Index

A

abs_size (sponge.function.Energy property) (sponge.function.Length property) acceleration_ref (sponge.function.Units property) add_atom() (sponge.system.Residue method) add_residue() (sponge.system.Molecule method)

append() (sponge.system.Molecule method) apply_to_point() (in module mindsponge.common) atom37_to_frames() (in module mindsponge.data_transform) atom37_to_torsion_angles() (in module mindsponge.data_transform) Attention (class in mindsponge.cell) avogadro (sponge.function.Units property)

B

backbone() (in module mindsponge.metrics) BalancedMSE (class in mindsponge.metrics) between_residue_bond() (in module mindsponge.metrics) between_residue_clash() (in module mindsponge.metrics) bias (sponge.core.RunOneStepCell property) (sponge.core.WithEnergyCell property) bias_function (sponge.core.RunOneStepCell property) bias_names (sponge.core.RunOneStepCell property) (sponge.core.WithEnergyCell property) bias_pace() (sponge.core.WithEnergyCell method) biases (sponge.core.RunOneStepCell property) (sponge.core.WithEnergyCell property) BinaryFocal (class in mindsponge.metrics) boltzmann (sponge.control.Controller property) (sponge.function.Units property) (sponge.optimizer.Updater property)

boltzmann_def (sponge.function.Units property) broadcast_multiplicity() (sponge.system.Residue method) build_angle() (sponge.system.Molecule method) build_atom_charge() (sponge.system.Molecule method) (sponge.system.Residue method) build_atom_mass() (sponge.system.Residue method) build_atom_type() (sponge.system.Molecule method) (sponge.system.Residue method) build_atomic_number() (sponge.system.Residue method) build_bond() (sponge.system.Residue method) build_dihedrals() (sponge.system.Molecule method) build_h_bonds() (sponge.system.Molecule method) build_improper() (sponge.system.Molecule method) build_settle() (sponge.system.Residue method) build_space() (sponge.system.Molecule method) build_system() (sponge.system.Molecule method)

C

calc_angle() (in module sponge.function) calc_angle_by_vectors() (in module sponge.function) calc_angle_nopbc() (in module sponge.function) calc_angle_pbc() (in module sponge.function) calc_biases() (sponge.core.WithEnergyCell method) calc_colvar() (sponge.system.Molecule method) calc_distance() (in module sponge.function) calc_distance_nopbc() (in module sponge.function) calc_distance_pbc() (in module sponge.function) calc_energies() (sponge.core.WithEnergyCell method) calc_image() (sponge.system.Molecule method) calc_torsion() (in module sponge.function) calc_torsion_by_vectors() (in module sponge.function) calc_torsion_nopbc() (in module sponge.function) calc_torsion_pbc() (in module sponge.function) calc_vector() (in module sponge.function) calc_vector_default() (sponge.function.GetVector method) calc_vector_nopbc() (in module sponge.function) (sponge.function.GetVector method)

calc_vector_pbc() (in module sponge.function) (sponge.function.GetVector method) change_unit() (sponge.function.Energy method) (sponge.function.Length method) check_system() (sponge.potential.EnergyCell static method) compute_renamed_ground_truth() (in module mindsponge.metrics) Controller (class in sponge.control) convert_energy_from() (sponge.function.Units method) (sponge.potential.EnergyCell method) convert_energy_to() (sponge.function.Units method) (sponge.potential.EnergyCell method) convert_length_from() (sponge.function.Units method) (sponge.system.Molecule method) convert_length_to() (sponge.function.Units method) (sponge.system.Molecule method) coordinate_in_pbc() (sponge.system.Molecule method) copy() (sponge.system.Molecule method) coulomb (sponge.function.Units property) cutoff (sponge.core.WithEnergyCell property)

D

decay_and_scale_grad() (sponge.optimizer.Updater method)

E

energies (sponge.core.RunOneStepCell property) (sponge.core.WithEnergyCell property) Energy (class in sponge.function) energy() (sponge.function.Units method) energy_convert() (in module sponge.function) energy_cutoff (sponge.core.RunOneStepCell property) energy_names (sponge.core.RunOneStepCell property) (sponge.core.WithEnergyCell property) (sponge.potential.PotentialCell property)

energy_ref (sponge.function.Units property) energy_unit (sponge.core.RunOneStepCell property) (sponge.core.WithEnergyCell property) (sponge.function.Units property) (sponge.potential.EnergyCell property) energy_unit_name (sponge.function.Units property) EnergyCell (class in sponge.potential) exclude_index (sponge.potential.PotentialCell property)

