Diffusion Transformation Product Prediction 2e9999e8b851

ADD: TP prediction, documentation
2e9999e8b851
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Authored by Jasmin on Dec 15 2022, 08:51.

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ADD: TP prediction, documentation

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Jasmin

Dec 15 2022, 08:51

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hafnerja

Dec 15 2022, 08:53

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R12460:e657508bacb1: update readme

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Jasmin committed R12460:2e9999e8b851: ADD: TP prediction, documentation (authored by Jasmin).Dec 15 2022, 08:51

Changes (84)

		Path
A		.gitignore
A	(dir)	Additional_analyses/
A	(dir)	Additional_analyses/Analyse_cutoff_thresholds/
A		Additional_analyses/Analyse_cutoff_thresholds/analyse_cutoff_thresholds.py
A	(dir)	Additional_analyses/Analyse_cutoff_thresholds/input/
A		Additional_analyses/Analyse_cutoff_thresholds/input/TP_prediction_BBD+SLUDGE_top_50.tsv
A		Additional_analyses/Analyse_cutoff_thresholds/input/TP_prediction_BBD+SOIL+SLUDGE_top_50.tsv
A		Additional_analyses/Analyse_cutoff_thresholds/input/TP_prediction_BBD+SOIL_top_50.tsv
A		Additional_analyses/Analyse_cutoff_thresholds/input/TP_prediction_BBD_top_50.tsv
A		Additional_analyses/Analyse_cutoff_thresholds/input/confirmed_TPs.txt
A		Additional_analyses/Analyse_cutoff_thresholds/input/results_EAWAG-PPS.tsv
A	(dir)	Additional_analyses/Analyse_cutoff_thresholds/output/
A		Additional_analyses/Analyse_cutoff_thresholds/output/Cutoff_thresholds_Combined probability threshold.txt
A		Additional_analyses/Analyse_cutoff_thresholds/output/Cutoff_thresholds_Generation threshold.txt
A		Additional_analyses/Analyse_cutoff_thresholds/output/Cutoff_thresholds_Maximum TP threshold.txt
A		Additional_analyses/Analyse_cutoff_thresholds/output/Cutoff_thresholds_Probability threshold.txt
A		Additional_analyses/Analyse_cutoff_thresholds/output/TP_list_cutoff_analysis.txt
A	(dir)	Additional_analyses/Compare_methods/
A		Additional_analyses/Compare_methods/README.txt
A		Additional_analyses/Compare_methods/compare_method_pps.py
A	(dir)	Additional_analyses/Compare_methods/input/
A		Additional_analyses/Compare_methods/input/data_dict_com_with_CAS.pickle
A		Additional_analyses/Compare_methods/input/data_dict_com_without_CAS.pickle
A		Additional_analyses/Compare_methods/input/found_TP_SMILES.txt
A	(dir)	Additional_analyses/Compare_methods/output/
A		Additional_analyses/Compare_methods/output/number_of_predicted_TPs_per_parent.tsv
A		Additional_analyses/Compare_methods/output/precision_of_methods.tsv
A		Additional_analyses/Compare_methods/output/predicted_and_found_TPs.csv
A		Additional_analyses/Compare_methods/output/sources_of_TPs.tsv
A		Additional_analyses/Compare_methods/output/used_rules.txt
A	(dir)	File_conversion/
A	(dir)	File_conversion/Prediction_output_to_mass_list/
A		File_conversion/Prediction_output_to_mass_list/README.md
A		File_conversion/Prediction_output_to_mass_list/get_mass_list_from_prediction.py
A	(dir)	File_conversion/Prediction_output_to_mass_list/input/
A		File_conversion/Prediction_output_to_mass_list/input/SMILES_selected_comp.txt
A		File_conversion/Prediction_output_to_mass_list/input/code_subst.txt
A		File_conversion/Prediction_output_to_mass_list/input/name_subst.txt
A	(dir)	File_conversion/Prediction_output_to_mass_list/input/round 2/
