Python Module Index

t


	t
	`torchref`
	`torchref.base`
	`torchref.base.alignment`
	`torchref.base.alignment.normalization`
	`torchref.base.alignment.rotation`
	`torchref.base.alignment.scoring`
	`torchref.base.alignment.superposition`
	`torchref.base.CCTBX_related`
	`torchref.base.chain_closure`
	`torchref.base.chain_closure.backbone_utils`
	`torchref.base.chain_closure.closure`
	`torchref.base.coordinates`
	`torchref.base.coordinates.periodic_boundary`
	`torchref.base.coordinates.transforms_numpy`
	`torchref.base.coordinates.transforms_torch`
	`torchref.base.direct_summation`
	`torchref.base.direct_summation.anisotropic`
	`torchref.base.direct_summation.corrections`
	`torchref.base.direct_summation.isotropic`
	`torchref.base.electron_density`
	`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`
	`torchref.base.fourier.fft`
	`torchref.base.fourier.grid`
	`torchref.base.french_wilson`
	`torchref.base.get_scattering_factor_torch`
	`torchref.base.kernels`
	`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`
	`torchref.base.metrics.loss`
	`torchref.base.metrics.rfactor`
	`torchref.base.reciprocal`
	`torchref.base.reciprocal.basis`
	`torchref.base.reciprocal.grid_operations`
	`torchref.base.reciprocal.hkl`
	`torchref.base.reciprocal.interpolation`
	`torchref.base.reciprocal.symmetry`
	`torchref.base.scattering`
	`torchref.base.scattering.anomalous_table`
	`torchref.base.scattering.itc92`
	`torchref.base.scattering.scattering_table`
	`torchref.base.targets`
	`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`
	`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`
	`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`
	`torchref.io.cif`
	`torchref.io.cif_readers`
	`torchref.io.data_router`
	`torchref.io.datasets`
	`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`
	`torchref.kinetic.kinetics`
	`torchref.kinetic.occupancies`
	`torchref.kinetic.refinement`
	`torchref.kinetic.targets`
	`torchref.maps`
	`torchref.maps.difference_map`
	`torchref.maps.map`
	`torchref.model`
	`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`
	`torchref.refinement.base_refinement`
	`torchref.refinement.lbfgs_refinement`
	`torchref.refinement.logger`
	`torchref.refinement.loss_state`
	`torchref.refinement.optimizers`
	`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`
	`torchref.refinement.targets.adp`
	`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`
	`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`
	`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`
	`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`
	`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`
	`torchref.scaling.collection_scaler`
	`torchref.scaling.scaler`
	`torchref.scaling.scaler_base`
	`torchref.scaling.solvent`
	`torchref.scripts`
	`torchref.scripts.generate_scattering_table`
	`torchref.symmetry`
	`torchref.symmetry.cell`
	`torchref.symmetry.grid_utils`
	`torchref.symmetry.map_symmetry`
	`torchref.symmetry.map_symmetry_interpolation`
	`torchref.symmetry.reciprocal_symmetry`
	`torchref.symmetry.spacegroup`
	`torchref.symmetry.symmetry`
	`torchref.utils`
	`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.pse`
	`torchref.utils.serialization`
	`torchref.utils.stats`
	`torchref.utils.timing`
	`torchref.utils.utils`