Focused Library - Core Input

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

  • Solution-based/Hit to Lead/Generative Design/Reaction-based Libraries

  • Task-based/Library Prep & Design/Reaction-based Enumeration

  • Task-based/Virtual Screening - Structure-Based

  • Role-based/Medicinal Chemist

Description

This floe uses weighted ensemble molecular dynamics to sample the conformational dynamics of a target protein. Sampling is enhanced along a given set of normal modes (Tutorial: how to select normal modes as progress coordinates ). Note that the job can cost a few thousand dollars if the number of iterations for the simulation is too high (>500).

Promoted Parameters

Title in user interface (promoted name)

Inputs

Library Core Input (ui_result): Draw or load a library core to use for a virtual library enumeration. Starting with a lead molecule, edit it to include one or more Rn groups using the sketcher. Each Rgroup will be replaced with a set of reaction-specific reagents per the selection(s) below.

  • Required

  • Type: fragment_input

Reaction & Reagent Database (enum_rxndb): The name of the reaction & reagent database to use

  • Required

  • Type: file_in

Outputs

Product Dataset (products): Product dataset from the enumeration.

  • Required

  • Type: dataset_out

  • Default: libenum_products

Output Product Dataset (prod_dataset): If OFF, just counts records, but does not output them.

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

R1 Site

R1 Reagent Selection (enum_r1): A reagent selection from the sample reaction database list

