.__getitem__()
CIFReader.__setitem__()
CIFReader.__contains__()
CIFReader.__len__()
CIFReader.keys()
CIFReader.values()
CIFReader.items()
CIFReader.get()
CIFReader.__repr__()
CIFReader.summary()
ReflectionCIFReader
ReflectionCIFReader.__init__()
ReflectionCIFReader.read()
ReflectionCIFReader.__call__()
ReflectionCIFReader.get_reflection_data()
ReflectionCIFReader.has_miller_indices()
ReflectionCIFReader.has_amplitudes()
ReflectionCIFReader.has_intensities()
ReflectionCIFReader.has_phases()
ReflectionCIFReader.has_rfree_flags()
ReflectionCIFReader.get_miller_indices()
ReflectionCIFReader.get_amplitudes()
ReflectionCIFReader.get_intensities()
ReflectionCIFReader.get_cell_parameters()
ReflectionCIFReader.get_space_group()
ModelCIFReader
ModelCIFReader.__init__()
ModelCIFReader.read()
ModelCIFReader.__call__()
ModelCIFReader.get_atom_data()
ModelCIFReader.get_atom_data_by_model()
ModelCIFReader.get_cell_parameters()
ModelCIFReader.get_space_group()
ModelCIFReader.has_coordinates()
ModelCIFReader.has_cell_parameters()
ModelCIFReader.has_space_group()
ModelCIFReader.has_occupancy()
ModelCIFReader.has_bfactor()
ModelCIFReader.has_anisotropic_data()
ModelCIFReader.get_coordinates()
ModelCIFReader.get_atom_info()
RestraintCIFReader
RestraintCIFReader.__init__()
RestraintCIFReader.get_all_restraints()
RestraintCIFReader.get_compound_restraints()
RestraintCIFReader.get_bond_restraints()
RestraintCIFReader.get_compound_id()
RestraintCIFReader.has_bond_restraints()
RestraintCIFReader.has_angle_restraints()
RestraintCIFReader.has_torsion_restraints()
RestraintCIFReader.has_plane_restraints()
RestraintCIFReader.has_chirality_restraints()
DataRouter
DataRouter.filepath
DataRouter.verbose
DataRouter.data_type
DataRouter.file_format
DataRouter.reader
DataRouter.MTZ_EXTENSIONS
DataRouter.PDB_EXTENSIONS
DataRouter.CIF_EXTENSIONS
DataRouter.__init__()
DataRouter.get_reader()
DataRouter.get_data()
DataRouter.route()
DataRouter.__repr__()
DataRouter.__str__()
DataRouterError
IHMEnsembleMapping
IHMEnsembleMapping.states
IHMEnsembleMapping.model_groups
IHMEnsembleMapping.cell
IHMEnsembleMapping.spacegroup
IHMEnsembleMapping.atom_data_per_state
IHMEnsembleMapping.get_state_ids()
IHMEnsembleMapping.get_timepoint_names()
IHMEnsembleMapping.get_fractions_for_group()
IHMEnsembleMapping.identify_dark_group()
IHMEnsembleMapping.get_state_by_id()
IHMEnsembleMapping.get_group_by_name()
IHMEnsembleMapping.validate()
IHMEnsembleMapping.__init__()
IHMStateInfo
IHMStateInfo.state_id
IHMStateInfo.name
IHMStateInfo.details
IHMStateInfo.model_num
IHMStateInfo.__init__()
IHMModelGroupInfo
IHMModelGroupInfo.group_id
IHMModelGroupInfo.name
IHMModelGroupInfo.state_fractions
IHMModelGroupInfo.time_delay
IHMModelGroupInfo.time_delay_units
IHMModelGroupInfo.__init__()
RefinementMetadata
RefinementMetadata.program
RefinementMetadata.program_version
RefinementMetadata.refinement_method
RefinementMetadata.resolution_high
RefinementMetadata.resolution_low
RefinementMetadata.n_reflections_work
RefinementMetadata.n_reflections_test
RefinementMetadata.n_reflections_all
RefinementMetadata.percent_free
RefinementMetadata.r_work
RefinementMetadata.r_free
RefinementMetadata.b_mean_overall
RefinementMetadata.b_min
RefinementMetadata.b_max
RefinementMetadata.rmsd_bond_lengths
RefinementMetadata.rmsd_bond_angles
RefinementMetadata.n_atoms_total
RefinementMetadata.n_atoms_protein
RefinementMetadata.n_atoms_solvent
RefinementMetadata.solvent_model_ksol
RefinementMetadata.solvent_model_bsol
RefinementMetadata.cell
RefinementMetadata.spacegroup
RefinementMetadata.title
RefinementMetadata.authors
RefinementMetadata.passthrough_pdb_remarks
RefinementMetadata.passthrough_cif_categories
RefinementMetadata.custom_remarks
RefinementMetadata.to_dict()
RefinementMetadata.from_dict()
RefinementMetadata.from_refinement()
RefinementMetadata.from_pdb_file()
RefinementMetadata.from_cif_file()
RefinementMetadata.merge()
RefinementMetadata.render_pdb_header()
RefinementMetadata.render_cif_categories()
RefinementMetadata.__init__()
MTZ
PDB
read_reflections()
read_model()
read_restraints()
list_data_blocks()
