deepdrivemd
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__del__() (deepdrivemd.data.stream.aggregator_reader.AdiosReader method)
__init__() (deepdrivemd.data.stream.adios_utils.AdiosStreamStepRW method)
(deepdrivemd.data.stream.aggregator_reader.AdiosReader method)
(deepdrivemd.data.stream.aggregator_reader.Streams method)
(deepdrivemd.data.stream.aggregator_reader.StreamVariable method)
(deepdrivemd.data.stream.OutlierDB.OutlierDB method)
(deepdrivemd.models.aae_stream.utils.CenterOfMassTransform method)
(deepdrivemd.models.aae_stream.utils.PointCloudDatasetInMemory method)
A
adios (deepdrivemd.data.stream.aggregator_reader.AdiosReader attribute)
adios_cfg (deepdrivemd.sim.openmm_stream.config.OpenMMConfig attribute)
adios_xml_agg (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
(deepdrivemd.aggregation.stream.config.StreamAggregation attribute)
(deepdrivemd.config.StreamingExperimentConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
(deepdrivemd.models.keras_cvae_stream.config.KerasCVAEModelConfig attribute)
adios_xml_agg_4ml (deepdrivemd.config.StreamingExperimentConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
adios_xml_file (deepdrivemd.config.StreamingExperimentConfig attribute)
(deepdrivemd.sim.openmm_stream.config.OpenMMConfig attribute)
adios_xml_sim (deepdrivemd.config.StreamingExperimentConfig attribute)
(deepdrivemd.sim.openmm_stream.config.OpenMMConfig attribute)
AdiosReader (class in deepdrivemd.data.stream.aggregator_reader)
AdiosStreamStepRW (class in deepdrivemd.data.stream.adios_utils)
AGENT_DIR (deepdrivemd.data.api.DeepDriveMD_API attribute)
AGENT_PIPELINE_NAME (deepdrivemd.deepdrivemd_stream.PipelineManager attribute)
agent_stage (deepdrivemd.config.ExperimentConfig attribute)
(deepdrivemd.config.StreamingExperimentConfig attribute)
AGENT_STAGE_NAME (deepdrivemd.deepdrivemd.PipelineManager attribute)
(deepdrivemd.deepdrivemd_stream.PipelineManager attribute)
agg_dir (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
(deepdrivemd.models.keras_cvae_stream.config.KerasCVAEModelConfig attribute)
aggregate() (in module deepdrivemd.aggregation.stream.aggregator)
AGGREGATE_DIR (deepdrivemd.data.api.DeepDriveMD_API attribute)
AGGREGATION_PIPELINE_NAME (deepdrivemd.deepdrivemd_stream.PipelineManager attribute)
aggregation_stage (deepdrivemd.config.ExperimentConfig attribute)
(deepdrivemd.config.StreamingExperimentConfig attribute)
AGGREGATION_STAGE_NAME (deepdrivemd.deepdrivemd.PipelineManager attribute)
(deepdrivemd.deepdrivemd_stream.PipelineManager attribute)
apply_analysis_fn() (deepdrivemd.data.analysis.DeepDriveMD_Analysis method)
arguments (deepdrivemd.config.BaseStageConfig attribute)
array (deepdrivemd.data.stream.enumerations.DataStructure attribute)
B
batch (deepdrivemd.data.stream.aggregator_reader.Streams attribute)
batch_size (deepdrivemd.models.aae.config.AAEModelConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
(deepdrivemd.models.keras_cvae.config.KerasCVAEModelConfig attribute)
(deepdrivemd.models.keras_cvae_stream.config.KerasCVAEModelConfig attribute)
best_model (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
bestk() (in module deepdrivemd.utils)
bp_file (deepdrivemd.sim.openmm_stream.config.OpenMMConfig attribute)
build_model() (in module deepdrivemd.models.aae_stream.train)
C
CenterOfMassTransform (class in deepdrivemd.models.aae_stream.utils)
checkpoint_dir (deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
(deepdrivemd.models.keras_cvae_stream.config.KerasCVAEModelConfig attribute)
(deepdrivemd.selection.latest.config.LatestCheckpointConfig attribute)
checkpoint_suffix (deepdrivemd.selection.latest.config.LatestCheckpointConfig attribute)
cm (deepdrivemd.data.stream.aggregator_reader.Streams attribute)
cms_transform (deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
compute_number_of_nodes() (in module deepdrivemd.deepdrivemd_stream)
compute_rmsd (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
(deepdrivemd.aggregation.stream.config.StreamAggregation attribute)
(deepdrivemd.sim.openmm_stream.config.OpenMMConfig attribute)
compute_zcentroid (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
(deepdrivemd.aggregation.stream.config.StreamAggregation attribute)
(deepdrivemd.sim.openmm_stream.config.OpenMMConfig attribute)
