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improve conf files
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@albertbou92
albertbou92 committed Aug 10, 2024
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Showing 21 changed files with 105 additions and 43 deletions.
7 changes: 5 additions & 2 deletions scripts/a2c/config_denovo.yaml
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Expand Up @@ -11,8 +11,11 @@ total_smiles: 10_000 # Total number of smiles to generate

# Scoring function
molscore_mode: single # single, benchmark, or curriculum
molscore_task: MolOpt:Albuterol_similarity # task configuration (JSON), benchmark (preset only), or curriculum task (preset only)
custom_task: null # Requires custom_task mode to be set to null
molscore_task: MolOpt:Albuterol_similarity # selects the Albuterol_similarity task from the MolOpt benchmark
# molscore_task accepts task configuration files (JSON), benchmark (preset only), or curriculum task (preset only)
# Refer to MolScore documentation for more information
custom_task: null # Requires molscore_task mode to be set to null
# Reefr to the tutorials for more information on how to use custom scoring functions / tasks

# Promptsmiles configuration
prompt: null # e.g. c1ccccc # Fix the beginning of the generated molecules
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7 changes: 5 additions & 2 deletions scripts/a2c/config_fragment.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,11 @@ total_smiles: 10_000 # Total number of smiles to generate

# Scoring function
molscore_mode: single # single, benchmark, or curriculum
molscore_task: MolOpt:Celecoxxib_rediscovery # task configuration (JSON), benchmark (preset only), or curriculum task (preset only)
custom_task: null # Requires molscore_task to be set to null
molscore_task: MolOpt:Celecoxxib_rediscovery # selects the Celecoxxib_rediscovery task from the MolOpt benchmark
# molscore_task accepts task configuration files (JSON), benchmark (preset only), or curriculum task (preset only)
# Refer to MolScore documentation for more information
custom_task: null # Requires molscore_task mode to be set to null
# Reefr to the tutorials for more information on how to use custom scoring functions / tasks

# Promptsmiles configuration
promptsmiles: c1(C)ccc(*)cc1.NS(=O)(=O)(*)
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7 changes: 5 additions & 2 deletions scripts/a2c/config_scaffold.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,11 @@ total_smiles: 10_000 # Total number of smiles to generate

# Scoring function
molscore_mode: single # single, benchmark, or curriculum
molscore_task: LibINVENT_Exp1:DRD2_SelRF_SubFilt_DF # task configuration (JSON), benchmark (preset only), or curriculum task (preset only)
custom_task: null # Requires molscore_task to be set to null
molscore_task: LibINVENT_Exp1:DRD2_SelRF_SubFilt_DF # selects the DRD2_SelRF_SubFilt_DF task from the LibINVENT_Exp1 benchmark
# molscore_task accepts task configuration files (JSON), benchmark (preset only), or curriculum task (preset only)
# Refer to MolScore documentation for more information
custom_task: null # Requires molscore_task mode to be set to null
# Reefr to the tutorials for more information on how to use custom scoring functions / tasks

# Promptsmiles configuration
promptsmiles: N1(*)CCN(CC1)CCCCN(*)
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7 changes: 5 additions & 2 deletions scripts/ahc/config_denovo.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,11 @@ total_smiles: 10_000 # Total number of smiles to generate

# Scoring function
molscore_mode: single # single, benchmark, or curriculum
molscore_task: MolOpt:Albuterol_similarity # task configuration (JSON), benchmark (preset only), or curriculum task (preset only)
custom_task: null # Requires custom_task mode to be set to null
molscore_task: MolOpt:Albuterol_similarity # selects the Albuterol_similarity task from the MolOpt benchmark
# molscore_task accepts task configuration files (JSON), benchmark (preset only), or curriculum task (preset only)
# Refer to MolScore documentation for more information
custom_task: null # Requires molscore_task mode to be set to null
# Reefr to the tutorials for more information on how to use custom scoring functions / tasks

# Promptsmiles configuration
prompt: null # e.g. c1ccccc # Fix the beginning of the generated molecules
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7 changes: 5 additions & 2 deletions scripts/ahc/config_fragment.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,11 @@ total_smiles: 10_000 # Total number of smiles to generate

