Index

_

__getitem__() (conformer_rl.agents.storage.Storage method) _add_to_cache() (conformer_rl.logging.env_logger.EnvLogger method) _calculate_advantages() (conformer_rl.agents.base_ac_agent.BaseACAgent method) (conformer_rl.agents.base_ac_agent_recurrent.BaseACAgentRecurrent method) _done() (conformer_rl.environments.conformer_env.ConformerEnv method) _eval_episode() (conformer_rl.agents.base_ac_agent.BaseACAgent method) (conformer_rl.agents.base_ac_agent_recurrent.BaseACAgentRecurrent method) (conformer_rl.agents.base_agent.BaseAgent method) (conformer_rl.agents.base_agent_recurrent.BaseAgentRecurrent method) _eval_step() (conformer_rl.agents.base_ac_agent_recurrent.BaseACAgentRecurrent method) (conformer_rl.agents.base_agent_recurrent.BaseAgentRecurrent method) _info() (conformer_rl.environments.conformer_env.ConformerEnv method) _load_from_pickle() (in module conformer_rl.analysis.analysis)

_obs() (conformer_rl.environments.conformer_env.ConformerEnv method) (conformer_rl.environments.environment_components.obs_mixins.AtomCoordsTypeGraphObsMixin method) (conformer_rl.environments.environment_components.obs_mixins.AtomTypeGraphObsMixin method) (conformer_rl.environments.environment_components.obs_mixins.GraphObsMixin method) _reward() (conformer_rl.environments.conformer_env.ConformerEnv method) (conformer_rl.environments.environment_components.reward_mixins.GibbsEndPruningRewardMixin method) (conformer_rl.environments.environment_components.reward_mixins.GibbsLogPruningRewardMixin method) (conformer_rl.environments.environment_components.reward_mixins.GibbsPruningRewardMixin method) (conformer_rl.environments.environment_components.reward_mixins.GibbsRewardMixin method) _sample() (conformer_rl.agents.base_ac_agent.BaseACAgent method) (conformer_rl.agents.base_ac_agent_recurrent.BaseACAgentRecurrent method) _step() (conformer_rl.environments.conformer_env.ConformerEnv method) (conformer_rl.environments.environment_components.action_mixins.ContinuousActionMixin method) (conformer_rl.environments.environment_components.action_mixins.DiscreteActionMixin method)

A

A2CAgent (class in conformer_rl.agents.A2C.A2C_agent) A2CExternalCurriculumAgent (class in conformer_rl.agents.curriculum_agents) A2CRecurrentAgent (class in conformer_rl.agents.A2C.A2C_recurrent_agent) A2CRecurrentExternalCurriculumAgent (class in conformer_rl.agents.curriculum_agents) add_scalar() (conformer_rl.logging.train_logger.TrainLogger method)

append() (conformer_rl.agents.storage.Storage method) atom_coords() (in module conformer_rl.environments.environment_components.molecule_features) atom_type_CO() (in module conformer_rl.environments.environment_components.molecule_features) AtomCoordsTypeGraphObsMixin (class in conformer_rl.environments.environment_components.obs_mixins) AtomTypeGraphObsMixin (class in conformer_rl.environments.environment_components.obs_mixins)

B

bar_plot_episodic() (in module conformer_rl.analysis.analysis) BaseACAgent (class in conformer_rl.agents.base_ac_agent) BaseACAgentRecurrent (class in conformer_rl.agents.base_ac_agent_recurrent)

BaseAgent (class in conformer_rl.agents.base_agent) BaseAgentRecurrent (class in conformer_rl.agents.base_agent_recurrent) bond_type() (in module conformer_rl.environments.environment_components.molecule_features)