concatenate_last_n_h5() (in module deepdrivemd.aggregation.basic.aggregate)
concatenate_virtual_h5() (in module deepdrivemd.data.utils)
config_directory (deepdrivemd.config.StreamingExperimentConfig attribute)
config_path() (deepdrivemd.data.api.Stage_API method)
connect_to_input() (in module deepdrivemd.aggregation.stream.aggregator)
connections (deepdrivemd.data.stream.adios_utils.AdiosStreamStepRW attribute)
contact_map (deepdrivemd.aggregation.basic.config.BasicAggegation attribute)
(deepdrivemd.sim.openmm.config.OpenMMConfig attribute)
conv_filter_shapes (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
(deepdrivemd.models.keras_cvae.config.KerasCVAEModelConfig attribute)
(deepdrivemd.models.keras_cvae_stream.config.KerasCVAEModelConfig attribute)
conv_filters (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
(deepdrivemd.models.keras_cvae.config.KerasCVAEModelConfig attribute)
(deepdrivemd.models.keras_cvae_stream.config.KerasCVAEModelConfig attribute)
conv_layers (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
(deepdrivemd.models.keras_cvae.config.KerasCVAEModelConfig attribute)
(deepdrivemd.models.keras_cvae_stream.config.KerasCVAEModelConfig attribute)
conv_strides (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
(deepdrivemd.models.keras_cvae.config.KerasCVAEModelConfig attribute)
(deepdrivemd.models.keras_cvae_stream.config.KerasCVAEModelConfig attribute)
copy_velocities_p (deepdrivemd.sim.openmm_stream.config.OpenMMConfig attribute)
cpu_reqs (deepdrivemd.config.BaseStageConfig attribute)
cpus_per_node (deepdrivemd.config.ExperimentConfig attribute)
current_dir (deepdrivemd.sim.openmm_stream.config.OpenMMConfig attribute)
D
dataset_location (deepdrivemd.models.aae.config.AAEModelConfig attribute)
dataset_name (deepdrivemd.models.aae.config.AAEModelConfig attribute)
(deepdrivemd.models.keras_cvae.config.KerasCVAEModelConfig attribute)
DataStructure (class in deepdrivemd.data.stream.enumerations)
decoder_affine_widths (deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
decoder_bias (deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
decoder_relu_slope (deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
deepdrivemd
module
deepdrivemd.agents
module
deepdrivemd.agents.lof
module
deepdrivemd.agents.lof.config
module
deepdrivemd.agents.stream
module
deepdrivemd.agents.stream.config
module
deepdrivemd.aggregation
module
deepdrivemd.aggregation.basic
module
deepdrivemd.aggregation.basic.aggregate
module
deepdrivemd.aggregation.basic.config
module
deepdrivemd.aggregation.stream
module
deepdrivemd.aggregation.stream.aggregator
module
deepdrivemd.aggregation.stream.config
module
deepdrivemd.config
module
deepdrivemd.data
module
deepdrivemd.data.analysis
module
deepdrivemd.data.api
module
deepdrivemd.data.stream
module
deepdrivemd.data.stream.adios_utils
module
deepdrivemd.data.stream.aggregator_reader
module
deepdrivemd.data.stream.enumerations
module
deepdrivemd.data.stream.OutlierDB
module
deepdrivemd.data.utils
module
deepdrivemd.deepdrivemd
module
deepdrivemd.deepdrivemd_stream
module
deepdrivemd.models
module
deepdrivemd.models.aae
module
deepdrivemd.models.aae.config
module
deepdrivemd.models.aae_stream
module
deepdrivemd.models.aae_stream.config
module
deepdrivemd.models.aae_stream.train
module
deepdrivemd.models.aae_stream.utils
module
deepdrivemd.models.keras_cvae
module
deepdrivemd.models.keras_cvae.config
module
deepdrivemd.models.keras_cvae.utils
module
deepdrivemd.models.keras_cvae_stream
module
deepdrivemd.models.keras_cvae_stream.config
module
deepdrivemd.selection
module
deepdrivemd.selection.latest
module
deepdrivemd.selection.latest.config
module
deepdrivemd.selection.latest.select_model
module
deepdrivemd.sim
module
deepdrivemd.sim.openmm
module
deepdrivemd.sim.openmm.config
module
deepdrivemd.sim.openmm_stream
module
deepdrivemd.sim.openmm_stream.config
module
deepdrivemd.utils
module
DeepDriveMD_Analysis (class in deepdrivemd.data.analysis)
DeepDriveMD_API (class in deepdrivemd.data.api)
dense_dropouts (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
(deepdrivemd.models.keras_cvae.config.KerasCVAEModelConfig attribute)
(deepdrivemd.models.keras_cvae_stream.config.KerasCVAEModelConfig attribute)
dense_layers (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
(deepdrivemd.models.keras_cvae.config.KerasCVAEModelConfig attribute)
