Index

A

add_file() (rid.task.task.Task method)

add_property() (rid.task.task.Task method) AdjustTrustLevel (class in rid.op.adjust_trust_level)

B

build() (rid.task.builder.ConstrainedMDTaskBuilder method) (rid.task.builder.EnhcMDTaskBuilder method) (rid.task.builder.RestrainedMDTaskBuilder method) (rid.task.builder.TaskBuilder method) build_gmx() (rid.task.builder.ConstrainedMDTaskBuilder method) (rid.task.builder.EnhcMDTaskBuilder method) (rid.task.builder.RestrainedMDTaskBuilder method) build_gmx_constraint_dict() (in module rid.task.builder) build_gmx_dict() (in module rid.task.builder)

build_lmp() (rid.task.builder.ConstrainedMDTaskBuilder method) (rid.task.builder.EnhcMDTaskBuilder method) (rid.task.builder.RestrainedMDTaskBuilder method) build_lmp_dict() (in module rid.task.builder) build_plumed() (rid.task.builder.ConstrainedMDTaskBuilder method) (rid.task.builder.EnhcMDTaskBuilder method) (rid.task.builder.RestrainedMDTaskBuilder method) build_plumed_constraint_dict() (in module rid.task.builder) build_plumed_dict() (in module rid.task.builder) build_plumed_restraint_dict() (in module rid.task.builder)

C

check_basic_argument() (in module rid.common.gromacs.mdp) check_deepfe_input() (in module rid.common.plumed.check_plumed) check_port_status() (in module rid.entrypoint.server) CheckLabelInputs (class in rid.op.prep_label)

chooseClusterCenter() (in module rid.select.cluster) Cluster (class in rid.select.cluster) CollectData (class in rid.op.prep_data) ConstrainedMDTaskBuilder (class in rid.task.builder) cv_dist() (in module rid.select.cluster)

D

DataGenerator (class in rid.superop.data) distance() (in module rid.common.mol)

download_rid() (in module rid.entrypoint.download) dump_json() (in module rid.utils.files)

E

EnhcMDTaskBuilder (class in rid.task.builder) execute() (rid.op.adjust_trust_level.AdjustTrustLevel method) (rid.op.label_stats.LabelStats method) (rid.op.mcmc_plot.MCMCPlot method) (rid.op.prep_data.CollectData method) (rid.op.prep_data.MergeData method) (rid.op.prep_exploration.PrepExplore method) (rid.op.prep_label.CheckLabelInputs method) (rid.op.prep_label.PrepLabel method) (rid.op.prep_rid.PrepRiD method) (rid.op.prep_select.PrepSelect method) (rid.op.recorder.Recorder method)

Exploration (class in rid.superop.exploration)

F

files (rid.task.task.Task property)

final_dump() (in module rid.common.lammps.command) forward_ports() (in module rid.entrypoint.server)

G

generate_coords() (in module rid.common.gromacs.trjconv) generate_forces() (in module rid.common.gromacs.trjconv) get_cluster_selection() (rid.select.cluster.Cluster method) get_cv_dim() (rid.task.builder.EnhcMDTaskBuilder method) get_cv_name() (in module rid.common.plumed.make_plumed) get_dihedral_from_resid() (in module rid.common.mol) get_dihedral_info() (in module rid.common.mol) get_distance_from_atomid() (in module rid.common.mol) get_grompp_cmd() (in module rid.common.gromacs.command) (in module rid.common.sampler.command) get_input_sign() (rid.op.adjust_trust_level.AdjustTrustLevel class method) (rid.op.label_stats.LabelStats class method) (rid.op.mcmc_plot.MCMCPlot class method) (rid.op.prep_data.CollectData class method) (rid.op.prep_data.MergeData class method) (rid.op.prep_exploration.PrepExplore class method) (rid.op.prep_label.CheckLabelInputs class method) (rid.op.prep_label.PrepLabel class method) (rid.op.prep_rid.PrepRiD class method) (rid.op.prep_select.PrepSelect class method) (rid.op.recorder.Recorder class method)

get_mdrun_cmd() (in module rid.common.gromacs.command) (in module rid.common.sampler.command) get_output_sign() (rid.op.adjust_trust_level.AdjustTrustLevel class method) (rid.op.label_stats.LabelStats class method) (rid.op.mcmc_plot.MCMCPlot class method) (rid.op.prep_data.CollectData class method) (rid.op.prep_data.MergeData class method) (rid.op.prep_exploration.PrepExplore class method) (rid.op.prep_label.CheckLabelInputs class method) (rid.op.prep_label.PrepLabel class method) (rid.op.prep_rid.PrepRiD class method) (rid.op.prep_select.PrepSelect class method) (rid.op.recorder.Recorder class method) get_task() (rid.task.builder.ConstrainedMDTaskBuilder method) (rid.task.builder.EnhcMDTaskBuilder method) (rid.task.builder.RestrainedMDTaskBuilder method)