C

cache (conformer_rl.logging.env_logger.EnvLogger attribute) calculate_normalizers() (in module conformer_rl.utils.chem_utils) calculate_tfd() (in module conformer_rl.analysis.analysis) clear_data() (conformer_rl.logging.env_logger.EnvLogger method) clear_episode() (conformer_rl.logging.env_logger.EnvLogger method) Config (class in conformer_rl.config.agent_config) config (conformer_rl.agents.base_agent.BaseAgent attribute) (conformer_rl.environments.conformer_env.ConformerEnv attribute) config_from_molFile() (in module conformer_rl.molecule_generation.generate_molecule_config) config_from_rdkit() (in module conformer_rl.molecule_generation.generate_molecule_config) config_from_smiles() (in module conformer_rl.molecule_generation.generate_molecule_config) configs (conformer_rl.environments.curriculum_conformer_env.CurriculumConformerEnv attribute) conformer_rl.agents.A2C.A2C_agent module conformer_rl.agents.A2C.A2C_recurrent_agent module conformer_rl.agents.base_ac_agent module conformer_rl.agents.base_ac_agent_recurrent module conformer_rl.agents.base_agent module conformer_rl.agents.base_agent_recurrent module conformer_rl.agents.curriculum_agents module conformer_rl.agents.PPO.PPO_agent module conformer_rl.agents.PPO.PPO_recurrent_agent module conformer_rl.agents.storage module conformer_rl.analysis.analysis module conformer_rl.config.agent_config module conformer_rl.config.mol_config module conformer_rl.environments.conformer_env module conformer_rl.environments.curriculum_conformer_env module conformer_rl.environments.environment_components.action_mixins module conformer_rl.environments.environment_components.molecule_features module

conformer_rl.environments.environment_components.obs_mixins module conformer_rl.environments.environment_components.reward_mixins module conformer_rl.environments.environment_wrapper module conformer_rl.environments.environments module conformer_rl.logging.env_logger module conformer_rl.logging.train_logger module conformer_rl.models.graph_components module conformer_rl.models.RTGN module conformer_rl.models.RTGN_GAT module conformer_rl.models.RTGN_GAT_recurrent module conformer_rl.models.RTGN_recurrent module conformer_rl.molecule_generation.generate_alkanes module conformer_rl.molecule_generation.generate_lignin module conformer_rl.molecule_generation.generate_molecule_config module conformer_rl.molecule_generation.generate_xor_gate module conformer_rl.utils.chem_utils module conformer_rl.utils.misc_utils module ConformerEnv (class in conformer_rl.environments.conformer_env) ContinuousActionMixin (class in conformer_rl.environments.environment_components.action_mixins) current_step (conformer_rl.environments.conformer_env.ConformerEnv attribute) (conformer_rl.environments.curriculum_conformer_env.CurriculumConformerEnv attribute) current_time() (in module conformer_rl.utils.misc_utils) curriculum_agent_buffer_len (conformer_rl.config.agent_config.Config attribute) curriculum_agent_fail_rate (conformer_rl.config.agent_config.Config attribute) curriculum_agent_reward_thresh (conformer_rl.config.agent_config.Config attribute) curriculum_agent_success_rate (conformer_rl.config.agent_config.Config attribute) curriculum_max_index (conformer_rl.environments.curriculum_conformer_env.CurriculumConformerEnv attribute) CurriculumConformerEnv (class in conformer_rl.environments.curriculum_conformer_env)

D

data_dir (conformer_rl.config.agent_config.Config attribute) decrease_level() (conformer_rl.environments.curriculum_conformer_env.CurriculumConformerEnv method) discount (conformer_rl.config.agent_config.Config attribute)

DiscreteActionEnv (class in conformer_rl.environments.environments) DiscreteActionMixin (class in conformer_rl.environments.environment_components.action_mixins) drawConformer() (in module conformer_rl.analysis.analysis) drawConformer_episodic() (in module conformer_rl.analysis.analysis)

E

E0 (conformer_rl.config.mol_config.MolConfig attribute) entropy_weight (conformer_rl.config.agent_config.Config attribute) EnvLogger (class in conformer_rl.logging.env_logger) episode_data (conformer_rl.logging.env_logger.EnvLogger attribute) episode_info (conformer_rl.environments.conformer_env.ConformerEnv attribute) (conformer_rl.environments.curriculum_conformer_env.CurriculumConformerEnv attribute) eval_env (conformer_rl.config.agent_config.Config attribute) eval_episodes (conformer_rl.config.agent_config.Config attribute) eval_interval (conformer_rl.config.agent_config.Config attribute) eval_logger (conformer_rl.agents.base_agent.BaseAgent attribute) evaluate() (conformer_rl.agents.A2C.A2C_agent.A2CAgent method) (conformer_rl.agents.A2C.A2C_recurrent_agent.A2CRecurrentAgent method) (conformer_rl.agents.base_ac_agent.BaseACAgent method) (conformer_rl.agents.base_ac_agent_recurrent.BaseACAgentRecurrent method) (conformer_rl.agents.base_agent.BaseAgent method) (conformer_rl.agents.base_agent_recurrent.BaseAgentRecurrent method) (conformer_rl.agents.curriculum_agents.A2CExternalCurriculumAgent method) (conformer_rl.agents.curriculum_agents.A2CRecurrentExternalCurriculumAgent method) (conformer_rl.agents.curriculum_agents.PPOExternalCurriculumAgent method) (conformer_rl.agents.curriculum_agents.PPORecurrentExternalCurriculumAgent method) (conformer_rl.agents.PPO.PPO_agent.PPOAgent method) (conformer_rl.agents.PPO.PPO_recurrent_agent.PPORecurrentAgent method)

