@@ -502,7 +502,7 @@ <h1>Source code for torch_molecule.datasets.load_hf_dataset</h1><div class="high
502502< span class ="sd "> local_dir : str, optional</ span >
503503< span class ="sd "> Path where the data should be saved, by default "torchmol_data"</ span >
504504< span class ="sd "> target_cols : List[str], optional</ span >
505- < span class ="sd "> List of target column names, by default ["ABCB1", "ABL1", "ADRA1D", "ADRA2B", "ADRB2", "CA12", "CA2", "CA9", "CACNA1H", "CDK2", "CHRM1", "CHRM3", "CHRM4", "CNR1", "CYP1A2", "CYP2C19", "CYP2C9", "CYP2D6", "CYP3A4", "DRD2", "DRD3", "DRD4", "EGFR", "ESR1", "FLT1", "HRH1", "HTR1A", "HTR2A", "HTR2B", "HTR2C", "HTR6", "KCNH2", "KDR", "LCK", "MCL1", "OPRK1", "PPARG", "PTGS1", "SIGMAR1", "SLC6A2", "SLC6A4"] </ span >
505+ < span class ="sd "> List of target column names, by default all tasks </ span >
506506< span class ="sd "> return_local_data_path : bool, optional</ span >
507507< span class ="sd "> Whether to return the local data path, by default False</ span >
508508< span class ="sd "> </ span >
@@ -535,7 +535,7 @@ <h1>Source code for torch_molecule.datasets.load_hf_dataset</h1><div class="high
535535< a class ="viewcode-back " href ="../../../dataset.html#torch_molecule.datasets.load_toxcast "> [docs]</ a >
536536< span class ="k "> def</ span > < span class ="w "> </ span > < span class ="nf "> load_toxcast</ span > < span class ="p "> (</ span >
537537 < span class ="n "> local_dir</ span > < span class ="p "> :</ span > < span class ="nb "> str</ span > < span class ="o "> =</ span > < span class ="s2 "> "torchmol_data"</ span > < span class ="p "> ,</ span >
538- < span class ="n "> target_cols</ span > < span class ="p "> :</ span > < span class ="n "> Optional </ span > < span class =" p " > [ </ span > < span class =" n " > List</ span > < span class ="p "> [</ span > < span class ="nb "> str</ span > < span class ="p "> ]] </ span > < span class ="o "> =</ span > < span class ="kc " > None </ span > < span class ="p "> ,</ span >
538+ < span class ="n "> target_cols</ span > < span class ="p "> :</ span > < span class ="n "> List</ span > < span class ="p "> [</ span > < span class ="nb "> str</ span > < span class ="p "> ]</ span > < span class ="o "> =</ span > < span class ="n " > TOXCAST_TASKS </ span > < span class ="p "> ,</ span >
539539 < span class ="n "> return_local_data_path</ span > < span class ="p "> :</ span > < span class ="nb "> bool</ span > < span class ="o "> =</ span > < span class ="kc "> False</ span > < span class ="p "> ,</ span >
540540< span class ="p "> ):</ span >
541541< span class ="w "> </ span > < span class ="sd "> """</ span >
@@ -548,7 +548,7 @@ <h1>Source code for torch_molecule.datasets.load_hf_dataset</h1><div class="high
548548< span class ="sd "> local_dir : str, optional</ span >
549549< span class ="sd "> Path where the data should be saved, by default "torchmol_data"</ span >
550550< span class ="sd "> target_cols : List[str], optional</ span >
551- < span class ="sd "> List of target column names, by default None (i.e., all tasks) </ span >
551+ < span class ="sd "> List of target column names, by default all tasks</ span >
552552< span class ="sd "> return_local_data_path : bool, optional</ span >
553553< span class ="sd "> Whether to return the local data path, by default False</ span >
554554< span class ="sd "> </ span >
@@ -563,9 +563,6 @@ <h1>Source code for torch_molecule.datasets.load_hf_dataset</h1><div class="high
563563< span class ="sd "> - property_numpy: 2D numpy array with properties (rows=molecules, cols=targets)</ span >
564564< span class ="sd "> - local_data_path: Path where the data is saved</ span >
565565< span class ="sd "> """</ span >
566- < span class ="k "> if</ span > < span class ="n "> target_cols</ span > < span class ="ow "> is</ span > < span class ="kc "> None</ span > < span class ="p "> :</ span >
567- < span class ="n "> target_cols</ span > < span class ="o "> =</ span > < span class ="n "> TOXCAST_TASKS</ span > < span class ="o "> .</ span > < span class ="n "> copy</ span > < span class ="p "> ()</ span >
568-
569566 < span class ="n "> smiles_list</ span > < span class ="p "> ,</ span > < span class ="n "> property_numpy</ span > < span class ="p "> ,</ span > < span class ="n "> local_data_path</ span > < span class ="o "> =</ span > < span class ="n "> _load_from_hf</ span > < span class ="p "> (</ span >
570567 < span class ="n "> repo_id</ span > < span class ="o "> =</ span > < span class ="s2 "> "liuganghuggingface/toxcast"</ span > < span class ="p "> ,</ span >