(deepdrivemd.models.keras_cvae_stream.config.KerasCVAEModelConfig attribute)
dense_neurons (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
(deepdrivemd.models.keras_cvae.config.KerasCVAEModelConfig attribute)
(deepdrivemd.models.keras_cvae_stream.config.KerasCVAEModelConfig attribute)
dictionary (deepdrivemd.data.stream.OutlierDB.OutlierDB attribute)
dir (deepdrivemd.data.stream.OutlierDB.OutlierDB attribute)
discriminator_affine_widths (deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
discriminator_bias (deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
discriminator_filters (deepdrivemd.models.aae.config.AAEModelConfig attribute)
discriminator_relu_slope (deepdrivemd.models.aae.config.AAEModelConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
divisibleby (deepdrivemd.sim.openmm_stream.config.OpenMMConfig attribute)
dt_ps (deepdrivemd.sim.openmm.config.OpenMMConfig attribute)
(deepdrivemd.sim.openmm_stream.config.OpenMMConfig attribute)
dtype (deepdrivemd.data.stream.aggregator_reader.StreamVariable attribute)
dump_yaml() (deepdrivemd.config.BaseSettings method)
E
embed_interval (deepdrivemd.models.aae.config.AAEModelConfig attribute)
encoder_bias (deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
encoder_filters (deepdrivemd.models.aae.config.AAEModelConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
encoder_kernel_sizes (deepdrivemd.models.aae.config.AAEModelConfig attribute)
encoder_kernels (deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
encoder_relu_slope (deepdrivemd.models.aae.config.AAEModelConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
epochs (deepdrivemd.models.aae.config.AAEModelConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
(deepdrivemd.models.keras_cvae.config.KerasCVAEModelConfig attribute)
(deepdrivemd.models.keras_cvae_stream.config.KerasCVAEModelConfig attribute)
executable (deepdrivemd.config.BaseStageConfig attribute)
experiment_directory (deepdrivemd.config.AgentTaskConfig attribute)
(deepdrivemd.config.AggregationTaskConfig attribute)
(deepdrivemd.config.BaseTaskConfig attribute)
(deepdrivemd.config.ExperimentConfig attribute)
(deepdrivemd.config.ModelSelectionTaskConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
experiment_directory_cannot_exist() (deepdrivemd.config.ExperimentConfig class method)
explicit (deepdrivemd.sim.openmm.config.OpenMMConfig.MDSolvent attribute)
(deepdrivemd.sim.openmm_stream.config.OpenMMConfig.MDSolvent attribute)
explicit_solvent_requires_top_suffix() (deepdrivemd.sim.openmm.config.OpenMMConfig class method)
(deepdrivemd.sim.openmm_stream.config.OpenMMConfig class method)
extrinsic_score (deepdrivemd.agents.lof.config.OutlierDetectionConfig attribute)
F
final_shape (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
(deepdrivemd.models.keras_cvae.config.KerasCVAEModelConfig attribute)
(deepdrivemd.models.keras_cvae_stream.config.KerasCVAEModelConfig attribute)
find_input() (in module deepdrivemd.aggregation.stream.aggregator)
fnc (deepdrivemd.aggregation.basic.config.BasicAggegation attribute)
fnc_name (deepdrivemd.models.aae.config.AAEModelConfig attribute)
fraction_of_contacts (deepdrivemd.sim.openmm.config.OpenMMConfig attribute)
from_yaml() (deepdrivemd.config.BaseSettings class method)
func_condition() (deepdrivemd.deepdrivemd.PipelineManager method)
func_on_false() (deepdrivemd.deepdrivemd.PipelineManager method)
func_on_true() (deepdrivemd.deepdrivemd.PipelineManager method)
G
generate_agent_stage() (deepdrivemd.deepdrivemd.PipelineManager method)
(deepdrivemd.deepdrivemd_stream.PipelineManager method)
generate_aggregating_stage() (deepdrivemd.deepdrivemd.PipelineManager method)
(deepdrivemd.deepdrivemd_stream.PipelineManager method)
generate_machine_learning_stage() (deepdrivemd.deepdrivemd.PipelineManager method)
(deepdrivemd.deepdrivemd_stream.PipelineManager method)
generate_model_selection_stage() (deepdrivemd.deepdrivemd.PipelineManager method)
generate_molecular_dynamics_stage() (deepdrivemd.deepdrivemd.PipelineManager method)
(deepdrivemd.deepdrivemd_stream.PipelineManager method)
generate_pipelines() (deepdrivemd.deepdrivemd.PipelineManager method)
(deepdrivemd.deepdrivemd_stream.PipelineManager method)
generate_sample_config() (in module deepdrivemd.config)
generate_task() (in module deepdrivemd.deepdrivemd)