# Scoring function
molscore_mode: single # single, benchmark, or curriculum
molscore_task: MolOpt:Celecoxxib_rediscovery # task configuration (JSON), benchmark (preset only), or curriculum task (preset only)
custom_task: null # Requires molscore_task to be set to null
molscore_task: MolOpt:Celecoxxib_rediscovery # selects the Celecoxxib_rediscovery task from the MolOpt benchmark
# molscore_task accepts task configuration files (JSON), benchmark (preset only), or curriculum task (preset only)
# Refer to MolScore documentation for more information
custom_task: null # Requires molscore_task mode to be set to null
# Reefr to the tutorials for more information on how to use custom scoring functions / tasks

# Promptsmiles configuration
promptsmiles: c1(C)ccc(*)cc1.NS(=O)(=O)(*)
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7 changes: 5 additions & 2 deletions scripts/ahc/config_scaffold.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,11 @@ total_smiles: 10_000 # Total number of smiles to generate

# Scoring function
molscore_mode: single # single, benchmark, or curriculum
molscore_task: LibINVENT_Exp1:DRD2_SelRF_SubFilt_DF # task configuration (JSON), benchmark (preset only), or curriculum task (preset only)
custom_task: null # Requires molscore_task to be set to null
molscore_task: LibINVENT_Exp1:DRD2_SelRF_SubFilt_DF # selects the DRD2_SelRF_SubFilt_DF task from the LibINVENT_Exp1 benchmark
# molscore_task accepts task configuration files (JSON), benchmark (preset only), or curriculum task (preset only)
# Refer to MolScore documentation for more information
custom_task: null # Requires molscore_task mode to be set to null
# Reefr to the tutorials for more information on how to use custom scoring functions / tasks

# Promptsmiles configuration
promptsmiles: N1(*)CCN(CC1)CCCCN(*)
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7 changes: 5 additions & 2 deletions scripts/dpo/config_denovo.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,11 @@ total_smiles: 10_000 # Total number of smiles to generate

# Scoring function
molscore_mode: single # single, benchmark, or curriculum
molscore_task: MolOpt:Albuterol_similarity # task configuration (JSON), benchmark (preset only), or curriculum task (preset only)
custom_task: null # Requires custom_task mode to be set to null
molscore_task: MolOpt:Albuterol_similarity # selects the Albuterol_similarity task from the MolOpt benchmark
# molscore_task accepts task configuration files (JSON), benchmark (preset only), or curriculum task (preset only)
# Refer to MolScore documentation for more information
custom_task: null # Requires molscore_task mode to be set to null
# Reefr to the tutorials for more information on how to use custom scoring functions / tasks

# Promptsmiles configuration
prompt: null # e.g. c1ccccc # Fix the beginning of the generated molecules
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7 changes: 5 additions & 2 deletions scripts/dpo/config_fragment.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,11 @@ total_smiles: 10_000 # Total number of smiles to generate

# Scoring function
molscore_mode: single # single, benchmark, or curriculum
molscore_task: MolOpt:Celecoxxib_rediscovery # task configuration (JSON), benchmark (preset only), or curriculum task (preset only)
custom_task: null # Requires molscore_task to be set to null
molscore_task: MolOpt:Celecoxxib_rediscovery # selects the Celecoxxib_rediscovery task from the MolOpt benchmark
# molscore_task accepts task configuration files (JSON), benchmark (preset only), or curriculum task (preset only)
# Refer to MolScore documentation for more information
custom_task: null # Requires molscore_task mode to be set to null
# Reefr to the tutorials for more information on how to use custom scoring functions / tasks

# Promptsmiles configuration
promptsmiles: c1(C)ccc(*)cc1.NS(=O)(=O)(*)
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7 changes: 5 additions & 2 deletions scripts/dpo/config_scaffold.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,11 @@ total_smiles: 10_000 # Total number of smiles to generate