571568 < span class ="n "> filename</ span > < span class ="o "> =</ span > < span class ="s2 "> "toxcast_data.csv.gz"</ span > < span class ="p "> ,</ span >
@@ -585,7 +582,7 @@ <h1>Source code for torch_molecule.datasets.load_hf_dataset</h1><div class="high
585582< a class ="viewcode-back " href ="../../../dataset.html#torch_molecule.datasets.load_admet "> [docs]</ a >
586583< span class ="k "> def</ span > < span class ="w "> </ span > < span class ="nf "> load_admet</ span > < span class ="p "> (</ span >
587584 < span class ="n "> local_dir</ span > < span class ="p "> :</ span > < span class ="nb "> str</ span > < span class ="o "> =</ span > < span class ="s2 "> "torchmol_data"</ span > < span class ="p "> ,</ span >
588- < span class ="n "> target_cols</ span > < span class ="p "> :</ span > < span class ="n "> Optional</ span > < span class ="p "> [</ span > < span class ="n "> List</ span > < span class ="p "> [</ span > < span class ="nb "> str</ span > < span class ="p "> ]]</ span > < span class ="o "> =</ span > < span class ="kc "> None</ span > < span class ="p "> ,</ span >
585+ < span class ="n "> target_cols</ span > < span class ="p "> :</ span > < span class ="n "> List</ span > < span class ="p "> [</ span > < span class ="nb "> str</ span > < span class ="p "> ]</ span > < span class ="o "> =</ span > < span class ="p "> [</ span > < span class ="s2 "> "AMES"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "BBB_Martins"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "Bioavailability_Ma"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "CYP1A2_Veith"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "CYP2C19_Veith"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "CYP2C9_Substrate_CarbonMangels"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "CYP2C9_Veith"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "CYP2D6_Substrate_CarbonMangels"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "CYP2D6_Veith"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "CYP3A4_Substrate_CarbonMangels"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "CYP3A4_Veith"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "Caco2_Wang"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "Carcinogens_Lagunin"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "Clearance_Hepatocyte_AZ"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "Clearance_Microsome_AZ"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "ClinTox"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "DILI"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "HIA_Hou"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "Half_Life_Obach"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "HydrationFreeEnergy_FreeSolv"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "LD50_Zhu"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "Lipophilicity_AstraZeneca"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "NR-AR-LBD"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "NR-AR"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "NR-AhR"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "NR-Aromatase"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "NR-ER-LBD"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "NR-ER"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "NR-PPAR-gamma"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "PAMPA_NCATS"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "PPBR_AZ"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "Pgp_Broccatelli"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "SR-ARE"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "SR-ATAD5"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "SR-HSE"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "SR-MMP"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "SR-p53"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "Skin_Reaction"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "Solubility_AqSolDB"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "VDss_Lombardo"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "hERG"</ span > < span class ="p "> ],</ span >
589586 < span class ="n "> return_local_data_path</ span > < span class ="p "> :</ span > < span class ="nb "> bool</ span > < span class ="o "> =</ span > < span class ="kc "> False</ span > < span class ="p "> ,</ span >
590587< span class ="p "> ):</ span >
591588< span class ="w "> </ span > < span class ="sd "> """</ span >
@@ -598,7 +595,7 @@ <h1>Source code for torch_molecule.datasets.load_hf_dataset</h1><div class="high
598595< span class ="sd "> local_dir : str, optional</ span >