write_map()
dataframe_to_gemmi_structure()
write_model()
read()
IHMReader
IHMWriter
write()
find_header_length()
read_crystallographic_info()
load_as_dataframe()
extract_pdb_headers()
extract_link_records()
write_multi_model()
find_header_length_pdb_file()
load_pdb_as_pd()
FFT()
SfFFT
SfFFT.cell
SfFFT.spacegroup
SfFFT.symmetry
SfFFT.max_res
SfFFT.radius_angstrom
SfFFT.gridsize
SfFFT.real_space_grid
SfFFT.voxel_size
SfFFT.map_symmetry
SfFFT.__init__()
SfFFT.fractional_matrix
SfFFT.inv_fractional_matrix
SfFFT.set_cell_and_spacegroup()
SfFFT.compute_optimal_gridsize()
SfFFT.compute_real_space_grid()
SfFFT.setup_grid()
SfFFT.build_density_map()
SfFFT.map_to_structure_factors()
SfFFT.compute_structure_factors()
SfFFT.reset_cache()
SfFFT.copy()
SfDS
SfDS.cell
SfDS.spacegroup
SfDS.__init__()
SfDS.fractional_matrix
SfDS.inv_fractional_matrix
SfDS.set_cell_and_spacegroup()
SfDS.compute_structure_factors()
SfDS.reset_cache()
SfDS.copy()
InternalCoordinateTensor
InternalCoordinateTensor.n_atoms
InternalCoordinateTensor.n_chains
InternalCoordinateTensor.max_depth
InternalCoordinateTensor.bond_lengths
InternalCoordinateTensor.angles
InternalCoordinateTensor.torsions
InternalCoordinateTensor.chain_positions
InternalCoordinateTensor.chain_orientations
InternalCoordinateTensor.__init__()
InternalCoordinateTensor.dtype
InternalCoordinateTensor.device
InternalCoordinateTensor.to()
InternalCoordinateTensor.cuda()
InternalCoordinateTensor.cpu()
InternalCoordinateTensor.forward_slow()
InternalCoordinateTensor.forward()
InternalCoordinateTensor.shake()
InternalCoordinateTensor.fix()
InternalCoordinateTensor.freeze()
InternalCoordinateTensor.refine()
InternalCoordinateTensor.unfreeze()
InternalCoordinateTensor.fix_all()
InternalCoordinateTensor.freeze_all()
InternalCoordinateTensor.refine_all()
InternalCoordinateTensor.unfreeze_all()
InternalCoordinateTensor.n_refinable
InternalCoordinateTensor.n_fixed
InternalCoordinateTensor.forward_parallel()
MixedModel
MixedModel.models
MixedModel.fraction_params
MixedModel.__init__()
MixedModel.fractions
MixedModel.cell
MixedModel.spacegroup
MixedModel.device
MixedModel.dtype_float
MixedModel.real_space_grid
MixedModel.fft
MixedModel.gridsize
MixedModel.map_symmetry
MixedModel.inv_fractional_matrix
MixedModel.fractional_matrix
MixedModel.setup_grid()
MixedModel.get_radius()
MixedModel.build_complete_map()
MixedModel.freeze_fractions()
MixedModel.unfreeze_fractions()
MixedModel.forward()
MixedModel.get_individual_fcalc()
MixedModel.copy()
MixedModel.__repr__()
MixedModel.write_ihm()
MixedModel.get_vdw_radii()
MixedModel.xyz()
Model
Model.xyz
Model.adp
Model.u
Model.occupancy
Model.pdb
Model.cell
Model.spacegroup
Model.symmetry
Model.initialized
Model.__init__()
Model.__bool__()
Model.exclude_H_from_sf
Model.inv_fractional_matrix
Model.fractional_matrix
Model.recB
Model.Z
Model.get_P1_parameters_iso()
Model.get_MD_parameters()
Model.parametrization
Model.get_scattering_params_iso()
Model.get_scattering_params_aniso()
Model.set_restraints_cif()
Model.restraints
Model.bond_deviations()
Model.angle_deviations()
Model.torsion_deviations_with_sigmas()
Model.load()
Model.load_pdb()
Model.load_cif()
Model.chain_sequences
Model.get_chain_residues()
Model.update_pdb()
Model.get_vdw_radii()
Model.to()
Model.copy()
Model.write_pdb()
Model.write_cif()
Model.get_iso()
Model.set_default_masks()
Model.PARAM_TYPES
Model.parameters_of_types()
Model.freeze()
Model.freeze_all()
Model.unfreeze_all()
Model.unfreeze()
Model.update_mask_from_selection()
Model.apply_mask_to_parameter()
Model.freeze_selection()
Model.unfreeze_selection()
Model.get_aniso()
Model.parameters()
Model.named_mixed_tensors()
Model.print_parameters_info()
Model.register_alternative_conformations()
Model.shake_coords()
Model.shake_adp()
Model.generate_hydrogens()
Model.strip_altlocs()
Model.strip_hydrogens()
Model.hydrogenate()
Model.adp_loss()
Model.adp_nll_loss()
Model.adp_nll_loss_per_atom()
Model.adp_kl_divergence_loss()
Model.state_dict()
Model.save_state()
Model.load_state()
Model.create_from_state_dict()
Model.get_selection_mask()
Model.select()
