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_constraint() (sponge.control.Integrator method) add_residue() (sponge.system.Molecule method) all_none() (in module sponge.function) all_not_none() (in module sponge.function) all_periodic (sponge.colvar.Colvar property) AllAtoms (class in sponge.colvar) analyse() (sponge.core.Sponge method) AnalysisCell (class in sponge.core) AndersenBarostat (class in sponge.control)

Angle (class in sponge.colvar) any_none() (in module sponge.function) any_not_none() (in module sponge.function) any_periodic (sponge.colvar.Colvar property) append() (sponge.system.Molecule method) apply_to_point() (in module mindsponge.common) apply_transform() (sponge.control.SETTLE method) atom37_to_frames() (in module mindsponge.data_transform) atom37_to_torsion_angles() (in module mindsponge.data_transform) Atoms (class in sponge.colvar) AtomsBase (class in sponge.colvar) Attention (class in mindsponge.cell) avogadro (sponge.function.Units property)

B

backbone() (in module mindsponge.metrics) BalancedMSE (class in mindsponge.metrics) (class in sponge.metrics) Barostat (class in sponge.control) BatchedAtoms (class in sponge.colvar) BatchedPosition (class in sponge.colvar) BerendsenBarostat (class in sponge.control) BerendsenThermostat (class in sponge.control) 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) (class in sponge.metrics)

boltzmann (sponge.control.Controller property) (sponge.function.Units property) (sponge.optimizer.Updater property) boltzmann_def (sponge.function.Units property) bonds_in() (in module sponge.function) broadcast_multiplicity() (sponge.system.Residue method) Brownian (class in sponge.control) 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.Sponge method) (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.Sponge method) (sponge.core.WithEnergyCell method) calc_energy() (sponge.core.Sponge method) calc_image() (sponge.system.Molecule method) calc_max_neighbours() (sponge.partition.DistanceNeighbours static method) calc_potential() (sponge.core.Sponge 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) calculate() (sponge.partition.NeighbourList method) Center (class in sponge.colvar) change_optimizer() (sponge.core.Sponge method) change_potential() (sponge.core.Sponge method) change_unit() (sponge.function.Energy method) (sponge.function.Length method) check_broadcast() (in module sponge.function)

check_neighbour_list() (sponge.partition.DistanceNeighbours method) (sponge.partition.GridNeighbours method) check_system() (sponge.potential.EnergyCell static method) Colvar (class in sponge.colvar) ColvarCombine (class in sponge.colvar) ColvarGroup (class in sponge.colvar) CombineCV (class in sponge.colvar) compressibility (sponge.control.Barostat property) compute_renamed_ground_truth() (in module mindsponge.metrics) concat_first_dim() (in module sponge.function) concat_last_dim() (in module sponge.function) concat_penulti() (in module sponge.function) ConstantValue (class in sponge.colvar) Constraint (class in sponge.control) 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() (in module sponge.function) (sponge.colvar.AtomsBase method) (sponge.system.Molecule method) copy() (sponge.system.Molecule method) CosCV (class in sponge.colvar) coulomb (sponge.function.Units property) coulomb_interaction() (in module sponge.function) create_time (sponge.core.Sponge property) cutoff (sponge.core.WithEnergyCell property) (sponge.core.WithForceCell property)

D

decay_and_scale_grad() (sponge.optimizer.Updater method) Distance (class in sponge.colvar)

DistanceNeighbours (class in sponge.partition) dtype (sponge.colvar.Colvar property) DynamicUpdater (class in sponge.optimizer)

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.Sponge 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.core.WithForceCell 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) FullConnectNeighbours (class in sponge.partition) FunctionCV (class in sponge.colvar)

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_arguments() (in module sponge.function) get_atoms() (in module sponge.colvar) (sponge.system.Molecule method) get_barostat() (in module sponge.control) get_bias() (sponge.core.Sponge method) get_biases() (sponge.core.Sponge method) get_boltzmann() (sponge.function.Units method) get_colvar() (in module sponge.colvar) get_com() (sponge.control.Controller method) get_com_velocity() (sponge.control.Controller method) get_constraint() (in module sponge.control) get_coordinate() (sponge.system.Molecule method) get_coulomb() (sponge.function.Units method) get_dt() (sponge.optimizer.Updater method) get_energies() (sponge.core.Sponge method) get_energy() (in module sponge.function) 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_initializer() (in module sponge.function) get_integer() (in module sponge.function) get_integrator() (in module sponge.control) get_inverse() (sponge.control.SETTLE method) get_kinetics() (sponge.control.Controller method) (sponge.optimizer.Updater method) get_length() (in module sponge.function) get_length_ref() (in module sponge.function) get_length_unit() (in module sponge.function) get_length_unit_name() (in module sponge.function) get_mass_center() (sponge.control.SETTLE method)

