rm rxn with no agents set to F

sustainable-processes · Jan 15, 2024 · 6c577e2 · 6c577e2
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diff --git a/Makefile b/Makefile
@@ -161,10 +161,10 @@ paper_3: paper_plot_uspto_no_trust_unfiltered_num_rxn_components paper_plot_uspt
 # 4. clean (filtered)
 
 paper_clean_uspto_no_trust_filtered: #requires: paper_extract_uspto_no_trust
-	python -m orderly.clean --output_path="data/orderly/uspto_no_trust/filtered/filtered_orderly_ord.parquet" --ord_extraction_path="data/orderly/uspto_no_trust/extracted_ords" --molecules_to_remove_path="data/orderly/uspto_no_trust/all_molecule_names.csv" --min_frequency_of_occurrence=0 --map_rare_molecules_to_other=True --set_unresolved_names_to_none_if_mapped_rxn_str_exists_else_del_rxn=True --remove_rxn_with_unresolved_names=False --set_unresolved_names_to_none=False --num_product=1 --num_reactant=2 --num_solv=2 --num_agent=3 --num_cat=0 --num_reag=0 --consistent_yield=False --remove_reactions_with_no_solvents=False --remove_reactions_with_no_agents=True --train_size=0.0
+	python -m orderly.clean --output_path="data/orderly/uspto_no_trust/filtered/filtered_orderly_ord.parquet" --ord_extraction_path="data/orderly/uspto_no_trust/extracted_ords" --molecules_to_remove_path="data/orderly/uspto_no_trust/all_molecule_names.csv" --min_frequency_of_occurrence=0 --map_rare_molecules_to_other=True --set_unresolved_names_to_none_if_mapped_rxn_str_exists_else_del_rxn=True --remove_rxn_with_unresolved_names=False --set_unresolved_names_to_none=False --num_product=1 --num_reactant=2 --num_solv=2 --num_agent=3 --num_cat=0 --num_reag=0 --consistent_yield=False --remove_reactions_with_no_solvents=False --remove_reactions_with_no_agents=False --train_size=0.0
 
 paper_clean_uspto_with_trust_filtered: #requires: paper_extract_uspto_with_trust
-	python -m orderly.clean --output_path="data/orderly/uspto_with_trust/filtered/filtered_orderly_ord.parquet" --ord_extraction_path="data/orderly/uspto_with_trust/extracted_ords" --molecules_to_remove_path="data/orderly/uspto_with_trust/all_molecule_names.csv" --min_frequency_of_occurrence=0 --map_rare_molecules_to_other=True --set_unresolved_names_to_none_if_mapped_rxn_str_exists_else_del_rxn=True --remove_rxn_with_unresolved_names=False --set_unresolved_names_to_none=False --num_product=1 --num_reactant=2 --num_solv=2 --num_agent=0 --num_cat=1 --num_reag=2 --consistent_yield=False --remove_reactions_with_no_solvents=False --remove_reactions_with_no_agents=True --train_size=0.0
+	python -m orderly.clean --output_path="data/orderly/uspto_with_trust/filtered/filtered_orderly_ord.parquet" --ord_extraction_path="data/orderly/uspto_with_trust/extracted_ords" --molecules_to_remove_path="data/orderly/uspto_with_trust/all_molecule_names.csv" --min_frequency_of_occurrence=0 --map_rare_molecules_to_other=True --set_unresolved_names_to_none_if_mapped_rxn_str_exists_else_del_rxn=True --remove_rxn_with_unresolved_names=False --set_unresolved_names_to_none=False --num_product=1 --num_reactant=2 --num_solv=2 --num_agent=0 --num_cat=1 --num_reag=2 --consistent_yield=False --remove_reactions_with_no_solvents=False --remove_reactions_with_no_agents=False --train_size=0.0
 
 paper_4: paper_clean_uspto_no_trust_filtered paper_clean_uspto_with_trust_filtered
 

diff --git a/README.md b/README.md
@@ -167,7 +167,7 @@ If you would like to extract all data in ORD (instead of just USPTO data) simply
 
 ### ORDerly-condition
 
-```python -m orderly.clean --output_path="../orderly_generated_datasets/orderly_condition.parquet" --ord_extraction_path="data/orderly/extracted_ords" --molecules_to_remove_path="data/orderly/all_molecule_names.csv" --min_frequency_of_occurrence=100 --map_rare_molecules_to_other=False --set_unresolved_names_to_none_if_mapped_rxn_str_exists_else_del_rxn=True --remove_rxn_with_unresolved_names=False --set_unresolved_names_to_none=False --num_product=1 --num_reactant=2 --num_solv=2 --num_agent=3 --num_cat=0 --num_reag=0 --consistent_yield=False --scramble=False --train_test_split_fraction=0.9 --remove_reactions_with_no_reactants=True --remove_reactions_with_no_products=True --remove_reactions_with_no_solvents=False --remove_reactions_with_no_agents=True```
+```python -m orderly.clean --output_path="../orderly_generated_datasets/orderly_condition.parquet" --ord_extraction_path="data/orderly/extracted_ords" --molecules_to_remove_path="data/orderly/all_molecule_names.csv" --min_frequency_of_occurrence=100 --map_rare_molecules_to_other=False --set_unresolved_names_to_none_if_mapped_rxn_str_exists_else_del_rxn=True --remove_rxn_with_unresolved_names=False --set_unresolved_names_to_none=False --num_product=1 --num_reactant=2 --num_solv=2 --num_agent=3 --num_cat=0 --num_reag=0 --consistent_yield=False --scramble=False --train_test_split_fraction=0.9 --remove_reactions_with_no_reactants=True --remove_reactions_with_no_products=True --remove_reactions_with_no_solvents=False --remove_reactions_with_no_agents=False```
 
 ### ORDerly-forward
 

diff --git a/orderly/clean/cleaner.py b/orderly/clean/cleaner.py
@@ -945,7 +945,7 @@ def get_matching_indices(
 @click.option(
     "--remove_reactions_with_no_agents",
     type=bool,
-    default=True,
+    default=False,
     show_default=True,
     help="Remove reactions with no agents (ie no reagents AND no catalysts). Does not consider solvents",
 )