Model.xyz_fractional()
Model.rotate()
Model.translate()
Model.get_centroid()
Model.use_internal_coordinates()
ModelFT
ModelFT.max_res
ModelFT.radius_angstrom
ModelFT.wavelength
ModelFT.anomalous_threshold
ModelFT.gridsize
ModelFT.real_space_grid
ModelFT.map
ModelFT.parametrization
ModelFT.map_symmetry
ModelFT.__init__()
ModelFT.cell
ModelFT.spacegroup
ModelFT.load_pdb()
ModelFT.select()
ModelFT.load_cif()
ModelFT.setup_gridsize()
ModelFT.A
ModelFT.B
ModelFT.voxel_size
ModelFT.get_iso()
ModelFT.get_aniso()
ModelFT.setup_grid()
ModelFT.get_radius()
ModelFT.build_complete_map()
ModelFT.build_initial_map()
ModelFT.save_map()
ModelFT.get_map_statistics()
ModelFT.rebuild_map()
ModelFT.update_pdb()
ModelFT.reset_cache()
ModelFT.invalidate_cache()
ModelFT.get_structure_factor()
ModelFT.fft
ModelFT.forward()
ModelFT.copy()
ModelFT.state_dict()
ModelFT.create_from_state_dict()
MixedTensor
MixedTensor.refinable_mask
MixedTensor.fixed_mask
MixedTensor.fixed_values
MixedTensor.refinable_params
MixedTensor.__init__()
MixedTensor.forward()
MixedTensor.__getitem__()
MixedTensor.__setitem__()
MixedTensor.set()
MixedTensor.shape
MixedTensor.dtype
MixedTensor.device
MixedTensor.get_refinable_count()
MixedTensor.get_fixed_count()
MixedTensor.update_fixed_values()
MixedTensor.update_refinable_mask()
MixedTensor.detach()
MixedTensor.clone()
MixedTensor.copy()
MixedTensor.clip()
MixedTensor.to()
MixedTensor.refine()
MixedTensor.fix()
MixedTensor.refine_all()
MixedTensor.fix_all()
MixedTensor.name
MixedTensor.__str__()
MixedTensor.parameters()
PositiveMixedTensor
PositiveMixedTensor.__init__()
PositiveMixedTensor.forward()
PositiveMixedTensor.fix()
PositiveMixedTensor.refine()
PositiveMixedTensor.set()
PositiveMixedTensor.get_log_values()
PositiveMixedTensor.update_refinable_mask()
PositiveMixedTensor.copy()
PositiveMixedTensor.__str__()
PassThroughTensor
PassThroughTensor.__init__()
PassThroughTensor.forward()
OccupancyTensor
OccupancyTensor.expansion_mask
OccupancyTensor.linked_occ_sizes
OccupancyTensor.collapse_counts
OccupancyTensor.__init__()
OccupancyTensor.forward()
OccupancyTensor.shape
OccupancyTensor.collapsed_shape
OccupancyTensor.clamp()
OccupancyTensor.set_group_occupancy()
OccupancyTensor.get_group_occupancy()
OccupancyTensor.freeze()
OccupancyTensor.unfreeze()
OccupancyTensor.freeze_all()
OccupancyTensor.unfreeze_all()
OccupancyTensor.get_refinable_atoms()
OccupancyTensor.get_frozen_atoms()
OccupancyTensor.get_refinable_count()
OccupancyTensor.get_fixed_count()
OccupancyTensor.update_refinable_mask()
OccupancyTensor.from_residue_groups()
OccupancyTensor.copy()
SegmentedInternalCoordinateTensor
SegmentedInternalCoordinateTensor.n_atoms
SegmentedInternalCoordinateTensor.n_segments
SegmentedInternalCoordinateTensor.max_depth
SegmentedInternalCoordinateTensor.bond_lengths
SegmentedInternalCoordinateTensor.angles
SegmentedInternalCoordinateTensor.torsions
SegmentedInternalCoordinateTensor.segment_positions
SegmentedInternalCoordinateTensor.segment_orientations
SegmentedInternalCoordinateTensor.AA_NAMES
SegmentedInternalCoordinateTensor.__init__()
SegmentedInternalCoordinateTensor.dtype
SegmentedInternalCoordinateTensor.device
SegmentedInternalCoordinateTensor.forward()
SegmentedInternalCoordinateTensor.shake()
SegmentedInternalCoordinateTensor.fix()
SegmentedInternalCoordinateTensor.freeze()
SegmentedInternalCoordinateTensor.refine()
SegmentedInternalCoordinateTensor.unfreeze()
SegmentedInternalCoordinateTensor.fix_all()
SegmentedInternalCoordinateTensor.freeze_all()
SegmentedInternalCoordinateTensor.refine_all()
SegmentedInternalCoordinateTensor.unfreeze_all()
SegmentedInternalCoordinateTensor.n_refinable
SegmentedInternalCoordinateTensor.n_fixed
ClosedSegmentedInternalCoordinateTensor
ClosedSegmentedInternalCoordinateTensor.__init__()
ClosedSegmentedInternalCoordinateTensor.dtype
ClosedSegmentedInternalCoordinateTensor.device
ClosedSegmentedInternalCoordinateTensor.forward()
ClosedSegmentedInternalCoordinateTensor.shake()
ClosedSegmentedInternalCoordinateTensor.fix()
ClosedSegmentedInternalCoordinateTensor.freeze()