(in module deepdrivemd.deepdrivemd_stream)
generator_filters (deepdrivemd.models.aae.config.AAEModelConfig attribute)
generator_relu_slope (deepdrivemd.models.aae.config.AAEModelConfig attribute)
get_agent_h5() (deepdrivemd.data.analysis.DeepDriveMD_Analysis method)
get_agent_json() (deepdrivemd.data.analysis.DeepDriveMD_Analysis method)
get_count() (deepdrivemd.data.api.Stage_API static method)
get_frameinfo() (in module deepdrivemd.utils)
get_initial_pdbs() (deepdrivemd.data.api.DeepDriveMD_API static method)
get_last_n_md_runs() (deepdrivemd.data.api.DeepDriveMD_API method)
get_latest() (deepdrivemd.data.api.Stage_API static method)
get_model_path() (in module deepdrivemd.selection.latest.select_model)
get_restart_pdb() (deepdrivemd.data.api.DeepDriveMD_API method)
get_system_name() (deepdrivemd.data.api.DeepDriveMD_API static method)
get_system_pdb_name() (deepdrivemd.data.api.DeepDriveMD_API static method)
get_topology() (deepdrivemd.data.api.DeepDriveMD_API static method)
get_total_iterations() (deepdrivemd.data.api.DeepDriveMD_API method)
get_virtual_h5_file() (in module deepdrivemd.data.utils)
glob_file_from_dirs() (in module deepdrivemd.data.api)
gpu_reqs (deepdrivemd.config.BaseStageConfig attribute)
gpus_per_node (deepdrivemd.config.ExperimentConfig attribute)
H
hardware_threads_per_cpu (deepdrivemd.config.ExperimentConfig attribute)
hash2intarray() (in module deepdrivemd.utils)
heat_bath_friction_coef (deepdrivemd.sim.openmm.config.OpenMMConfig attribute)
(deepdrivemd.sim.openmm_stream.config.OpenMMConfig attribute)
I
implicit (deepdrivemd.sim.openmm.config.OpenMMConfig.MDSolvent attribute)
(deepdrivemd.sim.openmm_stream.config.OpenMMConfig.MDSolvent attribute)
in_memory (deepdrivemd.sim.openmm.config.OpenMMConfig attribute)
(deepdrivemd.sim.openmm_stream.config.OpenMMConfig attribute)
inference_batch_size (deepdrivemd.agents.lof.config.OutlierDetectionConfig attribute)
init_eps (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
init_min_samples (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
init_pdb_file (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
(deepdrivemd.config.StreamingExperimentConfig attribute)
init_weights (deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
init_weights_path (deepdrivemd.config.MachineLearningTaskConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
initial_epochs (deepdrivemd.models.aae.config.AAEModelConfig attribute)
(deepdrivemd.models.keras_cvae.config.KerasCVAEModelConfig attribute)
initial_pdb_dir (deepdrivemd.config.MolecularDynamicsTaskConfig attribute)
(deepdrivemd.sim.openmm_stream.config.OpenMMConfig attribute)
initial_shape (deepdrivemd.models.keras_cvae.config.KerasCVAEModelConfig attribute)
input_path (deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
intarray2hash() (in module deepdrivemd.utils)
intrinsic_score (deepdrivemd.agents.lof.config.OutlierDetectionConfig attribute)
io (deepdrivemd.data.stream.aggregator_reader.AdiosReader attribute)
J
json_path() (deepdrivemd.data.api.Stage_API method)
K
k_random_old_h5_files (deepdrivemd.agents.lof.config.OutlierDetectionConfig attribute)
(deepdrivemd.models.aae.config.AAEModelConfig attribute)
(deepdrivemd.models.keras_cvae.config.KerasCVAEModelConfig attribute)
L
lambda_gp (deepdrivemd.models.aae.config.AAEModelConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
lambda_rec (deepdrivemd.models.aae.config.AAEModelConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
last_n_h5_files (deepdrivemd.aggregation.basic.config.BasicAggegation attribute)
(deepdrivemd.models.aae.config.AAEModelConfig attribute)
(deepdrivemd.models.keras_cvae.config.KerasCVAEModelConfig attribute)
lastN (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
(deepdrivemd.data.stream.aggregator_reader.Streams attribute)
latent_dim (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
(deepdrivemd.models.aae.config.AAEModelConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
(deepdrivemd.models.keras_cvae.config.KerasCVAEModelConfig attribute)
(deepdrivemd.models.keras_cvae_stream.config.KerasCVAEModelConfig attribute)
latest_checkpoint() (in module deepdrivemd.selection.latest.select_model)
latest_model_checkpoint() (in module deepdrivemd.selection.latest.select_model)
ligand (deepdrivemd.sim.openmm_stream.config.OpenMMConfig attribute)