  • Type: string

  • Choices: [‘’, ‘3-nitrile-pyridine:Diones_2_4’, ‘Buchwald-Hartwig:Amines’, ‘Buchwald-Hartwig:Halides_aryl’, ‘Buchwald_cross_coupling1:Amines’, ‘Buchwald_cross_coupling1:Aryl_halides’, ‘Buchwald_cross_coupling2:Amines’, ‘Buchwald_cross_coupling2:Aryl_halides’, ‘Ester_hydrolysis-amide_synthesis1:Amines’, ‘Ester_hydrolysis-amide_synthesis1:Esters’, ‘Ester_hydrolysis-amide_synthesis2:Amines’, ‘Ester_hydrolysis-amide_synthesis2:Esters’, ‘Grignard_alcohol:Halides_alkyl’, ‘Grignard_alcohol:Ketones_aldehydes’, ‘Grignard_carbonyl:Halides_alkyl_aryl’, ‘Grignard_carbonyl:Nitriles’, ‘Heck_non-terminal_vinyl:Halide_vinyl_aryls’, ‘Heck_non-terminal_vinyl:Non_terminal_vinyls’, ‘Heck_terminal_vinyl:Halide_vinyl_aryls’, ‘Heck_terminal_vinyl:Terminal_vinyls’, ‘Huisgen_disubst-alkyne:Alkyl_halides_alcohols’, ‘Huisgen_disubst-alkyne:Alkynes_disubstituted’, ‘Mitsunobu_imide:Acetylacetamides’, ‘Mitsunobu_imide:Alcohols_primary_secondary’, ‘Mitsunobu_phenol:Alcohols_primary_secondary’, ‘Mitsunobu_phenol:Phenols’, ‘Mitsunobu_sulfonamide:Alcohols_primary_secondary’, ‘Mitsunobu_sulfonamide:Sulfonamides’, ‘Mitsunobu_tetrazole_1:Alcohols_primary_secondary’, ‘Mitsunobu_tetrazole_1:Tetrazoles’, ‘Mitsunobu_tetrazole_2:Alcohols_primary_secondary’, ‘Mitsunobu_tetrazole_2:Tetrazoles’, ‘N-alkylation1:Amines’, ‘N-alkylation1:Benzyl_halides’, ‘N-alkylation2:Amines’, ‘N-alkylation2:Benzyl_halides’, ‘N-arylation_heterocycles_1:Boronic_acids_aryl’, ‘N-arylation_heterocycles_1:Pyrrole_like_nitrogens’, ‘N-arylation_heterocycles_2:Boronic_acids_aryl’, ‘N-arylation_heterocycles_2:Pyrrole_like_nitrogens’, ‘Negishi:Alkyl_halides_primary1’, ‘Negishi:Alkyl_halides_primary2’, ‘Niementowski_quinazoline:Amides_primary’, ‘Niementowski_quinazoline:Aminobenzoic_acids’, ‘O-alkylation:Benzyl_halides’, ‘O-alkylation:Phenols’, ‘O-biarylation:Aryl_bromides’, ‘O-biarylation:Phenols’, ‘Pictet-Spengler:Aldehydes’, ‘Pictet-Spengler:Beta_amino_benzenes’, ‘Reductive_amination1:Aldehydes’, ‘Reductive_amination1:Amines’, ‘Reductive_amination2:Aldehydes’, ‘Reductive_amination2:Amines’, ‘Schotten-Baumann_amide:Amines’, ‘Schotten-Baumann_amide:Carboxylic_acids’, ‘SnAr1:Amines’, ‘SnAr1:Heterohalides’, ‘SnAr2:Amines’, ‘SnAr2:Heterohalides’, ‘Sonogashira:Alkynes’, ‘Sonogashira:Bromo_iodo_vinyls_aryls’, ‘Stille:Bromo_iodo_vinyls_aryls’, ‘Stille:Halides_aryl’, ‘Suzuki_cross_coupling:Aryl_bromides’, ‘Suzuki_cross_coupling:Suzuki_boronics’, ‘Wittig:Alkyl_halides_primary’, ‘Wittig:Ketones_aldehydes’, ‘benzimidazole_derivatives_aldehyde:Aldehydes’, ‘benzimidazole_derivatives_aldehyde:Aro_6_diamines’, ‘benzimidazole_derivatives_carboxylic-acid/ester:Aro_6_diamines’, ‘benzimidazole_derivatives_carboxylic-acid/ester:Carboxylic_acids’, ‘benzofuran:Alkynes’, ‘benzofuran:Halophenols’, ‘benzothiazole:Aldehydes’, ‘benzothiazole:Aro_6_thiamines’, ‘benzothiophene:Alkynes’, ‘benzothiophene:Halomethiols’, ‘benzoxazole_arom-aldehyde:Aminophenols’, ‘benzoxazole_arom-aldehyde:Benzaldehydes’, ‘benzoxazole_carboxylic-acid:Aminophenols’, ‘benzoxazole_carboxylic-acid:Carboxylic_acids’, ‘decarboxylative_coupling:Carbonyl_benzoic_acids’, ‘decarboxylative_coupling:Halides_aryl’, ‘heteroaromatic_nuc_sub:Amines’, ‘heteroaromatic_nuc_sub:Halo_aryls_activated’, ‘imidazole:Alpha_halo_ketones’, ‘imidazole:Aryl_amidines_guanidines’, ‘indole:Alkynes’, ‘indole:Haloanilines’, ‘nucl_sub_aromatic_ortho_nitro:Amines’, ‘nucl_sub_aromatic_ortho_nitro:Ortho_nitro_halides’, ‘nucl_sub_aromatic_para_nitro:Amines’, ‘nucl_sub_aromatic_para_nitro:Para_nitro_halides’, ‘oxadiazole:Carboxylic_acids’, ‘oxadiazole:Nitriles’, ‘phthalazinone:Hydrazines’, ‘phthalazinone:Ketobenzoic_acids’, ‘piperidine_indole:Indoles’, ‘piperidine_indole:Piperidines’, ‘pyrazole:Diones_2_4’, ‘pyrazole:Hydrazines’, ‘spiro-chromanone:Ketophenols’, ‘spiro-chromanone:Piperadone_ketones’, ‘sulfon_amide:Amines’, ‘sulfon_amide:Sulfonyl_chlorides’, ‘tetrazole_connect_regioisomere_1:Alkyl_bromides’, ‘tetrazole_connect_regioisomere_1:Nitriles’, ‘tetrazole_connect_regioisomere_2:Alkyl_bromides’, ‘tetrazole_connect_regioisomere_2:Nitriles’, ‘tetrazole_terminal:Nitriles’, ‘thiazole:Alpha_halo_ketones’, ‘thiazole:Thioamides’, ‘triaryl-imidazole:Aro_ethane_diones’, ‘triaryl-imidazole:Aroaldehydes’, ‘urea:Amines’, ‘urea:Isocyanates’]

Custom R1 Reagent Name (enum_r1_custom): A custom reagent specification from the reaction & reagent database. Any specification here supersedes any selection specified by the ‘R1 Reagent Selection’ parameter above.