ClosedSegmentedInternalCoordinateTensor.refine()
ClosedSegmentedInternalCoordinateTensor.unfreeze()
ClosedSegmentedInternalCoordinateTensor.fix_all()
ClosedSegmentedInternalCoordinateTensor.freeze_all()
ClosedSegmentedInternalCoordinateTensor.refine_all()
ClosedSegmentedInternalCoordinateTensor.unfreeze_all()
ClosedSegmentedInternalCoordinateTensor.n_refinable
ClosedSegmentedInternalCoordinateTensor.n_fixed
ClosedSegmentedInternalCoordinateTensor.closure_residuals
ClosedSegmentedInternalCoordinateTensor.max_closure_gap
ModelCollection
ModelCollection.__init__()
ModelCollection.add_timepoint()
ModelCollection.add_dark()
ModelCollection.from_kinetics()
ModelCollection.from_ihm()
ModelCollection.write_ihm()
ModelCollection.keys()
ModelCollection.values()
ModelCollection.items()
ModelCollection.get()
ModelCollection.dark_key
ModelCollection.dark_model
ModelCollection.base_models
ModelCollection.n_base_models
ModelCollection.timepoint_names
ModelCollection.cell
ModelCollection.spacegroup
ModelCollection.device
ModelCollection.get_all_fractions()
ModelCollection.get_fractions_matrix()
ModelCollection.freeze_all_fractions()
ModelCollection.unfreeze_all_fractions()
ModelCollection.freeze_structures()
ModelCollection.unfreeze_structures()
ModelCollection.write_pdbs()
CholeskyMixedTensor
Refinement
Refinement.device
Refinement.verbose
Refinement.reflection_data
Refinement.model
Refinement.scaler
Refinement.weighter
Refinement.__init__()
Refinement.set_xray_target_mode()
Refinement.data
Refinement.loss_state
Refinement.logger
Refinement.reset_loss_state()
Refinement.get_scales()
Refinement.setup_scaler()
Refinement.parameters()
Refinement.get_fcalc()
Refinement.get_fcalc_scaled()
Refinement.adp_loss()
Refinement.get_F_calc()
Refinement.get_F_calc_scaled()
Refinement.nll_xray()
Refinement.xray_loss_work()
Refinement.xray_loss_test()
Refinement.bond_loss()
Refinement.angle_loss()
Refinement.torsion_loss()
Refinement.geometry_loss()
Refinement.loss()
Refinement.setup_component_weighting()
Refinement.populate_state_meta()
Refinement.update_weights()
Refinement.create_loss_state()
Refinement.complete_loss_state()
Refinement.xray_loss()
Refinement.restraints_loss()
Refinement.collect_metrics()
Refinement.add_target_info_to_state()
Refinement.get_rfactor()
Refinement.update_outliers()
Refinement.plot_fcalc_vs_fobs()
Refinement.write_out_mtz()
Refinement.collect_deposition_metadata()
Refinement.write_out_pdb()
Refinement.write_out_cif()
Refinement.save_state()
Refinement.load_state()
Refinement.create_from_state_dict()
LBFGSRefinement
LBFGSRefinement.target_mode
LBFGSRefinement.LBFGS_DEFAULTS
LBFGSRefinement.__init__()
LBFGSRefinement.xray_loss()
LBFGSRefinement.refine_scaler()
LBFGSRefinement.refine_xyz()
LBFGSRefinement.refine_adp()
LBFGSRefinement.refine_joint()
LBFGSRefinement.run_training_trajectory()
LBFGSRefinement.run_training_trajectory_joint()
LBFGSRefinement.refine()
LBFGSRefinement.refine_everything()
LossState
LossState.device
LossState.targets
LossState.weights
LossState.history
LossState.meta
LossState.__getitem__()
LossState.__contains__()
LossState.get()
LossState.cache_losses()
LossState.update_meta()
LossState.register_target()
LossState.register_targets()
LossState.set_weight()
LossState.set_weights()
LossState.get_weight()
LossState.get_effective_weight()
LossState.mark_compilable()
LossState.compile_aggregate()
LossState.reset_compiled_aggregate()
LossState.log()
LossState.new_entry()
LossState.get_history()
LossState.aggregate()
LossState.get_loss()
LossState.active_parameters()
LossState.refresh_loss_leaves()
LossState.reset_caches()
LossState.restore_loss_leaf_grads()
LossState.run()
LossState.step()
LossState.get_breakdown()
LossState.get_group_totals()
LossState.format_breakdown()
LossState.summary()
LossState.to()
LossState.clear()
LossState.clear_history()
LossState.__init__()
Logger
Logger.state
Logger.verbose
Logger.pattern
Logger.record()
Logger.compare()
Logger.current()
Logger.get_record()
Logger.clear()
Logger.history
Logger.__init__()
Target
Target.name
Target.verbose
Target.__init__()
Target.forward()
Target.add_to_state()