I

init_executor() (in module rid.utils.set_config) init_keys (rid.flow.loop.ReinforcedDynamics property) InitBlock (class in rid.superop.blocks) input_artifacts (rid.flow.loop.ReinforcedDynamics property) (rid.flow.loop.ReinforcedDynamicsLoop property) (rid.superop.blocks.InitBlock property) (rid.superop.blocks.IterBlock property) (rid.superop.data.DataGenerator property) (rid.superop.exploration.Exploration property) (rid.superop.label.Label property) (rid.superop.mcmc.MCMC property) (rid.superop.selector.Selector property)

input_parameters (rid.flow.loop.ReinforcedDynamics property) (rid.flow.loop.ReinforcedDynamicsLoop property) (rid.superop.blocks.InitBlock property) (rid.superop.blocks.IterBlock property) (rid.superop.data.DataGenerator property) (rid.superop.exploration.Exploration property) (rid.superop.label.Label property) (rid.superop.mcmc.MCMC property) (rid.superop.selector.Selector property) IterBlock (class in rid.superop.blocks)

K

keys (rid.flow.loop.ReinforcedDynamicsLoop property) (rid.superop.blocks.InitBlock property) (rid.superop.blocks.IterBlock property) (rid.superop.data.DataGenerator property) (rid.superop.exploration.Exploration property) (rid.superop.label.Label property) (rid.superop.mcmc.MCMC property) (rid.superop.selector.Selector property)

L

Label (class in rid.superop.label) LabelStats (class in rid.op.label_stats) list_to_string() (in module rid.utils.format)

load_json() (in module rid.utils.files) load_pkl() (in module rid.utils.files) load_txt() (in module rid.utils.files) loop_keys (rid.flow.loop.ReinforcedDynamics property)

M

make_constraint_plumed() (in module rid.common.plumed.make_plumed) make_deepfe_bias() (in module rid.common.plumed.make_plumed) make_deepfe_plumed() (in module rid.common.plumed.make_plumed) make_distance() (in module rid.common.plumed.make_plumed) make_distance_list() (in module rid.common.plumed.make_plumed) make_distance_list_from_file() (in module rid.common.plumed.make_plumed) make_distance_name() (in module rid.common.plumed.make_plumed) make_md_mdp_from_config() (in module rid.common.gromacs.mdp) make_md_mdp_string() (in module rid.common.gromacs.mdp) make_mdp_from_json() (in module rid.common.gromacs.mdp) make_print() (in module rid.common.plumed.make_plumed) make_print_bias() (in module rid.common.plumed.make_plumed) make_restraint() (in module rid.common.plumed.make_plumed) make_restraint_list() (in module rid.common.plumed.make_plumed) make_restraint_plumed() (in module rid.common.plumed.make_plumed) make_threshold() (rid.select.cluster.Cluster method) make_torsion() (in module rid.common.plumed.make_plumed) make_torsion_list() (in module rid.common.plumed.make_plumed) make_torsion_list_from_file() (in module rid.common.plumed.make_plumed) make_torsion_name() (in module rid.common.plumed.make_plumed) make_wall_list() (in module rid.common.plumed.make_plumed) make_wholemolecules() (in module rid.common.plumed.make_plumed) MCMC (class in rid.superop.mcmc) MCMCPlot (class in rid.op.mcmc_plot) MergeData (class in rid.op.prep_data) mk_cluster() (in module rid.select.cluster) mk_dist() (in module rid.select.cluster) modify_define() (in module rid.common.gromacs.mdp) modify_output() (in module rid.common.gromacs.mdp) module rid rid.common rid.common.gromacs rid.common.gromacs.command rid.common.gromacs.gmx_constant rid.common.gromacs.mdp rid.common.gromacs.trjconv rid.common.lammps rid.common.lammps.command rid.common.lammps.lmp_constant rid.common.mol rid.common.mol_dpdata rid.common.plumed rid.common.plumed.check_plumed rid.common.plumed.make_plumed rid.common.plumed.plumed_constant rid.common.sampler rid.common.sampler.command rid.common.tensorflow rid.constants rid.entrypoint rid.entrypoint.cli rid.entrypoint.download rid.entrypoint.info rid.entrypoint.server rid.flow rid.flow.loop rid.main rid.mcmc rid.nn rid.op rid.op.adjust_trust_level rid.op.label_stats rid.op.mcmc_plot rid.op.prep_data rid.op.prep_exploration rid.op.prep_label rid.op.prep_rid rid.op.prep_select rid.op.recorder rid.select rid.select.cluster rid.superop rid.superop.blocks rid.superop.data rid.superop.exploration rid.superop.label rid.superop.mcmc rid.superop.selector rid.task rid.task.builder rid.task.task rid.tools rid.utils rid.utils.command rid.utils.files rid.utils.format rid.utils.path rid.utils.set_config