ExternalCurriculumAgentMixin (class in conformer_rl.agents.curriculum_agents)

F

forward() (conformer_rl.models.RTGN.RTGN method) (conformer_rl.models.RTGN_GAT.RTGNGat method) (conformer_rl.models.RTGN_GAT_recurrent.RTGNGatRecurrent method) (conformer_rl.models.RTGN_recurrent.RTGNRecurrent method)

G

gae_lambda (conformer_rl.config.agent_config.Config attribute) GAT (class in conformer_rl.models.graph_components) generate_branched_alkane() (in module conformer_rl.molecule_generation.generate_alkanes) generate_lignin() (in module conformer_rl.molecule_generation.generate_lignin) generate_straight_alkane() (in module conformer_rl.molecule_generation.generate_alkanes) generate_xor_gate() (in module conformer_rl.molecule_generation.generate_xor_gate) get_bond_pairs() (in module conformer_rl.environments.environment_components.molecule_features) get_conformer_energies() (in module conformer_rl.utils.chem_utils) get_conformer_energy() (in module conformer_rl.utils.chem_utils) GibbsEndPruningRewardMixin (class in conformer_rl.environments.environment_components.reward_mixins)

GibbsLogPruningRewardMixin (class in conformer_rl.environments.environment_components.reward_mixins) GibbsPruningRewardMixin (class in conformer_rl.environments.environment_components.reward_mixins) GibbsRewardMixin (class in conformer_rl.environments.environment_components.reward_mixins) GibbsScoreEndPruningEnv (class in conformer_rl.environments.environments) GibbsScoreEnv (class in conformer_rl.environments.environments) GibbsScoreLogPruningCurriculumEnv (class in conformer_rl.environments.environments) GibbsScoreLogPruningEnv (class in conformer_rl.environments.environments) GibbsScorePruningCurriculumEnv (class in conformer_rl.environments.environments) GibbsScorePruningEnv (class in conformer_rl.environments.environments) gradient_clip (conformer_rl.config.agent_config.Config attribute) GraphObsMixin (class in conformer_rl.environments.environment_components.obs_mixins)

H

heatmap_episodic() (in module conformer_rl.analysis.analysis)

histogram_episodic() (in module conformer_rl.analysis.analysis) histogram_select_episodes() (in module conformer_rl.analysis.analysis)

I

increase_level() (conformer_rl.environments.curriculum_conformer_env.CurriculumConformerEnv method)

L

list_keys() (in module conformer_rl.analysis.analysis) load() (conformer_rl.agents.A2C.A2C_agent.A2CAgent method) (conformer_rl.agents.A2C.A2C_recurrent_agent.A2CRecurrentAgent method) (conformer_rl.agents.base_ac_agent.BaseACAgent method) (conformer_rl.agents.base_ac_agent_recurrent.BaseACAgentRecurrent method) (conformer_rl.agents.base_agent.BaseAgent method) (conformer_rl.agents.base_agent_recurrent.BaseAgentRecurrent method) (conformer_rl.agents.curriculum_agents.A2CExternalCurriculumAgent method) (conformer_rl.agents.curriculum_agents.A2CRecurrentExternalCurriculumAgent method) (conformer_rl.agents.curriculum_agents.PPOExternalCurriculumAgent method) (conformer_rl.agents.curriculum_agents.PPORecurrentExternalCurriculumAgent method) (conformer_rl.agents.PPO.PPO_agent.PPOAgent method) (conformer_rl.agents.PPO.PPO_recurrent_agent.PPORecurrentAgent method)

load_data_from_pickle() (in module conformer_rl.analysis.analysis) load_model() (in module conformer_rl.utils.misc_utils) log_episode() (conformer_rl.logging.env_logger.EnvLogger method) log_episode_item() (conformer_rl.logging.env_logger.EnvLogger method) log_step() (conformer_rl.logging.env_logger.EnvLogger method) log_step_item() (conformer_rl.logging.env_logger.EnvLogger method)