Target.maintenance()
DataTarget
DataTarget.name
DataTarget._model
DataTarget._data
DataTarget._scaler
DataTarget.verbose
DataTarget.__init__()
DataTarget.model
DataTarget.data
DataTarget.scaler
DataTarget.has_model
DataTarget.get_fcalc()
DataTarget.get_fcalc_scaled()
DataTarget.get_F_calc_scaled()
DataTarget.get_rfactor()
ModelTarget
ModelTarget.name
ModelTarget._model
ModelTarget.verbose
ModelTarget.__init__()
ModelTarget.model
ModelTarget.restraints
AdamWithAdaptiveNoise
ExploratoryLBFGS
LangevinSA
MomentumStochasticSA
gaussian_nll()
von_mises_nll()
adp_similarity_nll()
XrayTarget
GaussianXrayTarget
MaximumLikelihoodXrayTarget
LeastSquaresXrayTarget
create_xray_target()
DifferenceXrayTarget
PhaseInformedDifferenceTarget
RiceDifferenceTarget
TaylorCorrectedDifferenceTarget
GeometryTarget
BondTarget
AngleTarget
TorsionTarget
PlanarityTarget
ChiralTarget
NonBondedTarget
NonBondedHTarget
RamachandranTarget
ADPTarget
ADPSimilarityTarget
RigidBondTarget
ADPEntropyTarget
ADPLocalityTarget
CombinedTargets
TotalGeometryTarget
TotalADPTarget
ForceFieldTarget
AmberTarget
OccupancyFloorDiagnostic
NegativeDensityPenalty
DisplacementRegularizer
DifferenceAmplitudeRegularizer
SampledMLPhaseTarget
SampledMLDifferenceTarget
create_sampled_ml_target()
create_sampled_ml_difference_target()
RealSpaceTarget
RealSpaceCorrelationTarget
RealSpaceDifferenceTarget
RealSpaceExtrapolatedTarget
CoordinateSimilarityTarget
BaseWeighting
WeightingScheme
ResolutionWeighting
OverfittingWeighting
ManualWeighting
ComponentWeighting
create_loss_state()
Restraints
ResidueIterator
ResidueIterator.pdb
ResidueIterator.groups
ResidueIterator.__init__()
ResidueIterator.__iter__()
ResidueIterator.__len__()
ResidueIterator.get_consecutive_pairs()
RestraintBuilder
RestraintBuilder._indices
RestraintBuilder._references
RestraintBuilder._sigmas
RestraintBuilder._count
RestraintBuilder.restraint_type
RestraintBuilder.atom_columns
RestraintBuilder.n_atoms
RestraintBuilder.__init__()
RestraintBuilder.reset()
RestraintBuilder.process_residue()
RestraintBuilder.finalize()
RestraintBuilder.count
BondRestraintBuilder
BondRestraintBuilder.restraint_type
BondRestraintBuilder.atom_columns
BondRestraintBuilder.n_atoms
BondRestraintBuilder.process_residue()
AngleRestraintBuilder
AngleRestraintBuilder.restraint_type
AngleRestraintBuilder.atom_columns
AngleRestraintBuilder.n_atoms
AngleRestraintBuilder.process_residue()
TorsionRestraintBuilder
TorsionRestraintBuilder._periods
TorsionRestraintBuilder.restraint_type
TorsionRestraintBuilder.atom_columns
TorsionRestraintBuilder.n_atoms
TorsionRestraintBuilder.__init__()
TorsionRestraintBuilder.reset()
TorsionRestraintBuilder.process_residue()
TorsionRestraintBuilder.finalize()
PlaneRestraintBuilder
PlaneRestraintBuilder._planes_by_count
PlaneRestraintBuilder.restraint_type
PlaneRestraintBuilder.atom_columns
PlaneRestraintBuilder.n_atoms
PlaneRestraintBuilder.__init__()
PlaneRestraintBuilder.reset()
PlaneRestraintBuilder.process_residue()
PlaneRestraintBuilder.finalize()
ChiralRestraintBuilder
ChiralRestraintBuilder._ideal_volumes
ChiralRestraintBuilder.ideal_volume
ChiralRestraintBuilder.sigma
ChiralRestraintBuilder.restraint_type
ChiralRestraintBuilder.atom_columns
ChiralRestraintBuilder.n_atoms
ChiralRestraintBuilder.__init__()
ChiralRestraintBuilder.reset()
ChiralRestraintBuilder.process_residue()
ChiralRestraintBuilder.finalize()
InterResidueBondBuilder
InterResidueBondBuilder._indices
InterResidueBondBuilder._references
InterResidueBondBuilder._sigmas
InterResidueBondBuilder.__init__()
InterResidueBondBuilder.reset()
InterResidueBondBuilder.process_peptide_bond()
InterResidueBondBuilder.process_disulfide_bond()
InterResidueBondBuilder.finalize()
InterResidueBondBuilder.count
InterResidueAngleBuilder
InterResidueAngleBuilder.__init__()
InterResidueAngleBuilder.reset()
InterResidueAngleBuilder.process_peptide_angles()
InterResidueAngleBuilder.process_disulfide_angles()
InterResidueAngleBuilder.finalize()
InterResidueAngleBuilder.count
InterResidueTorsionBuilder
InterResidueTorsionBuilder.__init__()
InterResidueTorsionBuilder.reset()