# Scoring function
molscore_mode: single # single, benchmark, or curriculum
molscore_task: LibINVENT_Exp1:DRD2_SelRF_SubFilt_DF # task configuration (JSON), benchmark (preset only), or curriculum task (preset only)
custom_task: null # Requires molscore_task to be set to null
molscore_task: LibINVENT_Exp1:DRD2_SelRF_SubFilt_DF # selects the DRD2_SelRF_SubFilt_DF task from the LibINVENT_Exp1 benchmark
# molscore_task accepts task configuration files (JSON), benchmark (preset only), or curriculum task (preset only)
# Refer to MolScore documentation for more information
custom_task: null # Requires molscore_task mode to be set to null
# Reefr to the tutorials for more information on how to use custom scoring functions / tasks

# Promptsmiles configuration
promptsmiles: N1(*)CCN(CC1)CCCCN(*)
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7 changes: 5 additions & 2 deletions scripts/hill_climb/config_denovo.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,11 @@ total_smiles: 10_000 # Total number of smiles to generate

# Scoring function
molscore_mode: single # single, benchmark, or curriculum
molscore_task: MolOpt:Albuterol_similarity # task configuration (JSON), benchmark (preset only), or curriculum task (preset only)
custom_task: null # Requires custom_task mode to be set to null
molscore_task: MolOpt:Albuterol_similarity # selects the Albuterol_similarity task from the MolOpt benchmark
# molscore_task accepts task configuration files (JSON), benchmark (preset only), or curriculum task (preset only)
# Refer to MolScore documentation for more information
custom_task: null # Requires molscore_task mode to be set to null
# Reefr to the tutorials for more information on how to use custom scoring functions / tasks

# Promptsmiles configuration
prompt: null # e.g. c1ccccc # Fix the beginning of the generated molecules
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7 changes: 5 additions & 2 deletions scripts/hill_climb/config_fragment.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,11 @@ total_smiles: 10_000 # Total number of smiles to generate

# Scoring function
molscore_mode: single # single, benchmark, or curriculum
molscore_task: MolOpt:Celecoxxib_rediscovery # task configuration (JSON), benchmark (preset only), or curriculum task (preset only)
custom_task: null # Requires molscore_task to be set to null
molscore_task: MolOpt:Celecoxxib_rediscovery # selects the Celecoxxib_rediscovery task from the MolOpt benchmark
# molscore_task accepts task configuration files (JSON), benchmark (preset only), or curriculum task (preset only)
# Refer to MolScore documentation for more information
custom_task: null # Requires molscore_task mode to be set to null
# Reefr to the tutorials for more information on how to use custom scoring functions / tasks

# Promptsmiles configuration
promptsmiles: c1(C)ccc(*)cc1.NS(=O)(=O)(*)
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7 changes: 5 additions & 2 deletions scripts/hill_climb/config_scaffold.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,11 @@ total_smiles: 10_000 # Total number of smiles to generate

# Scoring function
molscore_mode: single # single, benchmark, or curriculum
molscore_task: LibINVENT_Exp1:DRD2_SelRF_SubFilt_DF # task configuration (JSON), benchmark (preset only), or curriculum task (preset only)
custom_task: null # Requires molscore_task to be set to null
molscore_task: LibINVENT_Exp1:DRD2_SelRF_SubFilt_DF # selects the DRD2_SelRF_SubFilt_DF task from the LibINVENT_Exp1 benchmark
# molscore_task accepts task configuration files (JSON), benchmark (preset only), or curriculum task (preset only)
# Refer to MolScore documentation for more information
custom_task: null # Requires molscore_task mode to be set to null
# Reefr to the tutorials for more information on how to use custom scoring functions / tasks

# Promptsmiles configuration
promptsmiles: N1(*)CCN(CC1)CCCCN(*)
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7 changes: 5 additions & 2 deletions scripts/ppo/config_denovo.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,11 @@ total_smiles: 10_000 # Total number of smiles to generate

# Scoring function
molscore_mode: single # single, benchmark, or curriculum
molscore_task: MolOpt:Albuterol_similarity # task configuration (JSON), benchmark (preset only), or curriculum task (preset only)
custom_task: null # Requires custom_task mode to be set to null
molscore_task: MolOpt:Albuterol_similarity # selects the Albuterol_similarity task from the MolOpt benchmark
# molscore_task accepts task configuration files (JSON), benchmark (preset only), or curriculum task (preset only)
# Refer to MolScore documentation for more information
custom_task: null # Requires molscore_task mode to be set to null
# Reefr to the tutorials for more information on how to use custom scoring functions / tasks