M

max_steps (conformer_rl.config.agent_config.Config attribute) mini_batch_size (conformer_rl.config.agent_config.Config attribute) mkdir() (in module conformer_rl.utils.misc_utils) module conformer_rl.agents.A2C.A2C_agent conformer_rl.agents.A2C.A2C_recurrent_agent conformer_rl.agents.base_ac_agent conformer_rl.agents.base_ac_agent_recurrent conformer_rl.agents.base_agent conformer_rl.agents.base_agent_recurrent conformer_rl.agents.curriculum_agents conformer_rl.agents.PPO.PPO_agent conformer_rl.agents.PPO.PPO_recurrent_agent conformer_rl.agents.storage conformer_rl.analysis.analysis conformer_rl.config.agent_config conformer_rl.config.mol_config conformer_rl.environments.conformer_env conformer_rl.environments.curriculum_conformer_env conformer_rl.environments.environment_components.action_mixins conformer_rl.environments.environment_components.molecule_features conformer_rl.environments.environment_components.obs_mixins conformer_rl.environments.environment_components.reward_mixins conformer_rl.environments.environment_wrapper conformer_rl.environments.environments conformer_rl.logging.env_logger conformer_rl.logging.train_logger conformer_rl.models.graph_components conformer_rl.models.RTGN conformer_rl.models.RTGN_GAT conformer_rl.models.RTGN_GAT_recurrent conformer_rl.models.RTGN_recurrent conformer_rl.molecule_generation.generate_alkanes conformer_rl.molecule_generation.generate_lignin conformer_rl.molecule_generation.generate_molecule_config conformer_rl.molecule_generation.generate_xor_gate conformer_rl.utils.chem_utils conformer_rl.utils.misc_utils

mol (conformer_rl.config.mol_config.MolConfig attribute) MolConfig (class in conformer_rl.config.mol_config) MPNN (class in conformer_rl.models.graph_components)

N

network (conformer_rl.config.agent_config.Config attribute)

num_conformers (conformer_rl.config.mol_config.MolConfig attribute) num_workers (conformer_rl.config.agent_config.Config attribute)

O

optimization_epochs (conformer_rl.config.agent_config.Config attribute)

optimizer_fn (conformer_rl.config.agent_config.Config attribute) order() (conformer_rl.agents.storage.Storage method)

P

ppo_ratio_clip (conformer_rl.config.agent_config.Config attribute) PPOAgent (class in conformer_rl.agents.PPO.PPO_agent) PPOExternalCurriculumAgent (class in conformer_rl.agents.curriculum_agents) PPORecurrentAgent (class in conformer_rl.agents.PPO.PPO_recurrent_agent)

PPORecurrentExternalCurriculumAgent (class in conformer_rl.agents.curriculum_agents) prune_conformers() (in module conformer_rl.utils.chem_utils) prune_last_conformer() (in module conformer_rl.utils.chem_utils) pruning_thresh (conformer_rl.config.mol_config.MolConfig attribute)

R

recurrence (conformer_rl.config.agent_config.Config attribute) reset() (conformer_rl.agents.storage.Storage method) (conformer_rl.environments.conformer_env.ConformerEnv method) (conformer_rl.environments.curriculum_conformer_env.CurriculumConformerEnv method) rollout_length (conformer_rl.config.agent_config.Config attribute) RTGN (class in conformer_rl.models.RTGN) RTGNGat (class in conformer_rl.models.RTGN_GAT) RTGNGatRecurrent (class in conformer_rl.models.RTGN_GAT_recurrent) RTGNRecurrent (class in conformer_rl.models.RTGN_recurrent) run_steps() (conformer_rl.agents.A2C.A2C_agent.A2CAgent method) (conformer_rl.agents.A2C.A2C_recurrent_agent.A2CRecurrentAgent method) (conformer_rl.agents.base_ac_agent.BaseACAgent method) (conformer_rl.agents.base_ac_agent_recurrent.BaseACAgentRecurrent method) (conformer_rl.agents.base_agent.BaseAgent method) (conformer_rl.agents.base_agent_recurrent.BaseAgentRecurrent method) (conformer_rl.agents.curriculum_agents.A2CExternalCurriculumAgent method) (conformer_rl.agents.curriculum_agents.A2CRecurrentExternalCurriculumAgent method) (conformer_rl.agents.curriculum_agents.PPOExternalCurriculumAgent method) (conformer_rl.agents.curriculum_agents.PPORecurrentExternalCurriculumAgent method) (conformer_rl.agents.PPO.PPO_agent.PPOAgent method) (conformer_rl.agents.PPO.PPO_recurrent_agent.PPORecurrentAgent method)