InterResidueTorsionBuilder.process_peptide_torsions()
InterResidueTorsionBuilder.process_disulfide_torsions()
InterResidueTorsionBuilder.finalize_phi()
InterResidueTorsionBuilder.finalize_psi()
InterResidueTorsionBuilder.finalize_omega()
InterResidueTorsionBuilder.finalize_disulfide()
InterResiduePlaneBuilder
InterResiduePlaneBuilder.__init__()
InterResiduePlaneBuilder.reset()
InterResiduePlaneBuilder.process_peptide_planes()
InterResiduePlaneBuilder.finalize()
InterResiduePlaneBuilder.count
get_library_manager()
PreprocessedPDB
PreprocessedCIF
build_all_restraints()
PreprocessedLinkData
find_atom_index()
match_bonds_numba()
match_angles_numba()
match_torsions_numba()
match_chirals_numba()
FastResidueIterator
FastBondBuilder
FastAngleBuilder
FastTorsionBuilder
FastPlaneBuilder
FastChiralBuilder
build_all_restraints_fast()
HydrogenTopology
build_hydrogen_topology()
place_riding_hydrogens()
build_h_candidate_pairs()
MonomerLibraryManager
prefilter_symop_offsets()
assign_to_grid()
build_cell_list()
find_pairs_periodic_grid()
find_pairs_periodic_grid_v2()
exclusion_set_to_hash()
filter_pairs()
build_vdw_restraints_gpu()
find_h_vdw_pairs_gpu()
load_nll_surfaces()
classify_residue()
RestraintsNew
validate_restraint_data()
read_cif()
split_respecting_quotes()
find_cif_file_in_library()
read_link_definitions()
build_restraints_bondlength()
build_restraints_angles()
build_restraints_torsion()
build_restraints_planes()
build_restraints()
calculate_restraints_bondlength()
calculate_restraints_angles()
calculate_restraints_torsion()
calculate_restraints_all()
read_for_component()
read_comp_list()
Scaler
Scaler.device
Scaler.nbins
Scaler.__init__()
Scaler.model
Scaler.set_model_and_data()
Scaler.initialize()
Scaler.compute_fcalc()
Scaler.calc_initial_scale()
Scaler.fit_anisotropy()
Scaler.setup_solvent()
Scaler.fit_all_scales()
Scaler.screen_solvent_params()
Scaler.refine_lbfgs()
Scaler.rfactor()
Scaler.bin_wise_rfactor()
Scaler.get_binwise_mean_intensity()
Scaler.state_dict()
Scaler.load_state_dict()
ScalerBase
ScalerBase.device
ScalerBase.nbins
ScalerBase.__init__()
ScalerBase.set_data()
ScalerBase.initialize()
ScalerBase.hkl
ScalerBase.calc_initial_scale()
ScalerBase.setup_anisotropy_correction()
ScalerBase.anisotropy_correction()
ScalerBase.fit_anisotropy()
ScalerBase.set_solvent_model()
ScalerBase.setup_binwise_solvent_scale()
ScalerBase.fit_all_scales()
ScalerBase.fit_simple()
ScalerBase.get_scale()
ScalerBase.rfactor()
ScalerBase.bin_wise_rfactor()
ScalerBase.setup_bin_wise_bfactor()
ScalerBase.bin_wise_bfactor_correction()
ScalerBase.get_binwise_mean_intensity()
ScalerBase.screen_solvent_params()
ScalerBase.refine_lbfgs()
ScalerBase.estimate_sigma_eff()
ScalerBase.forward()
ScalerBase.state_dict()
ScalerBase.load_state_dict()
ScalerBase.save_state()
ScalerBase.load_state()
SolventModel
SolventModel.model
SolventModel.device
SolventModel.verbose
SolventModel.float_type
SolventModel.solvent_radius
SolventModel.erosion_radius
SolventModel.optimize_phase
SolventModel.log_k_solvent
SolventModel.b_solvent
SolventModel.phase_offset
SolventModel.__init__()
SolventModel.get_solvent_mask()
SolventModel.update_solvent()
SolventModel.smooth_solvent_mask()
SolventModel.get_rec_solvent()
SolventModel.forward()
SolventModel.parameters()
CollectionScaler
CollectionScaler.__init__()
CollectionScaler.initialize()
CollectionScaler.get_mixed_solvent_raw()
CollectionScaler.forward_mixed()
CollectionScaler.refine_lbfgs_joint()
CollectionScaler.screen_solvent_params_joint()
CollectionScaler.update_all_solvent()
CollectionScaler.invalidate_solvent_cache()
CollectionScaler.component_solvent_models
Cell
Cell.__init__()
Cell.reset_cache()
Cell.detach()
Cell.clone()
Cell.device
Cell.dtype
Cell.data
Cell.requires_grad
Cell.a
Cell.b
Cell.c
Cell.alpha
Cell.beta
Cell.gamma
Cell.fractional_matrix
Cell.inv_fractional_matrix
Cell.volume
Cell.reciprocal_basis_matrix
Cell.compute_grid_size()
Cell.tolist()
Cell.fractional_to_cartesian()
Cell.cartesian_to_fractional()
Cell.__repr__()
Cell.__getitem__()
Cell.__len__()
SpaceGroup
SpaceGroup.matrices
SpaceGroup.translations