A		File_conversion/Prediction_output_to_mass_list/input/round 2/Eawag_PPS_BBD_results.tsv
A		File_conversion/Prediction_output_to_mass_list/input/round 2/Eawag_PPS_BBD_results_edited.tsv
A		File_conversion/Prediction_output_to_mass_list/input/round 2/enviPath_BBD_SOIL_results.tsv
A		File_conversion/Prediction_output_to_mass_list/input/round 2/enviPath_BBD_results.tsv
A	(dir)	File_conversion/Prediction_output_to_mass_list/input/round 2b/
A		File_conversion/Prediction_output_to_mass_list/input/round 2b/Eawag_PPS_BBD_results.tsv
A		File_conversion/Prediction_output_to_mass_list/input/round 2b/enviPath_BBD_SOIL_results.tsv
A		File_conversion/Prediction_output_to_mass_list/input/round 2b/enviPath_BBD_results.tsv
A	(dir)	File_conversion/Prediction_output_to_mass_list/input/updated predictions/
A		File_conversion/Prediction_output_to_mass_list/input/updated predictions/TP_prediction_BBD+SLUDGE_top_50.tsv
A		File_conversion/Prediction_output_to_mass_list/input/updated predictions/TP_prediction_BBD+SOIL+SLUDGE_top_50.tsv
A		File_conversion/Prediction_output_to_mass_list/input/updated predictions/TP_prediction_BBD+SOIL_top_50.tsv
A		File_conversion/Prediction_output_to_mass_list/input/updated predictions/TP_prediction_BBD_top_50.tsv
A		File_conversion/Prediction_output_to_mass_list/input/updated predictions/links.txt
A	(dir)	File_conversion/Prediction_output_to_mass_list/output/
A		File_conversion/Prediction_output_to_mass_list/output/CD_masslist_EAWAG_BBD-PPS_round_2.csv
A		File_conversion/Prediction_output_to_mass_list/output/CD_masslist_EAWAG_BBD-PPS_round_2b.csv
A		File_conversion/Prediction_output_to_mass_list/output/CD_masslist_combined.csv
A		File_conversion/Prediction_output_to_mass_list/output/CD_masslist_enviPath-BBD+SLUDGE_updated.csv
A		File_conversion/Prediction_output_to_mass_list/output/CD_masslist_enviPath-BBD+SOIL+SLUDGE_updated.csv
A		File_conversion/Prediction_output_to_mass_list/output/CD_masslist_enviPath-BBD+SOIL_round_2.csv
A		File_conversion/Prediction_output_to_mass_list/output/CD_masslist_enviPath-BBD+SOIL_updated.csv
A		File_conversion/Prediction_output_to_mass_list/output/CD_masslist_enviPath-BBD_round_2.csv
A		File_conversion/Prediction_output_to_mass_list/output/CD_masslist_enviPath-BBD_updated.csv
A		File_conversion/Prediction_output_to_mass_list/output/combined_overview.csv
A		File_conversion/Prediction_output_to_mass_list/output/inclusion_list_neg.csv
A		File_conversion/Prediction_output_to_mass_list/output/inclusion_list_pos.csv
A		File_conversion/Prediction_output_to_mass_list/output/max_element_count.txt
A	(dir)	File_conversion/SMILES_to_mass_and_inclusion_list/
P		File_conversion/SMILES_to_mass_and_inclusion_list/README.md Copied from readme.md
V		{File_conversion/SMILES_to_mass_and_inclusion_list ← }/smiles.txt
V		{File_conversion/SMILES_to_mass_and_inclusion_list ← }/smiles_to_mass_and_inclusion_list.py
A		LICENSE.txt
A		Makefile
A	(dir)	TP_prediction/
A		TP_prediction/README.md
A		TP_prediction/find_atom_fate.py
A		TP_prediction/find_best_TPs.py
A	(dir)	TP_prediction/input/
A		TP_prediction/input/input_structures.tsv
A		TP_prediction/util.py
P		readme.md Copied to File_conversion/SMILES_to_mass_and_inclusion_list/README.md
A		requirements.txt
V		{ → File_conversion/SMILES_to_mass_and_inclusion_list}/smiles.txt
V		{ → File_conversion/SMILES_to_mass_and_inclusion_list}/smiles_to_mass_and_inclusion_list.py