M
MACHINE_LEARNING_DIR (deepdrivemd.data.api.DeepDriveMD_API attribute)
MACHINE_LEARNING_PIPELINE_NAME (deepdrivemd.deepdrivemd_stream.PipelineManager attribute)
machine_learning_stage (deepdrivemd.config.ExperimentConfig attribute)
(deepdrivemd.config.StreamingExperimentConfig attribute)
MACHINE_LEARNING_STAGE_NAME (deepdrivemd.deepdrivemd.PipelineManager attribute)
(deepdrivemd.deepdrivemd_stream.PipelineManager attribute)
main() (in module deepdrivemd.models.aae_stream.train)
max_iteration (deepdrivemd.config.ExperimentConfig attribute)
max_loss (deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
(deepdrivemd.models.keras_cvae_stream.config.KerasCVAEModelConfig attribute)
max_steps (deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
(deepdrivemd.models.keras_cvae_stream.config.KerasCVAEModelConfig attribute)
md5 (deepdrivemd.data.stream.aggregator_reader.Streams attribute)
mda_selection (deepdrivemd.sim.openmm.config.OpenMMConfig attribute)
(deepdrivemd.sim.openmm_stream.config.OpenMMConfig attribute)
min_step_increment (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
(deepdrivemd.models.keras_cvae_stream.config.KerasCVAEModelConfig attribute)
model (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
(deepdrivemd.aggregation.stream.config.StreamAggregation attribute)
(deepdrivemd.config.StreamingExperimentConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
(deepdrivemd.models.keras_cvae_stream.config.KerasCVAEModelConfig attribute)
MODEL_SELECTION_DIR (deepdrivemd.data.api.DeepDriveMD_API attribute)
model_selection_stage (deepdrivemd.config.ExperimentConfig attribute)
(deepdrivemd.config.StreamingExperimentConfig attribute)
MODEL_SELECTION_STAGE_NAME (deepdrivemd.deepdrivemd.PipelineManager attribute)
model_tag (deepdrivemd.config.MachineLearningTaskConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
model_type (deepdrivemd.agents.lof.config.OutlierDetectionConfig attribute)
model_type_check() (deepdrivemd.agents.lof.config.OutlierDetectionConfig class method)
module
deepdrivemd
deepdrivemd.agents
deepdrivemd.agents.lof
deepdrivemd.agents.lof.config
deepdrivemd.agents.stream
deepdrivemd.agents.stream.config
deepdrivemd.aggregation
deepdrivemd.aggregation.basic
deepdrivemd.aggregation.basic.aggregate
deepdrivemd.aggregation.basic.config
deepdrivemd.aggregation.stream
deepdrivemd.aggregation.stream.aggregator
deepdrivemd.aggregation.stream.config
deepdrivemd.config
deepdrivemd.data
deepdrivemd.data.analysis
deepdrivemd.data.api
deepdrivemd.data.stream
deepdrivemd.data.stream.adios_utils
deepdrivemd.data.stream.aggregator_reader
deepdrivemd.data.stream.enumerations
deepdrivemd.data.stream.OutlierDB
deepdrivemd.data.utils
deepdrivemd.deepdrivemd
deepdrivemd.deepdrivemd_stream
deepdrivemd.models
deepdrivemd.models.aae
deepdrivemd.models.aae.config
deepdrivemd.models.aae_stream
deepdrivemd.models.aae_stream.config
deepdrivemd.models.aae_stream.train
deepdrivemd.models.aae_stream.utils
deepdrivemd.models.keras_cvae
deepdrivemd.models.keras_cvae.config
deepdrivemd.models.keras_cvae.utils
deepdrivemd.models.keras_cvae_stream
deepdrivemd.models.keras_cvae_stream.config
deepdrivemd.selection
deepdrivemd.selection.latest
deepdrivemd.selection.latest.config
deepdrivemd.selection.latest.select_model
deepdrivemd.sim
deepdrivemd.sim.openmm
deepdrivemd.sim.openmm.config
deepdrivemd.sim.openmm_stream
deepdrivemd.sim.openmm_stream.config
deepdrivemd.utils
MOLECULAR_DYNAMICS_DIR (deepdrivemd.data.api.DeepDriveMD_API attribute)
MOLECULAR_DYNAMICS_PIPELINE_NAME (deepdrivemd.deepdrivemd_stream.PipelineManager attribute)
molecular_dynamics_stage (deepdrivemd.config.ExperimentConfig attribute)
MOLECULAR_DYNAMICS_STAGE_NAME (deepdrivemd.deepdrivemd.PipelineManager attribute)
(deepdrivemd.deepdrivemd_stream.PipelineManager attribute)
multi_ligand_table (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
(deepdrivemd.aggregation.stream.config.StreamAggregation attribute)
(deepdrivemd.config.StreamingExperimentConfig attribute)
(deepdrivemd.sim.openmm_stream.config.OpenMMConfig attribute)
N
n_most_recent_h5_files (deepdrivemd.agents.lof.config.OutlierDetectionConfig attribute)
n_sim (deepdrivemd.aggregation.stream.config.StreamAggregation attribute)
n_traj_frames (deepdrivemd.agents.lof.config.OutlierDetectionConfig attribute)