SpaceGroup.n_ops
SpaceGroup.__init__()
SpaceGroup.name
SpaceGroup.hm
SpaceGroup.xhm
SpaceGroup.number
SpaceGroup.gemmi
SpaceGroup.point_group
SpaceGroup.crystal_system
SpaceGroup.centrosymmetric
SpaceGroup.dtype
SpaceGroup.device
SpaceGroup.spacegroup
SpaceGroup.space_group
SpaceGroup.space_group_name
SpaceGroup.space_group_number
SpaceGroup.short_name()
SpaceGroup.operations()
SpaceGroup.apply()
SpaceGroup.apply_to_hkl()
SpaceGroup.expand_coords_to_P1()
SpaceGroup.forward()
SpaceGroup.get_grid_requirements()
SpaceGroup.check_grid_compatibility()
SpaceGroup.suggest_grid_size()
SpaceGroup.__hash__()
SpaceGroup.__eq__()
SpaceGroup.copy()
spacegroup_to_str()
get_symmetry_operations()
get_operations_as_tensors()
is_same_spacegroup()
get_point_group()
get_crystal_system()
is_centrosymmetric()
n_operations()
Symmetry
MapSymmetry()
MapSymmetryDirect
MapSymmetryDirect.__init__()
MapSymmetryDirect.get_symmetry_mate()
MapSymmetryDirect.forward()
MapSymmetryDirect.__call__()
MapSymmetryDirect.get_symmetry_info()
ReciprocalSymmetry()
ReciprocalSymmetryGrid
ReciprocalSymmetryGrid.space_group
ReciprocalSymmetryGrid.grid_shape
ReciprocalSymmetryGrid.symmetry
ReciprocalSymmetryGrid.n_ops
ReciprocalSymmetryGrid.__init__()
ReciprocalSymmetryGrid.apply_to_indices()
ReciprocalSymmetryGrid.get_phase_shift()
ReciprocalSymmetryGrid.get_symmetry_mate()
ReciprocalSymmetryGrid.get_all_symmetry_mates()
ReciprocalSymmetryGrid.symmetry_average()
ReciprocalSymmetryGrid.expand_to_p1()
ReciprocalSymmetryGrid.apply_friedel()
ReciprocalSymmetryGrid.is_systematic_absence()
ReciprocalSymmetryGrid.is_centric()
ReciprocalSymmetryGrid.get_epsilon()
ReciprocalSymmetryGrid.forward()
ReciprocalSymmetryGrid.__call__()
ReciprocalSymmetryGrid.get_symmetry_info()
expand_hkl()
complete_hkl()
reduce_hkl()
canonicalize_hkl()
expand_reflections()
expand_reciprocal_grid()
get_symmetry_grid_requirements()
check_grid_compatibility()
recommend_grid_size()
find_fft_friendly_size()
is_fft_friendly()
calculate_optimal_grid_size()
CellTensor
MapSymmetry
get_grid_requirements()
suggest_grid_size()
FrenchWilson
FrenchWilson.hkl
FrenchWilson.d_spacings
FrenchWilson.is_centric
FrenchWilson.__init__()
FrenchWilson.forward()
CachedRadiusMask
CachedRadiusMask._cache
CachedRadiusMask.__init__()
CachedRadiusMask.get_offsets()
ReciprocalSymmetryExtractor
ReciprocalSymmetryExtractor.__init__()
ReciprocalSymmetryExtractor.__call__()
ReciprocalSymmetryExtractor.extract()
ReciprocalSymmetryExtractor.extract_from_grid()
cartesian_to_fractional_torch()
fractional_to_cartesian_torch()
get_fractional_matrix()
get_inv_fractional_matrix_torch()
cartesian_to_fractional()
fractional_to_cartesian()
get_inv_fractional_matrix()
convert_coords_to_fractional()
smallest_diff()
smallest_diff_aniso()
reciprocal_basis_matrix()
reciprocal_basis_matrix_numpy()
get_scattering_vectors()
get_scattering_vectors_numpy()
get_s()
get_d_spacing()
compute_d_spacing_batch()
generate_possible_hkl()
place_on_grid()
extract_structure_factor_from_grid()
apply_translation_phase()
interpolate_structure_factor_from_grid()
interpolate_complex_from_grid()
trilinear_interpolate_patterson()
compute_symmetry_equivalent_hkls()
compute_translation_phases()
extract_structure_factors_with_symmetry()
interpolate_for_rotation()
smooth_reciprocal_grid()
iso_structure_factor_torched()
iso_structure_factor_torched_no_complex()
aniso_structure_factor_torched()
aniso_structure_factor_torched_no_complex()
anharmonic_correction()
anharmonic_correction_no_complex()
core_deformation()
multiplication_quasi_complex_tensor()
vectorized_add_to_map()
vectorized_add_to_map_aniso()
scatter_add_nd()
scatter_add_nd_super_slow()
find_relevant_voxels()
excise_angstrom_radius_around_coord()
add_to_solvent_mask()
add_to_phenix_mask()
find_solvent_voids()
fft()
ifft()
get_real_grid()
find_grid_size()
get_real_grid_numpy()
get_grids()
put_hkl_on_grid()
get_scattering_factors()
get_scattering_factors_unique()
get_parametrization_for_elements()
calc_scattering_factors_paramtetrization()
compute_radial_shells()
assign_to_shells()
compute_anisotropy_correction()