  • Type: string

R1 Maximum Reagents (enum_r1_max): (required) Maximum number of R1 reagents to process (0 for all)

  • Type: integer

R2 Site

R2 Reagent Name (enum_r2): A reagent selection from the sample reaction database list

  • Type: string

  • Choices: [‘’, ‘3-nitrile-pyridine:Diones_2_4’, ‘Buchwald-Hartwig:Amines’, ‘Buchwald-Hartwig:Halides_aryl’, ‘Buchwald_cross_coupling1:Amines’, ‘Buchwald_cross_coupling1:Aryl_halides’, ‘Buchwald_cross_coupling2:Amines’, ‘Buchwald_cross_coupling2:Aryl_halides’, ‘Ester_hydrolysis-amide_synthesis1:Amines’, ‘Ester_hydrolysis-amide_synthesis1:Esters’, ‘Ester_hydrolysis-amide_synthesis2:Amines’, ‘Ester_hydrolysis-amide_synthesis2:Esters’, ‘Grignard_alcohol:Halides_alkyl’, ‘Grignard_alcohol:Ketones_aldehydes’, ‘Grignard_carbonyl:Halides_alkyl_aryl’, ‘Grignard_carbonyl:Nitriles’, ‘Heck_non-terminal_vinyl:Halide_vinyl_aryls’, ‘Heck_non-terminal_vinyl:Non_terminal_vinyls’, ‘Heck_terminal_vinyl:Halide_vinyl_aryls’, ‘Heck_terminal_vinyl:Terminal_vinyls’, ‘Huisgen_disubst-alkyne:Alkyl_halides_alcohols’, ‘Huisgen_disubst-alkyne:Alkynes_disubstituted’, ‘Mitsunobu_imide:Acetylacetamides’, ‘Mitsunobu_imide:Alcohols_primary_secondary’, ‘Mitsunobu_phenol:Alcohols_primary_secondary’, ‘Mitsunobu_phenol:Phenols’, ‘Mitsunobu_sulfonamide:Alcohols_primary_secondary’, ‘Mitsunobu_sulfonamide:Sulfonamides’, ‘Mitsunobu_tetrazole_1:Alcohols_primary_secondary’, ‘Mitsunobu_tetrazole_1:Tetrazoles’, ‘Mitsunobu_tetrazole_2:Alcohols_primary_secondary’, ‘Mitsunobu_tetrazole_2:Tetrazoles’, ‘N-alkylation1:Amines’, ‘N-alkylation1:Benzyl_halides’, ‘N-alkylation2:Amines’, ‘N-alkylation2:Benzyl_halides’, ‘N-arylation_heterocycles_1:Boronic_acids_aryl’, ‘N-arylation_heterocycles_1:Pyrrole_like_nitrogens’, ‘N-arylation_heterocycles_2:Boronic_acids_aryl’, ‘N-arylation_heterocycles_2:Pyrrole_like_nitrogens’, ‘Negishi:Alkyl_halides_primary1’, ‘Negishi:Alkyl_halides_primary2’, ‘Niementowski_quinazoline:Amides_primary’, ‘Niementowski_quinazoline:Aminobenzoic_acids’, ‘O-alkylation:Benzyl_halides’, ‘O-alkylation:Phenols’, ‘O-biarylation:Aryl_bromides’, ‘O-biarylation:Phenols’, ‘Pictet-Spengler:Aldehydes’, ‘Pictet-Spengler:Beta_amino_benzenes’, ‘Reductive_amination1:Aldehydes’, ‘Reductive_amination1:Amines’, ‘Reductive_amination2:Aldehydes’, ‘Reductive_amination2:Amines’, ‘Schotten-Baumann_amide:Amines’, ‘Schotten-Baumann_amide:Carboxylic_acids’, ‘SnAr1:Amines’, ‘SnAr1:Heterohalides’, ‘SnAr2:Amines’, ‘SnAr2:Heterohalides’, ‘Sonogashira:Alkynes’, ‘Sonogashira:Bromo_iodo_vinyls_aryls’, ‘Stille:Bromo_iodo_vinyls_aryls’, ‘Stille:Halides_aryl’, ‘Suzuki_cross_coupling:Aryl_bromides’, ‘Suzuki_cross_coupling:Suzuki_boronics’, ‘Wittig:Alkyl_halides_primary’, ‘Wittig:Ketones_aldehydes’, ‘benzimidazole_derivatives_aldehyde:Aldehydes’, ‘benzimidazole_derivatives_aldehyde:Aro_6_diamines’, ‘benzimidazole_derivatives_carboxylic-acid/ester:Aro_6_diamines’, ‘benzimidazole_derivatives_carboxylic-acid/ester:Carboxylic_acids’, ‘benzofuran:Alkynes’, ‘benzofuran:Halophenols’, ‘benzothiazole:Aldehydes’, ‘benzothiazole:Aro_6_thiamines’, ‘benzothiophene:Alkynes’, ‘benzothiophene:Halomethiols’, ‘benzoxazole_arom-aldehyde:Aminophenols’, ‘benzoxazole_arom-aldehyde:Benzaldehydes’, ‘benzoxazole_carboxylic-acid:Aminophenols’, ‘benzoxazole_carboxylic-acid:Carboxylic_acids’, ‘decarboxylative_coupling:Carbonyl_benzoic_acids’, ‘decarboxylative_coupling:Halides_aryl’, ‘heteroaromatic_nuc_sub:Amines’, ‘heteroaromatic_nuc_sub:Halo_aryls_activated’, ‘imidazole:Alpha_halo_ketones’, ‘imidazole:Aryl_amidines_guanidines’, ‘indole:Alkynes’, ‘indole:Haloanilines’, ‘nucl_sub_aromatic_ortho_nitro:Amines’, ‘nucl_sub_aromatic_ortho_nitro:Ortho_nitro_halides’, ‘nucl_sub_aromatic_para_nitro:Amines’, ‘nucl_sub_aromatic_para_nitro:Para_nitro_halides’, ‘oxadiazole:Carboxylic_acids’, ‘oxadiazole:Nitriles’, ‘phthalazinone:Hydrazines’, ‘phthalazinone:Ketobenzoic_acids’, ‘piperidine_indole:Indoles’, ‘piperidine_indole:Piperidines’, ‘pyrazole:Diones_2_4’, ‘pyrazole:Hydrazines’, ‘spiro-chromanone:Ketophenols’, ‘spiro-chromanone:Piperadone_ketones’, ‘sulfon_amide:Amines’, ‘sulfon_amide:Sulfonyl_chlorides’, ‘tetrazole_connect_regioisomere_1:Alkyl_bromides’, ‘tetrazole_connect_regioisomere_1:Nitriles’, ‘tetrazole_connect_regioisomere_2:Alkyl_bromides’, ‘tetrazole_connect_regioisomere_2:Nitriles’, ‘tetrazole_terminal:Nitriles’, ‘thiazole:Alpha_halo_ketones’, ‘thiazole:Thioamides’, ‘triaryl-imidazole:Aro_ethane_diones’, ‘triaryl-imidazole:Aroaldehydes’, ‘urea:Amines’, ‘urea:Isocyanates’]