F

fill_water() (sponge.system.Molecule method) find_optimal_renaming() (in module mindsponge.common) force_cutoff (sponge.core.RunOneStepCell property) force_ref (sponge.function.Units property)

force_unit (sponge.function.Units property) force_unit_name (sponge.function.Units property) frame_aligned_point_error() (in module mindsponge.metrics) frame_aligned_point_error_map() (in module mindsponge.metrics)

G

gas_constant (sponge.function.Units property) gather_value() (in module sponge.function) gather_vector() (in module sponge.function) get_aligned_seq() (in module mindsponge.common) get_atoms() (sponge.system.Molecule method) get_boltzmann() (sponge.function.Units method) get_com() (sponge.control.Controller method) get_com_velocity() (sponge.control.Controller method) get_coordinate() (sponge.system.Molecule method) get_coulomb() (sponge.function.Units method) get_dt() (sponge.optimizer.Updater method) get_energy_ref() (in module sponge.function) get_energy_unit() (in module sponge.function) get_energy_unit_name() (in module sponge.function) get_fasta_info() (in module mindsponge.common) get_integer() (in module sponge.function) get_kinetics() (sponge.control.Controller method) (sponge.optimizer.Updater method) get_length_ref() (in module sponge.function)

get_length_unit() (in module sponge.function) get_length_unit_name() (in module sponge.function) get_ndarray() (in module sponge.function) get_neighbour_list() (sponge.core.WithEnergyCell method) get_pbc_box() (sponge.system.Molecule method) get_pdb_info() (in module mindsponge.common) get_pressure() (sponge.control.Controller method) (sponge.optimizer.Updater method) get_structural_violations() (in module mindsponge.metrics) get_temperature() (sponge.control.Controller method) (sponge.optimizer.Updater method) get_velocity() (sponge.optimizer.Updater method) get_volume() (sponge.control.Controller method) (sponge.system.Molecule method) GetDistance (class in sponge.function) GetDistanceShift (class in sponge.function) GetShiftGrad (class in sponge.function) GetVector (class in sponge.function) GlobalAttention (class in mindsponge.cell)

H

heavy_atom_mask (sponge.system.Molecule property)

I

initial_affine() (in module mindsponge.common) InvariantPointAttention (class in mindsponge.cell)

invert_point() (in module mindsponge.common) invert_rigids() (in module mindsponge.common) invert_rots() (in module mindsponge.common)

K

kinetic_ref (sponge.function.Units property)

L

Length (class in sponge.function) length() (sponge.function.Units method) length_convert() (in module sponge.function) length_ref (sponge.function.Units property) length_unit (sponge.core.RunOneStepCell property) (sponge.core.WithEnergyCell property) (sponge.function.Units property) (sponge.potential.EnergyCell property) (sponge.system.Molecule property)

length_unit_name (sponge.function.Units property) local_distance_difference_test() (in module mindsponge.metrics)

M

make_atom14_positions() (in module mindsponge.common) make_transform_from_reference() (in module mindsponge.common) Molecule (class in sponge.system) move() (sponge.system.Molecule method)

MSAColumnAttention (class in mindsponge.cell) MSAColumnGlobalAttention (class in mindsponge.cell) MSARowAttentionWithPairBias (class in mindsponge.cell) MultiClassFocal (class in mindsponge.metrics)

N

name (sponge.potential.EnergyCell property) (sponge.system.Residue property) ndim (sponge.system.Molecule property) neighbour_list_pace (sponge.core.RunOneStepCell property) (sponge.core.WithEnergyCell property)

next_step() (sponge.optimizer.Updater method) num_biases (sponge.core.RunOneStepCell property) (sponge.core.WithEnergyCell property) num_energies (sponge.core.RunOneStepCell property) (sponge.core.WithEnergyCell property) (sponge.potential.PotentialCell property)

O

OuterProductMean (class in mindsponge.cell)

P

pbc_box_reshape() (in module sponge.function) pbc_image() (in module sponge.function) PotentialCell (class in sponge.potential)

pre_compose() (in module mindsponge.common) press_unit_scale (sponge.optimizer.Updater property) pressure_ref (sponge.function.Units property)

Q

quat_affine() (in module mindsponge.common) quat_multiply_by_vec() (in module mindsponge.common)

quat_to_rot() (in module mindsponge.common) quaternion_from_tensor() (in module mindsponge.common) quaternion_to_tensor() (in module mindsponge.common)