get_ms_array() (in module sponge.function) get_name() (sponge.control.Integrator class method) get_ndarray() (in module sponge.function) get_neighbour_list() (sponge.core.WithEnergyCell method) (sponge.core.WithForceCell method) (sponge.partition.NeighbourList method) get_neighbours_from_grids() (sponge.partition.GridNeighbours 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_ref_kinetics() (sponge.control.Thermostat method) get_structural_violations() (in module mindsponge.metrics) get_temperature() (sponge.control.Controller method) (sponge.optimizer.Updater method) get_tensor() (in module sponge.function) get_thermostat() (in module sponge.control) get_transform() (sponge.control.SETTLE method) get_unit() (sponge.colvar.AtomsBase method) (sponge.colvar.Colvar method) (sponge.colvar.Distance method) (sponge.metrics.MetricCV method) get_vector_transform() (sponge.control.SETTLE method) get_vel_force_update() (sponge.control.SETTLE 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) GridNeighbours (class in sponge.partition) Group (class in sponge.colvar) group_hamiltonian_product() (sponge.control.SETTLE method)

H

hamiltonian_product() (in module sponge.function) (sponge.control.SETTLE method)

heavy_atom_mask (sponge.system.Molecule property)

I

identity() (in module sponge.function) IndexColvar (class in sponge.partition) IndexDistances (class in sponge.partition) IndexVectors (class in sponge.partition) initial_affine() (in module mindsponge.common)

Integrator (class in sponge.control) InvariantPointAttention (class in mindsponge.cell) invert_point() (in module mindsponge.common) invert_rigids() (in module mindsponge.common) invert_rots() (in module mindsponge.common)

K

keepdims_mean() (in module sponge.function) keepdims_prod() (in module sponge.function)

keepdims_sum() (in module sponge.function) kinetic_ref (sponge.function.Units property)

L

Langevin (class in sponge.control) LeapFrog (class in sponge.control) 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.core.WithForceCell property) (sponge.function.Units property) (sponge.potential.EnergyCell property) (sponge.system.Molecule property)

length_unit_name (sponge.function.Units property) lennard_jones_potential() (in module sponge.function) lennard_jones_potential2() (in module sponge.function) Lincs (class in sponge.control) local_distance_difference_test() (in module mindsponge.metrics)

M

make_atom14_positions() (in module mindsponge.common) make_transform_from_reference() (in module mindsponge.common) Metric (class in sponge.metrics) MetricCV (class in sponge.metrics) 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) (class in sponge.metrics)

N

name (sponge.colvar.Colvar property) (sponge.potential.EnergyCell property) (sponge.system.Residue property) ndim (sponge.colvar.AtomsBase property) (sponge.colvar.Colvar property) (sponge.colvar.Vector property) (sponge.system.Molecule property) neighbour_list_pace (sponge.core.RunOneStepCell property) (sponge.core.WithEnergyCell property) (sponge.core.WithForceCell property)

NeighbourList (class in sponge.partition) next_step() (sponge.optimizer.Updater method) num_biases (sponge.core.RunOneStepCell property) (sponge.core.Sponge property) (sponge.core.WithEnergyCell property) num_energies (sponge.core.RunOneStepCell property) (sponge.core.Sponge property) (sponge.core.WithEnergyCell property) (sponge.potential.PotentialCell property)

O

OuterProductMean (class in mindsponge.cell)

P

pace (sponge.partition.NeighbourList property) pbc_box_reshape() (in module sponge.function) pbc_image() (in module sponge.function) periodic (sponge.colvar.Colvar property) periodic_difference() (in module sponge.function) periodic_variable() (in module sponge.function) Position (class in sponge.colvar) PotentialCell (class in sponge.potential)

pre_compose() (in module mindsponge.common) press_unit_scale (sponge.optimizer.Updater property) pressure (sponge.control.Barostat property) pressure_ref (sponge.function.Units property) pressure_scale() (sponge.control.Barostat method) print_info() (sponge.partition.DistanceNeighbours method) (sponge.partition.GridNeighbours method) (sponge.partition.NeighbourList method)

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_inverse() (in module sponge.function) quaternion_multiply() (in module sponge.function) (sponge.control.SETTLE method) quaternion_to_tensor() (in module mindsponge.common)

R

recompile() (sponge.core.Sponge method) reconstruct_pressure() (sponge.control.Barostat method) reconstruct_temperature() (sponge.control.Thermostat method) reduce_all() (in module sponge.function) reduce_any() (in module sponge.function) reduce_prod() (in module sponge.function) reduplicate() (sponge.system.Molecule method) ref (sponge.function.Energy property) (sponge.function.Length property) ref_kinetics (sponge.control.Thermostat property) ref_press (sponge.optimizer.UpdaterMD property) ref_temp (sponge.optimizer.UpdaterMD property) repeat_box() (sponge.system.Molecule method) reshape() (sponge.colvar.Atoms method) (sponge.colvar.AtomsBase method) (sponge.colvar.Colvar method) (sponge.colvar.Position 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) run() (sponge.core.Sponge method) RunOneStepCell (class in sponge.core)