name (deepdrivemd.data.stream.aggregator_reader.StreamVariable attribute)
next() (deepdrivemd.data.stream.aggregator_reader.AdiosReader method)
(deepdrivemd.data.stream.aggregator_reader.StreamContactMapVariable method)
(deepdrivemd.data.stream.aggregator_reader.Streams method)
(deepdrivemd.data.stream.aggregator_reader.StreamScalarVariable method)
(deepdrivemd.data.stream.aggregator_reader.StreamVariable method)
next_input() (in module deepdrivemd.models.aae_stream.train)
next_random() (deepdrivemd.data.stream.OutlierDB.OutlierDB method)
node_local_path (deepdrivemd.config.AgentTaskConfig attribute)
(deepdrivemd.config.AggregationTaskConfig attribute)
(deepdrivemd.config.BaseTaskConfig attribute)
(deepdrivemd.config.ExperimentConfig attribute)
(deepdrivemd.config.ModelSelectionTaskConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
noise_mu (deepdrivemd.models.aae.config.AAEModelConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
noise_std (deepdrivemd.models.aae.config.AAEModelConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
num_agg (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
(deepdrivemd.models.keras_cvae_stream.config.KerasCVAEModelConfig attribute)
num_data_workers (deepdrivemd.models.aae.config.AAEModelConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
num_extrinsic_outliers (deepdrivemd.agents.lof.config.OutlierDetectionConfig attribute)
num_features (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
(deepdrivemd.models.aae.config.AAEModelConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
num_intrinsic_outliers (deepdrivemd.agents.lof.config.OutlierDetectionConfig attribute)
num_outliers_check() (deepdrivemd.agents.lof.config.OutlierDetectionConfig class method)
num_points (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
(deepdrivemd.models.aae.config.AAEModelConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
num_sim (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
num_tasks (deepdrivemd.aggregation.stream.config.StreamAggregation attribute)
(deepdrivemd.config.MolecularDynamicsStageConfig attribute)
(deepdrivemd.config.StreamingAgentStageConfig attribute)
(deepdrivemd.config.StreamingAggregationStageConfig attribute)
(deepdrivemd.config.StreamingMachineLearningStageConfig attribute)
O
openmm_selection (deepdrivemd.sim.openmm.config.OpenMMConfig attribute)
(deepdrivemd.sim.openmm_stream.config.OpenMMConfig attribute)
OpenMMConfig.MDSolvent (class in deepdrivemd.sim.openmm.config)
(class in deepdrivemd.sim.openmm_stream.config)
optimizer_lr (deepdrivemd.models.aae.config.AAEModelConfig attribute)
optimizer_name (deepdrivemd.models.aae.config.AAEModelConfig attribute)
outlier_count (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
outlier_max (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
outlier_min (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
outlier_selection (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
OutlierDB (class in deepdrivemd.data.stream.OutlierDB)
outliers_dir (deepdrivemd.sim.openmm_stream.config.OpenMMConfig attribute)
output_path (deepdrivemd.config.AgentTaskConfig attribute)
(deepdrivemd.config.AggregationTaskConfig attribute)
(deepdrivemd.config.BaseTaskConfig attribute)
(deepdrivemd.config.ModelSelectionTaskConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
P
parse_args() (in module deepdrivemd.utils)
parse_h5() (in module deepdrivemd.data.utils)
pdb_file (deepdrivemd.config.MolecularDynamicsTaskConfig attribute)
pickle_db (deepdrivemd.sim.openmm_stream.config.OpenMMConfig attribute)
PIPELINE_NAME (deepdrivemd.deepdrivemd.PipelineManager attribute)
PipelineManager (class in deepdrivemd.deepdrivemd)
(class in deepdrivemd.deepdrivemd_stream)
Point3dAAEConfig (class in deepdrivemd.models.aae_stream.config)
point_cloud (deepdrivemd.aggregation.basic.config.BasicAggegation attribute)
(deepdrivemd.sim.openmm.config.OpenMMConfig attribute)
PointCloudDatasetInMemory (class in deepdrivemd.models.aae_stream.utils)
positions (deepdrivemd.data.stream.aggregator_reader.Streams attribute)
pre_exec (deepdrivemd.config.BaseStageConfig attribute)
prefetch_factor (deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
print() (deepdrivemd.data.stream.OutlierDB.OutlierDB method)
process_type (deepdrivemd.config.CPUReqs attribute)