599596< span class ="sd "> Path where the data should be saved, by default "torchmol_data"</ span >
600597< span class ="sd "> target_cols : List[str], optional</ span >
601- < span class ="sd "> List of target column names, by default None (i.e., all tasks) </ span >
598+ < span class ="sd "> List of target column names, by default all tasks</ span >
602599< span class ="sd "> return_local_data_path : bool, optional</ span >
603600< span class ="sd "> Whether to return the local data path, by default False</ span >
604601< span class ="sd "> </ span >
@@ -613,9 +610,6 @@ <h1>Source code for torch_molecule.datasets.load_hf_dataset</h1><div class="high
613610< span class ="sd "> - property_numpy: 2D numpy array with properties (rows=molecules, cols=targets)</ span >
614611< span class ="sd "> - local_data_path: Path where the data is saved</ span >
615612< span class ="sd "> """</ span >
616- < span class ="k "> if</ span > < span class ="n "> target_cols</ span > < span class ="ow "> is</ span > < span class ="kc "> None</ span > < span class ="p "> :</ span >
617- < span class ="n "> target_cols</ span > < span class ="o "> =</ span > < span class ="p "> [</ span > < span class ="s2 "> "AMES"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "BBB_Martins"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "Bioavailability_Ma"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "CYP1A2_Veith"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "CYP2C19_Veith"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "CYP2C9_Substrate_CarbonMangels"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "CYP2C9_Veith"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "CYP2D6_Substrate_CarbonMangels"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "CYP2D6_Veith"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "CYP3A4_Substrate_CarbonMangels"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "CYP3A4_Veith"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "Caco2_Wang"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "Carcinogens_Lagunin"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "Clearance_Hepatocyte_AZ"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "Clearance_Microsome_AZ"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "ClinTox"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "DILI"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "HIA_Hou"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "Half_Life_Obach"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "HydrationFreeEnergy_FreeSolv"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "LD50_Zhu"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "Lipophilicity_AstraZeneca"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "NR-AR-LBD"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "NR-AR"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "NR-AhR"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "NR-Aromatase"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "NR-ER-LBD"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "NR-ER"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "NR-PPAR-gamma"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "PAMPA_NCATS"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "PPBR_AZ"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "Pgp_Broccatelli"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "SR-ARE"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "SR-ATAD5"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "SR-HSE"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "SR-MMP"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "SR-p53"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "Skin_Reaction"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "Solubility_AqSolDB"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "VDss_Lombardo"</ span > < span class ="p "> ,</ span > < span class ="s2 "> "hERG"</ span > < span class ="p "> ]</ span >
618-
619613 < span class ="n "> smiles_list</ span > < span class ="p "> ,</ span > < span class ="n "> property_numpy</ span > < span class ="p "> ,</ span > < span class ="n "> local_data_path</ span > < span class ="o "> =</ span > < span class ="n "> _load_from_hf</ span > < span class ="p "> (</ span >
620614 < span class ="n "> repo_id</ span > < span class ="o "> =</ span > < span class ="s2 "> "liuganghuggingface/admet"</ span > < span class ="p "> ,</ span >
621615 < span class ="n "> filename</ span > < span class ="o "> =</ span > < span class ="s2 "> "admet.csv"</ span > < span class ="p "> ,</ span >
0 commit comments