R

reduplicate() (sponge.system.Molecule method) ref (sponge.function.Energy property) (sponge.function.Length property) repeat_box() (sponge.system.Molecule method) Residue (class in sponge.system) residue_bond() (sponge.system.Molecule method) residue_coordinate() (sponge.system.Molecule method) residue_head() (sponge.system.Molecule method) residue_index() (sponge.system.Molecule method) residue_tail() (sponge.system.Molecule method) rigids_from_3_points() (in module mindsponge.common)

rigids_mul_rigids() (in module mindsponge.common) rigids_mul_rots() (in module mindsponge.common) rigids_mul_vecs() (in module mindsponge.common) rots_expand_dims() (in module mindsponge.common) rots_from_tensor() (in module mindsponge.common) rots_from_two_vecs() (in module mindsponge.common) rots_mul_rots() (in module mindsponge.common) rots_mul_vecs() (in module mindsponge.common) rots_scale() (in module mindsponge.common) rots_to_tensor() (in module mindsponge.common) RunOneStepCell (class in sponge.core)

S

set_atom_charge() (sponge.system.Molecule method) set_bond_length() (sponge.system.Molecule method) set_coordianate() (sponge.system.Molecule method) set_cutoff() (sponge.potential.EnergyCell method) set_degrees_of_freedom() (sponge.control.Controller method) (sponge.optimizer.Updater method) set_energy_unit() (sponge.function.Units method) set_exclude_index() (sponge.potential.PotentialCell method) set_global_energy_unit() (in module sponge.function) set_global_length_unit() (in module sponge.function) set_global_units() (in module sponge.function) set_input_unit() (sponge.potential.EnergyCell method) set_length_unit() (sponge.function.Units method) (sponge.system.Molecule method) set_name() (sponge.system.Residue method) set_pbc() (sponge.function.GetVector method) (sponge.potential.EnergyCell method) (sponge.potential.PotentialCell method)

set_pbc_box() (sponge.system.Molecule method) set_pbc_grad() (sponge.core.RunOneStepCell method) (sponge.core.WithEnergyCell method) (sponge.system.Molecule method) set_start_index() (sponge.system.Residue method) set_step() (sponge.optimizer.Updater method) set_steps() (sponge.core.RunOneStepCell method) set_temperature() (sponge.function.VelocityGenerator method) set_time_step() (sponge.control.Controller method) set_units() (sponge.function.Units method) (sponge.potential.EnergyCell method) shape (sponge.system.Molecule property) sidechain() (in module mindsponge.metrics) space_parameters() (sponge.system.Molecule method) supervised_chi() (in module mindsponge.metrics)

T

trainable_params() (sponge.system.Molecule method) Transition (class in mindsponge.cell)

TriangleAttention (class in mindsponge.cell) TriangleMultiplication (class in mindsponge.cell)

U

unit (sponge.function.Energy property) (sponge.function.Length property) unit_name (sponge.function.Energy property) (sponge.function.Length property) Units (class in sponge.function) update_bias() (sponge.core.RunOneStepCell method) (sponge.core.WithEnergyCell method) update_coordinate() (sponge.control.Controller method) (sponge.optimizer.Updater method) (sponge.system.Molecule method) update_image() (sponge.system.Molecule method) update_kinetics() (sponge.optimizer.Updater method) update_modifier() (sponge.core.RunOneStepCell method)

update_neighbour_list() (sponge.core.RunOneStepCell method) (sponge.core.WithEnergyCell method) update_pbc_box() (sponge.control.Controller method) (sponge.optimizer.Updater method) (sponge.system.Molecule method) update_pressure() (sponge.optimizer.Updater method) update_temperature() (sponge.optimizer.Updater method) update_velocity() (sponge.optimizer.Updater method) update_virial() (sponge.optimizer.Updater method) update_wrapper() (sponge.core.RunOneStepCell method) (sponge.core.WithEnergyCell method) Updater (class in sponge.optimizer) use_pbc (sponge.function.GetVector property) (sponge.potential.EnergyCell property)

V

value (sponge.function.Energy property) (sponge.function.Length property) vecs_cross_vecs() (in module mindsponge.common) vecs_dot_vecs() (in module mindsponge.common) vecs_expand_dims() (in module mindsponge.common) vecs_from_tensor() (in module mindsponge.common) vecs_robust_norm() (in module mindsponge.common) vecs_robust_normalize() (in module mindsponge.common)

vecs_scale() (in module mindsponge.common) vecs_sub() (in module mindsponge.common) vecs_to_tensor() (in module mindsponge.common) vector_in_pbc() (in module sponge.function) velocity_unit (sponge.function.Units property) velocity_unit_name (sponge.function.Units property) VelocityGenerator (class in sponge.function) volume_unit (sponge.function.Units property) volume_unit_name (sponge.function.Units property)

W

WithEnergyCell (class in sponge.core)

within_residue_violations() (in module mindsponge.metrics)