(deepdrivemd.config.GPUReqs attribute)
process_type_check() (deepdrivemd.config.CPUReqs class method)
(deepdrivemd.config.GPUReqs class method)
processes (deepdrivemd.config.CPUReqs attribute)
(deepdrivemd.config.GPUReqs attribute)
project (deepdrivemd.config.ExperimentConfig attribute)
project_gpu (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
project_lastN (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
published_model_dir (deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
(deepdrivemd.models.keras_cvae_stream.config.KerasCVAEModelConfig attribute)
Q
queue (deepdrivemd.config.ExperimentConfig attribute)
R
read_adios_file() (in module deepdrivemd.models.aae_stream.utils)
read_batch (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
(deepdrivemd.models.keras_cvae_stream.config.KerasCVAEModelConfig attribute)
read_step() (deepdrivemd.data.stream.adios_utils.AdiosStreamStepRW method)
read_task_json() (deepdrivemd.data.api.Stage_API method)
readers (deepdrivemd.data.stream.aggregator_reader.Streams attribute)
ref_pdb_file (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
(deepdrivemd.config.StreamingExperimentConfig attribute)
reference_pdb_file (deepdrivemd.sim.openmm.config.OpenMMConfig attribute)
(deepdrivemd.sim.openmm_stream.config.OpenMMConfig attribute)
reinit (deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
(deepdrivemd.models.keras_cvae_stream.config.KerasCVAEModelConfig attribute)
report_interval_ps (deepdrivemd.sim.openmm.config.OpenMMConfig attribute)
(deepdrivemd.sim.openmm_stream.config.OpenMMConfig attribute)
resource (deepdrivemd.config.ExperimentConfig attribute)
resume_checkpoint (deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
retrain_freq (deepdrivemd.config.MachineLearningStageConfig attribute)
(deepdrivemd.selection.latest.config.LatestCheckpointConfig attribute)
rmsd (deepdrivemd.aggregation.basic.config.BasicAggegation attribute)
rmsd_name (deepdrivemd.models.aae.config.AAEModelConfig attribute)
rmsds (deepdrivemd.data.stream.aggregator_reader.Streams attribute)
runs_dir (deepdrivemd.data.api.Stage_API property)
S
sample_interval (deepdrivemd.models.aae.config.AAEModelConfig attribute)
scalar (deepdrivemd.data.stream.enumerations.DataStructure attribute)
scalar_dset_names (deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
scalar_requires_grad (deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
schema_ (deepdrivemd.config.ExperimentConfig attribute)
scoring_method_check() (deepdrivemd.agents.lof.config.OutlierDetectionConfig class method)
seed (deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
setup_mpi() (in module deepdrivemd.utils)
setup_mpi_comm() (in module deepdrivemd.utils)
shuffle (deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
(deepdrivemd.models.keras_cvae.config.KerasCVAEModelConfig attribute)
(deepdrivemd.models.keras_cvae_stream.config.KerasCVAEModelConfig attribute)
simulation_length_ns (deepdrivemd.sim.openmm.config.OpenMMConfig attribute)
(deepdrivemd.sim.openmm_stream.config.OpenMMConfig attribute)
skip_aggregation (deepdrivemd.config.AggregationStageConfig attribute)
sklearn_num_jobs (deepdrivemd.agents.lof.config.OutlierDetectionConfig attribute)
sleeptime_bpfiles (deepdrivemd.aggregation.stream.config.StreamAggregation attribute)
software_directory (deepdrivemd.config.StreamingExperimentConfig attribute)
solvent_type (deepdrivemd.sim.openmm.config.OpenMMConfig attribute)
(deepdrivemd.sim.openmm_stream.config.OpenMMConfig attribute)
sorted_index (deepdrivemd.data.stream.OutlierDB.OutlierDB attribute)
sparse_to_dense() (in module deepdrivemd.models.keras_cvae.utils)
split_pct (deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
(deepdrivemd.models.keras_cvae.config.KerasCVAEModelConfig attribute)
(deepdrivemd.models.keras_cvae_stream.config.KerasCVAEModelConfig attribute)
Stage_API (class in deepdrivemd.data.api)
stage_dir() (deepdrivemd.data.api.Stage_API method)
stage_dir_count() (deepdrivemd.data.api.Stage_API method)
stage_idx (deepdrivemd.config.AgentTaskConfig attribute)
(deepdrivemd.config.AggregationTaskConfig attribute)
(deepdrivemd.config.BaseTaskConfig attribute)
(deepdrivemd.config.ModelSelectionTaskConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
stage_name() (deepdrivemd.data.api.Stage_API static method)