compute_shell_cv()
fit_anisotropy_correction()
apply_anisotropy_correction()
F_squared_to_E_values()
rotate_coords_torch()
rotate_coords_numpy()
axis_angle_to_rotation_matrix()
rotation_matrix_to_axis_angle()
quaternion_to_rotation_matrix()
random_rotation_uniform()
superpose_vectors_robust_torch()
superpose_vectors_robust()
align_torch()
align_pdbs()
get_alignment_matrix()
apply_transformation()
apply_transformation_numpy()
invert_transformation_matrix()
get_rfactor_torch()
get_rfactor()
rfactor()
get_rfactors()
bin_wise_rfactors()
calc_outliers()
calc_outliers_numpy()
nll_xray()
nll_xray_sum()
nll_xray_lognormal()
log_loss()
estimate_sigma_I()
estimate_sigma_F()
gaussian_to_lognormal_sigma()
gaussian_to_lognormal_mu()
compute_metric_tensor()
precompute_fractional_coords()
warmup()
get_cache_dir()
clear_cache()
warmup_cuda_operations()
get_cached_radius_offsets()
get_alignement_matrix()
rotation_matrix_euler_zyz()
identify_backbone_atoms()
get_chain_residues()
compute_backbone_torsions()
estimate_secondary_structure()
plan_junction_placement()
get_junction_backbone_indices()
backbone_fk_junction()
closure_residual()
JunctionClosure
JunctionSolver
get_fractional_matrix_numpy()
build_electron_density()
vectorized_add_to_map_optimized()
fused_add_to_map_gpu()
fused_find_and_place_atoms()
separable_density_gpu()
get_scattering_itc92()
get_parameterization()
get_parameterization_extended()
get_parametrization_atom()
linear_interpolation()
load_scattering_table()
get_scattering_params_by_z()
get_element_to_z_mapping()
get_z_to_element_mapping()
get_scattering_params_for_ion()
elements_to_z()
get_anomalous_correction()
get_significant_elements()
get_anomalous_corrections_by_indices()
adp_kl_math()
adp_locality_math()
adp_simu_math()
angle_math()
bhattacharyya_xray_loss_math()
bond_math()
chiral_math()
gaussian_xray_loss_math()
ls_xray_loss_math()
ml_xray_loss_math()
nonbonded_heavy_math()
planarity_math()
ramachandran_math()
torsion_omega_math()
torsion_unimodal_math()
calculate_scattering_factor_cctbx()
interpolate_table()
french_wilson_acentric()
french_wilson_centric()
french_wilson()
is_centric_from_hkl()
get_centric_acentric_masks()
estimate_mean_intensity_by_resolution()
french_wilson_auto()
get_res_for_dataset()
U_to_matrix()
deterministic_tensor_digest()
hash_tensors()
french_wilson_conversion()
ParameterFingerprint
ParameterFingerprint.__init__()
ParameterFingerprint.matches()
CachedForwardMixin
CachedForwardMixin.__call__()
CachedForwardMixin.reset_forward_cache()
DeviceMixin
DeviceMixin.to()
DeviceMixin.cuda()
DeviceMixin.cpu()
DeviceMovementMixin
resolve_device()
TensorMasks
TensorMasks.__init__()
TensorMasks.__setitem__()
TensorMasks.reset_cache()
TensorMasks.__call__()
TensorDict
TensorDict.__init__()
TensorDict.keys()
TensorDict.values()
TensorDict.items()
ModuleReference
ModuleReference._wrapped_module
ModuleReference.__init__()
ModuleReference.module
ModuleReference.__getattr__()
ModuleReference.__call__()
save_map()
sanitize_pdb_dataframe()
parse_phenix_selection()
create_selection_mask()
DebugMixin
DebugMixin.print_debug_summary()
DebugMixin.debug_on_error()
print_module_summary()
StatEntry
StatEntry.value
StatEntry.verbosity
StatEntry.__json__()
StatEntry.__init__()
stat()
filter_stats()
flatten_stats()
format_stats_table()
HyperparameterMixin
HyperparameterMixin.__init__()
HyperparameterMixin.register_hyperparameter()
HyperparameterMixin.get_hyperparameter()
HyperparameterMixin.set_hyperparameter()
HyperparameterMixin.hyperparameters()
HyperparameterMixin.named_hyperparameters()
HyperparameterMixin.hyperparameter_state_dict()
HyperparameterMixin.load_hyperparameter_state_dict()
HyperparameterMixin.hyperparameter_dict()
HyperparameterMixin.print_hyperparameters()
convert_to_serializable()
gradnorm()
validate_loss()
NonFiniteLossError
reset_diagnostic_budget()
collect_loss_leaves()
gather_with_index_add()
create_hyperparameter_property()
register_timing()
state_dict_to_json_serializable()
dict_to_state_dict()
json_to_state_dicts_separate()
disable_grad_outside_optimizer()
Development
Period Table Data