N

normalize_resources() (in module rid.utils.set_config)

O

output_artifacts (rid.flow.loop.ReinforcedDynamics property) (rid.flow.loop.ReinforcedDynamicsLoop property) (rid.superop.blocks.InitBlock property) (rid.superop.blocks.IterBlock property) (rid.superop.data.DataGenerator property) (rid.superop.exploration.Exploration property) (rid.superop.label.Label property) (rid.superop.mcmc.MCMC property) (rid.superop.selector.Selector property)

output_parameters (rid.flow.loop.ReinforcedDynamics property) (rid.flow.loop.ReinforcedDynamicsLoop property) (rid.superop.blocks.InitBlock property) (rid.superop.blocks.IterBlock property) (rid.superop.data.DataGenerator property) (rid.superop.exploration.Exploration property) (rid.superop.label.Label property) (rid.superop.mcmc.MCMC property) (rid.superop.selector.Selector property)

P

prep_confs() (in module rid.op.prep_rid) PrepExplore (class in rid.op.prep_exploration)

PrepLabel (class in rid.op.prep_label) PrepRiD (class in rid.op.prep_rid) PrepSelect (class in rid.op.prep_select)

R

read_binary() (in module rid.utils.files) read_txt() (in module rid.utils.files) Recorder (class in rid.op.recorder) ReinforcedDynamics (class in rid.flow.loop) ReinforcedDynamicsLoop (class in rid.flow.loop) RestrainedMDTaskBuilder (class in rid.task.builder) rid module rid.common module rid.common.gromacs module rid.common.gromacs.command module rid.common.gromacs.gmx_constant module rid.common.gromacs.mdp module rid.common.gromacs.trjconv module rid.common.lammps module rid.common.lammps.command module rid.common.lammps.lmp_constant module rid.common.mol module rid.common.mol_dpdata module rid.common.plumed module rid.common.plumed.check_plumed module rid.common.plumed.make_plumed module rid.common.plumed.plumed_constant module rid.common.sampler module rid.common.sampler.command module rid.common.tensorflow module rid.constants module rid.entrypoint module rid.entrypoint.cli module rid.entrypoint.download module rid.entrypoint.info module rid.entrypoint.server module rid.flow module rid.flow.loop module rid.main module rid.mcmc module

rid.nn module rid.op module rid.op.adjust_trust_level module rid.op.label_stats module rid.op.mcmc_plot module rid.op.prep_data module rid.op.prep_exploration module rid.op.prep_label module rid.op.prep_rid module rid.op.prep_select module rid.op.recorder module rid.select module rid.select.cluster module rid.superop module rid.superop.blocks module rid.superop.data module rid.superop.exploration module rid.superop.label module rid.superop.mcmc module rid.superop.selector module rid.task module rid.task.builder module rid.task.task module rid.tools module rid.utils module rid.utils.command module rid.utils.files module rid.utils.format module rid.utils.path module rid.utils.set_config module rid_ls() (in module rid.entrypoint.cli) rid_rm() (in module rid.entrypoint.cli) run_command() (in module rid.utils.command)

S

save_pkl() (in module rid.utils.files) save_txt() (in module rid.utils.files) sel_from_cluster() (in module rid.select.cluster) Selector (class in rid.superop.selector) set_directory() (in module rid.utils.path)

slice_dump() (in module rid.common.mol_dpdata) slice_dump_dpdata() (in module rid.common.mol_dpdata) slice_trjconv() (in module rid.common.gromacs.trjconv) slice_xtc() (in module rid.common.mol) slice_xtc_mdtraj() (in module rid.common.mol)

T

Task (class in rid.task.task)

TaskBuilder (class in rid.task.builder)

U

user_plumed_def() (in module rid.common.plumed.make_plumed)

W

write_binary() (in module rid.utils.files)

write_txt() (in module rid.utils.files)