# Promptsmiles configuration
prompt: null # e.g. c1ccccc # Fix the beginning of the generated molecules
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7 changes: 5 additions & 2 deletions scripts/ppo/config_fragment.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,11 @@ total_smiles: 10_000 # Total number of smiles to generate

# Scoring function
molscore_mode: single # single, benchmark, or curriculum
molscore_task: MolOpt:Celecoxxib_rediscovery # task configuration (JSON), benchmark (preset only), or curriculum task (preset only)
custom_task: null # Requires molscore_task to be set to null
molscore_task: MolOpt:Celecoxxib_rediscovery # selects the Celecoxxib_rediscovery task from the MolOpt benchmark
# molscore_task accepts task configuration files (JSON), benchmark (preset only), or curriculum task (preset only)
# Refer to MolScore documentation for more information
custom_task: null # Requires molscore_task mode to be set to null
# Reefr to the tutorials for more information on how to use custom scoring functions / tasks

# Promptsmiles configuration
promptsmiles: c1(C)ccc(*)cc1.NS(=O)(=O)(*)
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7 changes: 5 additions & 2 deletions scripts/ppo/config_scaffold.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,11 @@ total_smiles: 10_000 # Total number of smiles to generate

# Scoring function
molscore_mode: single # single, benchmark, or curriculum
molscore_task: LibINVENT_Exp1:DRD2_SelRF_SubFilt_DF # task configuration (JSON), benchmark (preset only), or curriculum task (preset only)
custom_task: null # Requires molscore_task to be set to null
molscore_task: LibINVENT_Exp1:DRD2_SelRF_SubFilt_DF # selects the DRD2_SelRF_SubFilt_DF task from the LibINVENT_Exp1 benchmark
# molscore_task accepts task configuration files (JSON), benchmark (preset only), or curriculum task (preset only)
# Refer to MolScore documentation for more information
custom_task: null # Requires molscore_task mode to be set to null
# Reefr to the tutorials for more information on how to use custom scoring functions / tasks

# Promptsmiles configuration
promptsmiles: N1(*)CCN(CC1)CCCCN(*)
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7 changes: 5 additions & 2 deletions scripts/reinforce/config_denovo.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,11 @@ total_smiles: 10_000 # Total number of smiles to generate

# Scoring function
molscore_mode: single # single, benchmark, or curriculum
molscore_task: MolOpt:Albuterol_similarity # task configuration (JSON), benchmark (preset only), or curriculum task (preset only)
custom_task: null # Requires custom_task mode to be set to null
molscore_task: MolOpt:Albuterol_similarity # selects the Albuterol_similarity task from the MolOpt benchmark
# molscore_task accepts task configuration files (JSON), benchmark (preset only), or curriculum task (preset only)
# Refer to MolScore documentation for more information
custom_task: null # Requires molscore_task mode to be set to null
# Reefr to the tutorials for more information on how to use custom scoring functions / tasks

# Promptsmiles configuration
prompt: null # e.g. c1ccccc # Fix the beginning of the generated molecules
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7 changes: 5 additions & 2 deletions scripts/reinforce/config_fragment.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,11 @@ total_smiles: 10_000 # Total number of smiles to generate

# Scoring function
molscore_mode: single # single, benchmark, or curriculum
molscore_task: MolOpt:Celecoxxib_rediscovery # task configuration (JSON), benchmark (preset only), or curriculum task (preset only)
custom_task: null # Requires molscore_task to be set to null
molscore_task: MolOpt:Celecoxxib_rediscovery # selects the Celecoxxib_rediscovery task from the MolOpt benchmark
# molscore_task accepts task configuration files (JSON), benchmark (preset only), or curriculum task (preset only)
# Refer to MolScore documentation for more information
custom_task: null # Requires molscore_task mode to be set to null
# Reefr to the tutorials for more information on how to use custom scoring functions / tasks