S

set_atom_charge() (sponge.system.Molecule method) set_barostat() (sponge.control.Brownian method) (sponge.control.Integrator method) (sponge.optimizer.UpdaterMD method) set_bond_length() (sponge.system.Molecule method) set_constraint() (sponge.control.Brownian method) (sponge.control.Integrator method) (sponge.optimizer.UpdaterMD method) set_coordianate() (sponge.system.Molecule method) set_cutoff() (sponge.potential.EnergyCell method) set_degrees_of_freedom() (sponge.control.Controller method) (sponge.control.Integrator method) (sponge.control.Thermostat method) (sponge.optimizer.Updater method) set_dimension() (sponge.colvar.AtomsBase method) set_energy_unit() (sponge.function.Units method) set_exclude_index() (sponge.partition.DistanceNeighbours method) (sponge.partition.GridNeighbours method) (sponge.partition.NeighbourList method) (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_mass() (sponge.colvar.Center method) set_name() (sponge.colvar.Colvar method) (sponge.system.Residue method) set_num_neighbours() (sponge.partition.DistanceNeighbours method) set_pbc() (sponge.colvar.Colvar method) (sponge.colvar.ColvarGroup method) (sponge.colvar.CombineCV method) (sponge.colvar.FunctionCV method) (sponge.colvar.TransformCV method) (sponge.function.GetVector method) (sponge.partition.IndexColvar 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.core.WithForceCell method) (sponge.system.Molecule method)

set_pressure() (sponge.control.Barostat method) (sponge.optimizer.UpdaterMD method) set_start_index() (sponge.system.Residue method) set_step() (sponge.optimizer.Updater method) set_steps() (sponge.core.RunOneStepCell method) set_temperature() (sponge.control.Thermostat method) (sponge.function.VelocityGenerator method) (sponge.optimizer.UpdaterMD method) set_thermostat() (sponge.control.Brownian method) (sponge.control.Integrator method) (sponge.optimizer.UpdaterMD method) set_time_step() (sponge.control.BerendsenBarostat method) (sponge.control.BerendsenThermostat method) (sponge.control.Brownian method) (sponge.control.Controller method) (sponge.control.Integrator method) (sponge.control.Langevin method) set_units() (sponge.function.Units method) (sponge.potential.EnergyCell method) set_velocity_half() (sponge.control.VelocityVerlet method) SETTLE (class in sponge.control) shape (sponge.colvar.AtomsBase property) (sponge.colvar.Colvar property) (sponge.colvar.Vector property) (sponge.system.Molecule property) sidechain() (in module mindsponge.metrics) SimulationCell (class in sponge.core) SinCV (class in sponge.colvar) space_parameters() (sponge.system.Molecule method) Sponge (class in sponge.core) squeeze_first_dim() (in module sponge.function) squeeze_last_dim() (in module sponge.function) squeeze_penulti() (in module sponge.function) stack_first_dim() (in module sponge.function) stack_last_dim() (in module sponge.function) stack_penulti() (in module sponge.function) SteepestDescent (class in sponge.optimizer) supervised_chi() (in module mindsponge.metrics)

T

temperature (sponge.control.Thermostat property) Thermostat (class in sponge.control) Torsion (class in sponge.colvar) trainable_params() (sponge.system.Molecule method)

TransformCV (class in sponge.colvar) 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() (sponge.metrics.Metric method) (sponge.metrics.MetricCV method) (sponge.partition.NeighbourList method) update_bias() (sponge.core.RunOneStepCell method) (sponge.core.Sponge 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) (sponge.core.Sponge method) (sponge.core.WithForceCell method)

update_neighbour_list() (sponge.core.RunOneStepCell method) (sponge.core.Sponge method) (sponge.core.WithEnergyCell method) (sponge.core.WithForceCell 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.Sponge method) (sponge.core.WithEnergyCell method) Updater (class in sponge.optimizer) UpdaterMD (class in sponge.optimizer) use_pbc (sponge.colvar.Colvar property) (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 (class in sponge.colvar) vector_in_pbc() (in module sponge.function) (sponge.colvar.Colvar class method) (sponge.partition.IndexColvar method) velocity_scale() (sponge.control.Thermostat method) velocity_unit (sponge.function.Units property) velocity_unit_name (sponge.function.Units property) VelocityGenerator (class in sponge.function) VelocityVerlet (class in sponge.control) Volume (class in sponge.colvar) volume_unit (sponge.function.Units property) volume_unit_name (sponge.function.Units property)

W

WithEnergyCell (class in sponge.core)

WithForceCell (class in sponge.core) within_residue_violations() (in module mindsponge.metrics)