Custom R2 Reagent Name (enum_r2_custom): A custom reagent specification from the reaction & reagent database. Any specification here supersedes any selection specified by the ‘R2 Reagent Selection’ parameter above.

  • Type: string

R2 Maximum Reagents (enum_r2_max): (required) Maximum number of R2 reagents to process (0 for all)

  • Type: integer

R3 Site

R3 Reagent Name (enum_r3): A reagent selection from the sample reaction database list

  • Type: string

  • Choices: [‘’, ‘3-nitrile-pyridine:Diones_2_4’, ‘Buchwald-Hartwig:Amines’, ‘Buchwald-Hartwig:Halides_aryl’, ‘Buchwald_cross_coupling1:Amines’, ‘Buchwald_cross_coupling1:Aryl_halides’, ‘Buchwald_cross_coupling2:Amines’, ‘Buchwald_cross_coupling2:Aryl_halides’, ‘Ester_hydrolysis-amide_synthesis1:Amines’, ‘Ester_hydrolysis-amide_synthesis1:Esters’, ‘Ester_hydrolysis-amide_synthesis2:Amines’, ‘Ester_hydrolysis-amide_synthesis2:Esters’, ‘Grignard_alcohol:Halides_alkyl’, ‘Grignard_alcohol:Ketones_aldehydes’, ‘Grignard_carbonyl:Halides_alkyl_aryl’, ‘Grignard_carbonyl:Nitriles’, ‘Heck_non-terminal_vinyl:Halide_vinyl_aryls’, ‘Heck_non-terminal_vinyl:Non_terminal_vinyls’, ‘Heck_terminal_vinyl:Halide_vinyl_aryls’, ‘Heck_terminal_vinyl:Terminal_vinyls’, ‘Huisgen_disubst-alkyne:Alkyl_halides_alcohols’, ‘Huisgen_disubst-alkyne:Alkynes_disubstituted’, ‘Mitsunobu_imide:Acetylacetamides’, ‘Mitsunobu_imide:Alcohols_primary_secondary’, ‘Mitsunobu_phenol:Alcohols_primary_secondary’, ‘Mitsunobu_phenol:Phenols’, ‘Mitsunobu_sulfonamide:Alcohols_primary_secondary’, ‘Mitsunobu_sulfonamide:Sulfonamides’, ‘Mitsunobu_tetrazole_1:Alcohols_primary_secondary’, ‘Mitsunobu_tetrazole_1:Tetrazoles’, ‘Mitsunobu_tetrazole_2:Alcohols_primary_secondary’, ‘Mitsunobu_tetrazole_2:Tetrazoles’, ‘N-alkylation1:Amines’, ‘N-alkylation1:Benzyl_halides’, ‘N-alkylation2:Amines’, ‘N-alkylation2:Benzyl_halides’, ‘N-arylation_heterocycles_1:Boronic_acids_aryl’, ‘N-arylation_heterocycles_1:Pyrrole_like_nitrogens’, ‘N-arylation_heterocycles_2:Boronic_acids_aryl’, ‘N-arylation_heterocycles_2:Pyrrole_like_nitrogens’, ‘Negishi:Alkyl_halides_primary1’, ‘Negishi:Alkyl_halides_primary2’, ‘Niementowski_quinazoline:Amides_primary’, ‘Niementowski_quinazoline:Aminobenzoic_acids’, ‘O-alkylation:Benzyl_halides’, ‘O-alkylation:Phenols’, ‘O-biarylation:Aryl_bromides’, ‘O-biarylation:Phenols’, ‘Pictet-Spengler:Aldehydes’, ‘Pictet-Spengler:Beta_amino_benzenes’, ‘Reductive_amination1:Aldehydes’, ‘Reductive_amination1:Amines’, ‘Reductive_amination2:Aldehydes’, ‘Reductive_amination2:Amines’, ‘Schotten-Baumann_amide:Amines’, ‘Schotten-Baumann_amide:Carboxylic_acids’, ‘SnAr1:Amines’, ‘SnAr1:Heterohalides’, ‘SnAr2:Amines’, ‘SnAr2:Heterohalides’, ‘Sonogashira:Alkynes’, ‘Sonogashira:Bromo_iodo_vinyls_aryls’, ‘Stille:Bromo_iodo_vinyls_aryls’, ‘Stille:Halides_aryl’, ‘Suzuki_cross_coupling:Aryl_bromides’, ‘Suzuki_cross_coupling:Suzuki_boronics’, ‘Wittig:Alkyl_halides_primary’, ‘Wittig:Ketones_aldehydes’, ‘benzimidazole_derivatives_aldehyde:Aldehydes’, ‘benzimidazole_derivatives_aldehyde:Aro_6_diamines’, ‘benzimidazole_derivatives_carboxylic-acid/ester:Aro_6_diamines’, ‘benzimidazole_derivatives_carboxylic-acid/ester:Carboxylic_acids’, ‘benzofuran:Alkynes’, ‘benzofuran:Halophenols’, ‘benzothiazole:Aldehydes’, ‘benzothiazole:Aro_6_thiamines’, ‘benzothiophene:Alkynes’, ‘benzothiophene:Halomethiols’, ‘benzoxazole_arom-aldehyde:Aminophenols’, ‘benzoxazole_arom-aldehyde:Benzaldehydes’, ‘benzoxazole_carboxylic-acid:Aminophenols’, ‘benzoxazole_carboxylic-acid:Carboxylic_acids’, ‘decarboxylative_coupling:Carbonyl_benzoic_acids’, ‘decarboxylative_coupling:Halides_aryl’, ‘heteroaromatic_nuc_sub:Amines’, ‘heteroaromatic_nuc_sub:Halo_aryls_activated’, ‘imidazole:Alpha_halo_ketones’, ‘imidazole:Aryl_amidines_guanidines’, ‘indole:Alkynes’, ‘indole:Haloanilines’, ‘nucl_sub_aromatic_ortho_nitro:Amines’, ‘nucl_sub_aromatic_ortho_nitro:Ortho_nitro_halides’, ‘nucl_sub_aromatic_para_nitro:Amines’, ‘nucl_sub_aromatic_para_nitro:Para_nitro_halides’, ‘oxadiazole:Carboxylic_acids’, ‘oxadiazole:Nitriles’, ‘phthalazinone:Hydrazines’, ‘phthalazinone:Ketobenzoic_acids’, ‘piperidine_indole:Indoles’, ‘piperidine_indole:Piperidines’, ‘pyrazole:Diones_2_4’, ‘pyrazole:Hydrazines’, ‘spiro-chromanone:Ketophenols’, ‘spiro-chromanone:Piperadone_ketones’, ‘sulfon_amide:Amines’, ‘sulfon_amide:Sulfonyl_chlorides’, ‘tetrazole_connect_regioisomere_1:Alkyl_bromides’, ‘tetrazole_connect_regioisomere_1:Nitriles’, ‘tetrazole_connect_regioisomere_2:Alkyl_bromides’, ‘tetrazole_connect_regioisomere_2:Nitriles’, ‘tetrazole_terminal:Nitriles’, ‘thiazole:Alpha_halo_ketones’, ‘thiazole:Thioamides’, ‘triaryl-imidazole:Aro_ethane_diones’, ‘triaryl-imidazole:Aroaldehydes’, ‘urea:Amines’, ‘urea:Isocyanates’]