# Promptsmiles configuration
promptsmiles: c1(C)ccc(*)cc1.NS(=O)(=O)(*)
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7 changes: 5 additions & 2 deletions scripts/reinforce/config_scaffold.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,11 @@ total_smiles: 10_000 # Total number of smiles to generate

# Scoring function
molscore_mode: single # single, benchmark, or curriculum
molscore_task: LibINVENT_Exp1:DRD2_SelRF_SubFilt_DF # task configuration (JSON), benchmark (preset only), or curriculum task (preset only)
custom_task: null # Requires molscore_task to be set to null
molscore_task: LibINVENT_Exp1:DRD2_SelRF_SubFilt_DF # selects the DRD2_SelRF_SubFilt_DF task from the LibINVENT_Exp1 benchmark
# molscore_task accepts task configuration files (JSON), benchmark (preset only), or curriculum task (preset only)
# Refer to MolScore documentation for more information
custom_task: null # Requires molscore_task mode to be set to null
# Reefr to the tutorials for more information on how to use custom scoring functions / tasks

# Promptsmiles configuration
promptsmiles: N1(*)CCN(CC1)CCCCN(*)
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7 changes: 5 additions & 2 deletions scripts/reinvent/config_denovo.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,11 @@ total_smiles: 10_000 # Total number of smiles to generate

# Scoring function
molscore_mode: single # single, benchmark, or curriculum
molscore_task: MolOpt:Albuterol_similarity # task configuration (JSON), benchmark (preset only), or curriculum task (preset only)
custom_task: null # Requires custom_task mode to be set to null
molscore_task: MolOpt:Albuterol_similarity # selects the Albuterol_similarity task from the MolOpt benchmark
# molscore_task accepts task configuration files (JSON), benchmark (preset only), or curriculum task (preset only)
# Refer to MolScore documentation for more information
custom_task: null # Requires molscore_task mode to be set to null
# Reefr to the tutorials for more information on how to use custom scoring functions / tasks

# Promptsmiles configuration
prompt: null # e.g. c1ccccc # Fix the beginning of the generated molecules
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7 changes: 5 additions & 2 deletions scripts/reinvent/config_fragment.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,11 @@ total_smiles: 10_000 # Total number of smiles to generate

# Scoring function
molscore_mode: single # single, benchmark, or curriculum
molscore_task: MolOpt:Celecoxxib_rediscovery # task configuration (JSON), benchmark (preset only), or curriculum task (preset only)
custom_task: null # Requires molscore_task to be set to null
molscore_task: MolOpt:Celecoxxib_rediscovery # selects the Celecoxxib_rediscovery task from the MolOpt benchmark
# molscore_task accepts task configuration files (JSON), benchmark (preset only), or curriculum task (preset only)
# Refer to MolScore documentation for more information
custom_task: null # Requires molscore_task mode to be set to null
# Reefr to the tutorials for more information on how to use custom scoring functions / tasks

# Promptsmiles configuration
promptsmiles: c1(C)ccc(*)cc1.NS(=O)(=O)(*)
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8 changes: 5 additions & 3 deletions scripts/reinvent/config_scaffold.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,11 +9,13 @@ seed: 101 # multiple seeds can be provided as a list to multiple experiments seq
num_envs: 128 # Number of smiles to generate in parallel
total_smiles: 10_000 # Total number of smiles to generate

# Scoring function
# Scoring function
molscore_mode: single # single, benchmark, or curriculum
molscore_task: LibINVENT_Exp1:DRD2_SelRF_SubFilt_DF # task configuration (JSON), benchmark (preset only), or curriculum task (preset only)
custom_task: null # Requires molscore_task to be set to null
molscore_task: LibINVENT_Exp1:DRD2_SelRF_SubFilt_DF # selects the DRD2_SelRF_SubFilt_DF task from the LibINVENT_Exp1 benchmark
# molscore_task accepts task configuration files (JSON), benchmark (preset only), or curriculum task (preset only)
# Refer to MolScore documentation for more information
custom_task: null # Requires molscore_task mode to be set to null
# Reefr to the tutorials for more information on how to use custom scoring functions / tasks

# Promptsmiles configuration
promptsmiles: N1(*)CCN(CC1)CCCCN(*)
Expand Down

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