steps (deepdrivemd.data.stream.aggregator_reader.Streams attribute)
stream (deepdrivemd.data.stream.aggregator_reader.AdiosReader attribute)
StreamContactMapVariable (class in deepdrivemd.data.stream.aggregator_reader)
Streams (class in deepdrivemd.data.stream.aggregator_reader)
StreamScalarVariable (class in deepdrivemd.data.stream.aggregator_reader)
StreamVariable (class in deepdrivemd.data.stream.aggregator_reader)
string (deepdrivemd.data.stream.enumerations.DataStructure attribute)
structure (deepdrivemd.data.stream.aggregator_reader.StreamVariable attribute)
T
t1Dto2D() (in module deepdrivemd.utils)
t2Dto1D() (in module deepdrivemd.utils)
task_config (deepdrivemd.config.AgentStageConfig attribute)
(deepdrivemd.config.AggregationStageConfig attribute)
(deepdrivemd.config.MachineLearningStageConfig attribute)
(deepdrivemd.config.ModelSelectionStageConfig attribute)
(deepdrivemd.config.MolecularDynamicsStageConfig attribute)
task_dir() (deepdrivemd.data.api.Stage_API method)
task_idx (deepdrivemd.config.AgentTaskConfig attribute)
(deepdrivemd.config.AggregationTaskConfig attribute)
(deepdrivemd.config.BaseTaskConfig attribute)
(deepdrivemd.config.ModelSelectionTaskConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
task_name() (deepdrivemd.data.api.Stage_API static method)
temperature_kelvin (deepdrivemd.sim.openmm.config.OpenMMConfig attribute)
(deepdrivemd.sim.openmm_stream.config.OpenMMConfig attribute)
thread_type (deepdrivemd.config.CPUReqs attribute)
(deepdrivemd.config.GPUReqs attribute)
thread_type_check() (deepdrivemd.config.CPUReqs class method)
(deepdrivemd.config.GPUReqs class method)
threads_per_process (deepdrivemd.config.CPUReqs attribute)
(deepdrivemd.config.GPUReqs attribute)
threshold (deepdrivemd.sim.openmm.config.OpenMMConfig attribute)
(deepdrivemd.sim.openmm_stream.config.OpenMMConfig attribute)
timeout1 (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
(deepdrivemd.models.keras_cvae_stream.config.KerasCVAEModelConfig attribute)
timeout2 (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
(deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
(deepdrivemd.models.keras_cvae_stream.config.KerasCVAEModelConfig attribute)
Timer (class in deepdrivemd.utils)
timer() (in module deepdrivemd.utils)
title (deepdrivemd.config.ExperimentConfig attribute)
top_file1 (deepdrivemd.config.StreamingExperimentConfig attribute)
(deepdrivemd.sim.openmm_stream.config.OpenMMConfig attribute)
top_suffix (deepdrivemd.sim.openmm.config.OpenMMConfig attribute)
(deepdrivemd.sim.openmm_stream.config.OpenMMConfig attribute)
total (deepdrivemd.data.stream.aggregator_reader.StreamVariable attribute)
train() (in module deepdrivemd.models.aae_stream.train)
train_model() (in module deepdrivemd.models.aae_stream.train)
transform() (deepdrivemd.models.aae_stream.utils.CenterOfMassTransform method)
tsne_interval (deepdrivemd.models.aae.config.AAEModelConfig attribute)
U
unique_name() (deepdrivemd.data.api.Stage_API static method)
use_discriminator_bias (deepdrivemd.models.aae.config.AAEModelConfig attribute)
use_encoder_bias (deepdrivemd.models.aae.config.AAEModelConfig attribute)
use_generator_bias (deepdrivemd.models.aae.config.AAEModelConfig attribute)
use_model_checkpoint (deepdrivemd.models.aae_stream.config.Point3dAAEConfig attribute)
use_outliers (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
use_random_outliers (deepdrivemd.agents.stream.config.OutlierDetectionConfig attribute)
V
validate() (in module deepdrivemd.models.aae_stream.train)
variables (deepdrivemd.data.stream.adios_utils.AdiosStreamStepRW attribute)
velocities (deepdrivemd.data.stream.aggregator_reader.Streams attribute)
verbose (deepdrivemd.aggregation.basic.config.BasicAggegation attribute)
W
wait_for_input() (in module deepdrivemd.models.aae_stream.train)
walltime_min (deepdrivemd.config.ExperimentConfig attribute)
wandb_project_name (deepdrivemd.models.aae.config.AAEModelConfig attribute)
wrap (deepdrivemd.sim.openmm.config.OpenMMConfig attribute)
write_pdb() (deepdrivemd.data.api.DeepDriveMD_API static method)
write_step() (deepdrivemd.data.stream.adios_utils.AdiosStreamStepRW method)
write_task_json() (deepdrivemd.data.api.Stage_API method)
Z
zcentroid_atoms (deepdrivemd.sim.openmm_stream.config.OpenMMConfig attribute)
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