R12460:2e9999e8b851

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.gitignore

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Additional_analyses/Analyse_cutoff_thresholds/analyse_cutoff_thresholds.py

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Additional_analyses/Analyse_cutoff_thresholds/input/TP_prediction_BBD+SLUDGE_top_50.tsv

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Additional_analyses/Analyse_cutoff_thresholds/input/TP_prediction_BBD+SOIL+SLUDGE_top_50.tsv

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Additional_analyses/Analyse_cutoff_thresholds/input/TP_prediction_BBD+SOIL_top_50.tsv

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Additional_analyses/Analyse_cutoff_thresholds/input/TP_prediction_BBD_top_50.tsv

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Additional_analyses/Analyse_cutoff_thresholds/input/confirmed_TPs.txt

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Additional_analyses/Analyse_cutoff_thresholds/input/results_EAWAG-PPS.tsv

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Additional_analyses/Analyse_cutoff_thresholds/output/Cutoff_thresholds_Combined probability threshold.txt

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Additional_analyses/Analyse_cutoff_thresholds/output/Cutoff_thresholds_Generation threshold.txt

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Additional_analyses/Analyse_cutoff_thresholds/output/Cutoff_thresholds_Maximum TP threshold.txt

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Additional_analyses/Analyse_cutoff_thresholds/output/Cutoff_thresholds_Probability threshold.txt

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Additional_analyses/Analyse_cutoff_thresholds/output/TP_list_cutoff_analysis.txt

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Additional_analyses/Compare_methods/README.txt

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Additional_analyses/Compare_methods/compare_method_pps.py

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Additional_analyses/Compare_methods/input/data_dict_com_with_CAS.pickle

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Additional_analyses/Compare_methods/input/data_dict_com_without_CAS.pickle

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Additional_analyses/Compare_methods/input/found_TP_SMILES.txt

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Additional_analyses/Compare_methods/output/number_of_predicted_TPs_per_parent.tsv

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Additional_analyses/Compare_methods/output/precision_of_methods.tsv

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Additional_analyses/Compare_methods/output/predicted_and_found_TPs.csv

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Additional_analyses/Compare_methods/output/sources_of_TPs.tsv

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Additional_analyses/Compare_methods/output/used_rules.txt

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File_conversion/Prediction_output_to_mass_list/README.md

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File_conversion/Prediction_output_to_mass_list/get_mass_list_from_prediction.py

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File_conversion/Prediction_output_to_mass_list/input/SMILES_selected_comp.txt

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File_conversion/Prediction_output_to_mass_list/input/code_subst.txt

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File_conversion/Prediction_output_to_mass_list/input/name_subst.txt

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File_conversion/Prediction_output_to_mass_list/input/round 2/Eawag_PPS_BBD_results.tsv

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File_conversion/Prediction_output_to_mass_list/input/round 2/Eawag_PPS_BBD_results_edited.tsv

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File_conversion/Prediction_output_to_mass_list/input/round 2/enviPath_BBD_SOIL_results.tsv

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File_conversion/Prediction_output_to_mass_list/input/round 2/enviPath_BBD_results.tsv

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File_conversion/Prediction_output_to_mass_list/input/round 2b/Eawag_PPS_BBD_results.tsv

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File_conversion/Prediction_output_to_mass_list/input/round 2b/enviPath_BBD_SOIL_results.tsv

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File_conversion/Prediction_output_to_mass_list/input/round 2b/enviPath_BBD_results.tsv

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File_conversion/Prediction_output_to_mass_list/input/updated predictions/TP_prediction_BBD+SLUDGE_top_50.tsv

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File_conversion/Prediction_output_to_mass_list/input/updated predictions/TP_prediction_BBD+SOIL+SLUDGE_top_50.tsv

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File_conversion/Prediction_output_to_mass_list/input/updated predictions/TP_prediction_BBD+SOIL_top_50.tsv

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File_conversion/Prediction_output_to_mass_list/input/updated predictions/TP_prediction_BBD_top_50.tsv

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File_conversion/Prediction_output_to_mass_list/input/updated predictions/links.txt