Custom R3 Reagent Name (enum_r3_custom): A custom reagent specification from the reaction & reagent database. Any specification here supersedes any selection specified by the ‘R3 Reagent Selection’ parameter above.

  • Type: string

R3 Maximum Reagents (enum_r3_max): (required) Maximum number of R3 reagents to process (0 for all)

  • Type: integer

R4 Site

R4 Reagent Name (enum_r4): A reagent selection from the sample reaction database list

  • Type: string

  • Choices: [‘’, ‘3-nitrile-pyridine:Diones_2_4’, ‘Buchwald-Hartwig:Amines’, ‘Buchwald-Hartwig:Halides_aryl’, ‘Buchwald_cross_coupling1:Amines’, ‘Buchwald_cross_coupling1:Aryl_halides’, ‘Buchwald_cross_coupling2:Amines’, ‘Buchwald_cross_coupling2:Aryl_halides’, ‘Ester_hydrolysis-amide_synthesis1:Amines’, ‘Ester_hydrolysis-amide_synthesis1:Esters’, ‘Ester_hydrolysis-amide_synthesis2:Amines’, ‘Ester_hydrolysis-amide_synthesis2:Esters’, ‘Grignard_alcohol:Halides_alkyl’, ‘Grignard_alcohol:Ketones_aldehydes’, ‘Grignard_carbonyl:Halides_alkyl_aryl’, ‘Grignard_carbonyl:Nitriles’, ‘Heck_non-terminal_vinyl:Halide_vinyl_aryls’, ‘Heck_non-terminal_vinyl:Non_terminal_vinyls’, ‘Heck_terminal_vinyl:Halide_vinyl_aryls’, ‘Heck_terminal_vinyl:Terminal_vinyls’, ‘Huisgen_disubst-alkyne:Alkyl_halides_alcohols’, ‘Huisgen_disubst-alkyne:Alkynes_disubstituted’, ‘Mitsunobu_imide:Acetylacetamides’, ‘Mitsunobu_imide:Alcohols_primary_secondary’, ‘Mitsunobu_phenol:Alcohols_primary_secondary’, ‘Mitsunobu_phenol:Phenols’, ‘Mitsunobu_sulfonamide:Alcohols_primary_secondary’, ‘Mitsunobu_sulfonamide:Sulfonamides’, ‘Mitsunobu_tetrazole_1:Alcohols_primary_secondary’, ‘Mitsunobu_tetrazole_1:Tetrazoles’, ‘Mitsunobu_tetrazole_2:Alcohols_primary_secondary’, ‘Mitsunobu_tetrazole_2:Tetrazoles’, ‘N-alkylation1:Amines’, ‘N-alkylation1:Benzyl_halides’, ‘N-alkylation2:Amines’, ‘N-alkylation2:Benzyl_halides’, ‘N-arylation_heterocycles_1:Boronic_acids_aryl’, ‘N-arylation_heterocycles_1:Pyrrole_like_nitrogens’, ‘N-arylation_heterocycles_2:Boronic_acids_aryl’, ‘N-arylation_heterocycles_2:Pyrrole_like_nitrogens’, ‘Negishi:Alkyl_halides_primary1’, ‘Negishi:Alkyl_halides_primary2’, ‘Niementowski_quinazoline:Amides_primary’, ‘Niementowski_quinazoline:Aminobenzoic_acids’, ‘O-alkylation:Benzyl_halides’, ‘O-alkylation:Phenols’, ‘O-biarylation:Aryl_bromides’, ‘O-biarylation:Phenols’, ‘Pictet-Spengler:Aldehydes’, ‘Pictet-Spengler:Beta_amino_benzenes’, ‘Reductive_amination1:Aldehydes’, ‘Reductive_amination1:Amines’, ‘Reductive_amination2:Aldehydes’, ‘Reductive_amination2:Amines’, ‘Schotten-Baumann_amide:Amines’, ‘Schotten-Baumann_amide:Carboxylic_acids’, ‘SnAr1:Amines’, ‘SnAr1:Heterohalides’, ‘SnAr2:Amines’, ‘SnAr2:Heterohalides’, ‘Sonogashira:Alkynes’, ‘Sonogashira:Bromo_iodo_vinyls_aryls’, ‘Stille:Bromo_iodo_vinyls_aryls’, ‘Stille:Halides_aryl’, ‘Suzuki_cross_coupling:Aryl_bromides’, ‘Suzuki_cross_coupling:Suzuki_boronics’, ‘Wittig:Alkyl_halides_primary’, ‘Wittig:Ketones_aldehydes’, ‘benzimidazole_derivatives_aldehyde:Aldehydes’, ‘benzimidazole_derivatives_aldehyde:Aro_6_diamines’, ‘benzimidazole_derivatives_carboxylic-acid/ester:Aro_6_diamines’, ‘benzimidazole_derivatives_carboxylic-acid/ester:Carboxylic_acids’, ‘benzofuran:Alkynes’, ‘benzofuran:Halophenols’, ‘benzothiazole:Aldehydes’, ‘benzothiazole:Aro_6_thiamines’, ‘benzothiophene:Alkynes’, ‘benzothiophene:Halomethiols’, ‘benzoxazole_arom-aldehyde:Aminophenols’, ‘benzoxazole_arom-aldehyde:Benzaldehydes’, ‘benzoxazole_carboxylic-acid:Aminophenols’, ‘benzoxazole_carboxylic-acid:Carboxylic_acids’, ‘decarboxylative_coupling:Carbonyl_benzoic_acids’, ‘decarboxylative_coupling:Halides_aryl’, ‘heteroaromatic_nuc_sub:Amines’, ‘heteroaromatic_nuc_sub:Halo_aryls_activated’, ‘imidazole:Alpha_halo_ketones’, ‘imidazole:Aryl_amidines_guanidines’, ‘indole:Alkynes’, ‘indole:Haloanilines’, ‘nucl_sub_aromatic_ortho_nitro:Amines’, ‘nucl_sub_aromatic_ortho_nitro:Ortho_nitro_halides’, ‘nucl_sub_aromatic_para_nitro:Amines’, ‘nucl_sub_aromatic_para_nitro:Para_nitro_halides’, ‘oxadiazole:Carboxylic_acids’, ‘oxadiazole:Nitriles’, ‘phthalazinone:Hydrazines’, ‘phthalazinone:Ketobenzoic_acids’, ‘piperidine_indole:Indoles’, ‘piperidine_indole:Piperidines’, ‘pyrazole:Diones_2_4’, ‘pyrazole:Hydrazines’, ‘spiro-chromanone:Ketophenols’, ‘spiro-chromanone:Piperadone_ketones’, ‘sulfon_amide:Amines’, ‘sulfon_amide:Sulfonyl_chlorides’, ‘tetrazole_connect_regioisomere_1:Alkyl_bromides’, ‘tetrazole_connect_regioisomere_1:Nitriles’, ‘tetrazole_connect_regioisomere_2:Alkyl_bromides’, ‘tetrazole_connect_regioisomere_2:Nitriles’, ‘tetrazole_terminal:Nitriles’, ‘thiazole:Alpha_halo_ketones’, ‘thiazole:Thioamides’, ‘triaryl-imidazole:Aro_ethane_diones’, ‘triaryl-imidazole:Aroaldehydes’, ‘urea:Amines’, ‘urea:Isocyanates’]