S

save() (conformer_rl.agents.A2C.A2C_agent.A2CAgent method) (conformer_rl.agents.A2C.A2C_recurrent_agent.A2CRecurrentAgent method) (conformer_rl.agents.base_ac_agent.BaseACAgent method) (conformer_rl.agents.base_ac_agent_recurrent.BaseACAgentRecurrent method) (conformer_rl.agents.base_agent.BaseAgent method) (conformer_rl.agents.base_agent_recurrent.BaseAgentRecurrent method) (conformer_rl.agents.curriculum_agents.A2CExternalCurriculumAgent method) (conformer_rl.agents.curriculum_agents.A2CRecurrentExternalCurriculumAgent method) (conformer_rl.agents.curriculum_agents.PPOExternalCurriculumAgent method) (conformer_rl.agents.curriculum_agents.PPORecurrentExternalCurriculumAgent method) (conformer_rl.agents.PPO.PPO_agent.PPOAgent method) (conformer_rl.agents.PPO.PPO_recurrent_agent.PPORecurrentAgent method) save_episode() (conformer_rl.logging.env_logger.EnvLogger method) save_interval (conformer_rl.config.agent_config.Config attribute) save_model() (in module conformer_rl.utils.misc_utils) seed (conformer_rl.config.mol_config.MolConfig attribute) set_one_thread() (in module conformer_rl.utils.misc_utils) step() (conformer_rl.agents.A2C.A2C_agent.A2CAgent method) (conformer_rl.agents.A2C.A2C_recurrent_agent.A2CRecurrentAgent method) (conformer_rl.agents.base_ac_agent.BaseACAgent method) (conformer_rl.agents.base_ac_agent_recurrent.BaseACAgentRecurrent method) (conformer_rl.agents.base_agent.BaseAgent method) (conformer_rl.agents.base_agent_recurrent.BaseAgentRecurrent method) (conformer_rl.agents.curriculum_agents.A2CExternalCurriculumAgent method) (conformer_rl.agents.curriculum_agents.A2CRecurrentExternalCurriculumAgent method) (conformer_rl.agents.curriculum_agents.ExternalCurriculumAgentMixin method) (conformer_rl.agents.curriculum_agents.PPOExternalCurriculumAgent method) (conformer_rl.agents.curriculum_agents.PPORecurrentExternalCurriculumAgent method) (conformer_rl.agents.PPO.PPO_agent.PPOAgent method) (conformer_rl.agents.PPO.PPO_recurrent_agent.PPORecurrentAgent method) (conformer_rl.environments.conformer_env.ConformerEnv method)

step_data (conformer_rl.logging.env_logger.EnvLogger attribute) step_info (conformer_rl.environments.conformer_env.ConformerEnv attribute) (conformer_rl.environments.curriculum_conformer_env.CurriculumConformerEnv attribute) Storage (class in conformer_rl.agents.storage) storage (conformer_rl.agents.base_agent.BaseAgent attribute)

T

tag (conformer_rl.config.agent_config.Config attribute) Task() (in module conformer_rl.environments.environment_wrapper) tau (conformer_rl.config.mol_config.MolConfig attribute) tfd_matrix() (in module conformer_rl.utils.chem_utils) to_np() (in module conformer_rl.utils.misc_utils)

total_reward (conformer_rl.environments.conformer_env.ConformerEnv attribute) (conformer_rl.environments.curriculum_conformer_env.CurriculumConformerEnv attribute) total_steps (conformer_rl.agents.base_agent.BaseAgent attribute) train_env (conformer_rl.config.agent_config.Config attribute) train_logger (conformer_rl.agents.base_agent.BaseAgent attribute) TrainLogger (class in conformer_rl.logging.train_logger)

U

unique_tag (conformer_rl.agents.base_agent.BaseAgent attribute) update_curriculum() (conformer_rl.agents.curriculum_agents.A2CExternalCurriculumAgent method) (conformer_rl.agents.curriculum_agents.A2CRecurrentExternalCurriculumAgent method) (conformer_rl.agents.curriculum_agents.ExternalCurriculumAgentMixin method) (conformer_rl.agents.curriculum_agents.PPOExternalCurriculumAgent method) (conformer_rl.agents.curriculum_agents.PPORecurrentExternalCurriculumAgent method)

use_gae (conformer_rl.config.agent_config.Config attribute) use_tensorboard (conformer_rl.config.agent_config.Config attribute)

V

value_loss_coefficient (conformer_rl.config.agent_config.Config attribute)

Z

Z0 (conformer_rl.config.mol_config.MolConfig attribute)