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File_conversion/Prediction_output_to_mass_list/output/CD_masslist_EAWAG_BBD-PPS_round_2.csv

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File_conversion/Prediction_output_to_mass_list/output/CD_masslist_EAWAG_BBD-PPS_round_2b.csv

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File_conversion/Prediction_output_to_mass_list/output/CD_masslist_combined.csv

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File_conversion/Prediction_output_to_mass_list/output/CD_masslist_enviPath-BBD+SLUDGE_updated.csv

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File_conversion/Prediction_output_to_mass_list/output/CD_masslist_enviPath-BBD+SOIL+SLUDGE_updated.csv

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File_conversion/Prediction_output_to_mass_list/output/CD_masslist_enviPath-BBD+SOIL_round_2.csv

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File_conversion/Prediction_output_to_mass_list/output/CD_masslist_enviPath-BBD+SOIL_updated.csv

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File_conversion/Prediction_output_to_mass_list/output/CD_masslist_enviPath-BBD_round_2.csv

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File_conversion/Prediction_output_to_mass_list/output/CD_masslist_enviPath-BBD_updated.csv

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File_conversion/Prediction_output_to_mass_list/output/combined_overview.csv

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File_conversion/Prediction_output_to_mass_list/output/inclusion_list_neg.csv

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File_conversion/Prediction_output_to_mass_list/output/inclusion_list_pos.csv

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File_conversion/Prediction_output_to_mass_list/output/max_element_count.txt

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File_conversion/SMILES_to_mass_and_inclusion_list/README.md

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File_conversion/SMILES_to_mass_and_inclusion_list/smiles.txt

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File_conversion/SMILES_to_mass_and_inclusion_list/smiles_to_mass_and_inclusion_list.py

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LICENSE.txt

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Makefile

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TP_prediction/README.md

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TP_prediction/find_atom_fate.py

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TP_prediction/find_best_TPs.py

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TP_prediction/input/input_structures.tsv

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TP_prediction/util.py

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readme.md

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requirements.txt

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smiles.txt

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smiles_to_mass_and_inclusion_list.py

ADD: TP prediction, documentation2e9999e8b851Actions

Description

Details

Event Timeline

Changes (84)

R12460:2e9999e8b851

.gitignore

Additional_analyses/Analyse_cutoff_thresholds/analyse_cutoff_thresholds.py

Additional_analyses/Analyse_cutoff_thresholds/input/TP_prediction_BBD+SLUDGE_top_50.tsv

Additional_analyses/Analyse_cutoff_thresholds/input/TP_prediction_BBD+SOIL+SLUDGE_top_50.tsv

Additional_analyses/Analyse_cutoff_thresholds/input/TP_prediction_BBD+SOIL_top_50.tsv

Additional_analyses/Analyse_cutoff_thresholds/input/TP_prediction_BBD_top_50.tsv

Additional_analyses/Analyse_cutoff_thresholds/input/confirmed_TPs.txt

Additional_analyses/Analyse_cutoff_thresholds/input/results_EAWAG-PPS.tsv

Additional_analyses/Analyse_cutoff_thresholds/output/Cutoff_thresholds_Combined probability threshold.txt

Additional_analyses/Analyse_cutoff_thresholds/output/Cutoff_thresholds_Generation threshold.txt

Additional_analyses/Analyse_cutoff_thresholds/output/Cutoff_thresholds_Maximum TP threshold.txt

Additional_analyses/Analyse_cutoff_thresholds/output/Cutoff_thresholds_Probability threshold.txt

Additional_analyses/Analyse_cutoff_thresholds/output/TP_list_cutoff_analysis.txt

Additional_analyses/Compare_methods/README.txt

Additional_analyses/Compare_methods/compare_method_pps.py

Additional_analyses/Compare_methods/input/data_dict_com_with_CAS.pickle

Additional_analyses/Compare_methods/input/data_dict_com_without_CAS.pickle

Additional_analyses/Compare_methods/input/found_TP_SMILES.txt

Additional_analyses/Compare_methods/output/number_of_predicted_TPs_per_parent.tsv