Custom R4 Reagent Name (enum_r4_custom): A custom reagent specification from the reaction & reagent database. Any specification here supersedes any selection specified by the ‘R4 Reagent Selection’ parameter above.

  • Type: string

R4 Maximum Reagents (enum_r4_max): (required) Maximum number of R4 reagents to process (0 for all)

  • Type: integer

Enumeration Options

Core ID (enum_coreid): An optional specification of the name for the library core. If explicitly provided, this name will supersede any molecule name for the core that may be present. If not provided, the molecule name of the core is used. When sketching a molecule de novo, this field should be specified to give the library core a name. The core molecule name is incorporated into the name of each enumerated product.

  • Type: string

Output Molecule Fieldname (enum_outmol): An (optional) output molecule fieldname, or blank to suppress

  • Type: string

  • Default: Product

Max Products (enum_prod_max): The maximum number of enumerated products allowed to be generated. If the Rgroup reagent limits chosen would generate more than this number of products, the floe will fail.

  • Required

  • Type: integer

  • Default: 1000000

Focused Library Filtering Options

Filter Products (enum_prod_filter): If ON, performs filtering on the generated products

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Product Filter (enum_prod_filtertype): Default type of molecule filter to apply to the generated products

  • Type: string

  • Default: BlockBuster

  • Choices: [‘Lead’, ‘Drug’, ‘BlockBuster’, ‘BlockBuster+PAINS’, ‘PAINS’, ‘Custom’]

Custom Product Filter (enum_prod_filterfile): If filtering is ON and set to [Custom], a filter file resource to use for custom product filtering

  • Type: file_in

Product Filter Summary Report (enum_prod_filtersummary): if ON, will generate a summary report of the rules that filtered product molecules

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Focused Library Property Generation

Compute Product Properties (enum_prod_props): Which molecule properties to calculate

  • Type: string

  • Default: []

  • Choices: [‘HeavyAtoms’, ‘MedChemInterest’, ‘MolComplexity’, ‘MolWeight’, ‘TPSA’, ‘XLogP’]

Advanced Enumeration Options

Duplicates Dataset (duplicates): Duplicates generated from the enumeration.

  • Type: dataset_out

  • Default: libenum_duplicates

Output Duplicate Dataset (dupe_dataset): If OFF, just counts records, but does not output them.

  • Required

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Failures Dataset (failures): Failures generated from the enumeration.

  • Type: dataset_out

  • Default: libenum_failures

Output Failure Dataset (fail_dataset): If OFF, just counts records, but does not output them.

  • Required

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Sample Seed (enum_sampleseed): Use the specified random seed for any sampling activities

  • Type: integer

Sample Reagents (enum_samplepcnt): Sample this percentage of the total reagents available, capped by the Maximum Reagents total

  • Type: integer

  • Default: 100

Verbosity (enum_verbosity): Sets the output logging verbosity

  • Type: string

  • Default: warning

  • Choices: [‘info’, ‘warning’, ‘error’, ‘debug’, ‘ddebug’]

Advanced Product Options

Check Valences (enum_checkval): How to handle valence issues for the final products: reject: reject valence errors, allow: ignore valence errors, fix: repair valence issues

  • Required

  • Type: string

  • Default: fix

  • Choices: [‘ignore’, ‘fix’, ‘reject’]

Dedupe Products (enum_dedupe): Simple canonical product SMI deduplication, or suppress if downstream floes will deduplicate

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Dedupe Products Memory (enum_dedupe_mem): Product deduplication may require significant memory, specify the desired amount in Mb

  • Type: decimal

  • Default: 10240

Classifier Memory Limit (enum_classifiermem): The memory limit for the reaction classifier - may need to be increased for large R&R databases

  • Required

  • Type: decimal

  • Default: 10240