Additional_analyses/Compare_methods/output/precision_of_methods.tsv

Additional_analyses/Compare_methods/output/predicted_and_found_TPs.csv

Additional_analyses/Compare_methods/output/sources_of_TPs.tsv

Additional_analyses/Compare_methods/output/used_rules.txt

File_conversion/Prediction_output_to_mass_list/README.md

File_conversion/Prediction_output_to_mass_list/get_mass_list_from_prediction.py

File_conversion/Prediction_output_to_mass_list/input/SMILES_selected_comp.txt

File_conversion/Prediction_output_to_mass_list/input/code_subst.txt

File_conversion/Prediction_output_to_mass_list/input/name_subst.txt

File_conversion/Prediction_output_to_mass_list/input/round 2/Eawag_PPS_BBD_results.tsv

File_conversion/Prediction_output_to_mass_list/input/round 2/Eawag_PPS_BBD_results_edited.tsv

File_conversion/Prediction_output_to_mass_list/input/round 2/enviPath_BBD_SOIL_results.tsv

File_conversion/Prediction_output_to_mass_list/input/round 2/enviPath_BBD_results.tsv

File_conversion/Prediction_output_to_mass_list/input/round 2b/Eawag_PPS_BBD_results.tsv

File_conversion/Prediction_output_to_mass_list/input/round 2b/enviPath_BBD_SOIL_results.tsv

File_conversion/Prediction_output_to_mass_list/input/round 2b/enviPath_BBD_results.tsv

File_conversion/Prediction_output_to_mass_list/input/updated predictions/TP_prediction_BBD+SLUDGE_top_50.tsv

File_conversion/Prediction_output_to_mass_list/input/updated predictions/TP_prediction_BBD+SOIL+SLUDGE_top_50.tsv

File_conversion/Prediction_output_to_mass_list/input/updated predictions/TP_prediction_BBD+SOIL_top_50.tsv

File_conversion/Prediction_output_to_mass_list/input/updated predictions/TP_prediction_BBD_top_50.tsv

File_conversion/Prediction_output_to_mass_list/input/updated predictions/links.txt

File_conversion/Prediction_output_to_mass_list/output/CD_masslist_EAWAG_BBD-PPS_round_2.csv

File_conversion/Prediction_output_to_mass_list/output/CD_masslist_EAWAG_BBD-PPS_round_2b.csv

File_conversion/Prediction_output_to_mass_list/output/CD_masslist_combined.csv

File_conversion/Prediction_output_to_mass_list/output/CD_masslist_enviPath-BBD+SLUDGE_updated.csv

File_conversion/Prediction_output_to_mass_list/output/CD_masslist_enviPath-BBD+SOIL+SLUDGE_updated.csv

File_conversion/Prediction_output_to_mass_list/output/CD_masslist_enviPath-BBD+SOIL_round_2.csv

File_conversion/Prediction_output_to_mass_list/output/CD_masslist_enviPath-BBD+SOIL_updated.csv

File_conversion/Prediction_output_to_mass_list/output/CD_masslist_enviPath-BBD_round_2.csv

File_conversion/Prediction_output_to_mass_list/output/CD_masslist_enviPath-BBD_updated.csv

File_conversion/Prediction_output_to_mass_list/output/combined_overview.csv

File_conversion/Prediction_output_to_mass_list/output/inclusion_list_neg.csv

File_conversion/Prediction_output_to_mass_list/output/inclusion_list_pos.csv

File_conversion/Prediction_output_to_mass_list/output/max_element_count.txt

File_conversion/SMILES_to_mass_and_inclusion_list/README.md

File_conversion/SMILES_to_mass_and_inclusion_list/smiles.txt

File_conversion/SMILES_to_mass_and_inclusion_list/smiles_to_mass_and_inclusion_list.py

LICENSE.txt

Makefile

TP_prediction/README.md

TP_prediction/find_atom_fate.py

TP_prediction/find_best_TPs.py

TP_prediction/input/input_structures.tsv

TP_prediction/util.py

readme.md

requirements.txt

smiles.txt

smiles_to_mass_and_inclusion_list.py

ADD: TP prediction, documentation
2e9999e8b851
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