Focused Library - Reagent Join

Category Paths

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

  • Solution-based/Hit to Lead/Generative Design/Fragment-based

  • Task-based/Virtual Screening - Structure-Based

  • Role-based/Medicinal Chemist

Description

This floe retrieves and applies the selected reagents from the specified Reaction & Reagent Database to a user-specified site on a lead molecule.

Promoted Parameters

Title in user interface (promoted name)

Inputs

Lead Molecule (coremol): Input lead molecule for joining reagents: select a specific site in the Sketcher.

  • Required

  • Type: fragment_input

Reaction & Reagent Database (rxndb): The name of the Reaction & Reagent Database to use.

  • Required

  • Type: file_in

Outputs

Output Data (outdata): If OFF, just counts records, but does not output them.

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Output Dataset (output): Output dataset containing retrieved reagents.

  • Required

  • Type: dataset_out

  • Default: Reaction_reagents

Output Mol Field (outmolfield): Desired name of the output structure field containing the joined products.

  • Type: field_parameter::mol

Output SMI File Resource (smifile): If provided, saves the extracted reagents as a simple SMILES file resource.

  • Type: file_out

Output CSV File Resource (csvfile): If provided, saves the extracted reagents as a simple CSV file resource.

  • Type: file_out

Reagent Join Options

Reagent Class (reagclass): A fully qualified reagent classification from the sample Reaction & Reagent 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:Boronic_acids_aryl’, ‘N-arylation_heterocycles: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 Reagent Class (customreagclass): A fully qualified reagent specification from the Reaction & Reagent Database. Any value for this parameter supersedes a Reagent Class selection above.

  • Type: string

Maximum Reagents (maxreagents): Limit for the number of reagents to extract.

  • Type: integer

Focused Library Filtering Options

Filter Reagents (filter_ureag): If ON, performs filtering on the unprepared reagents from the Reaction & Reagent Database.

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Custom Reagent Filter (filter_ureag_file): If reagent filtering is active AND a filter file is provided, the unprepared reagents will be filtered using the designated custom filter.

  • Type: file_in

Filter Prepared Reagents (filter_preag): If ON, performs filtering on the prepared reagents from the Reaction & Reagent Database.

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Custom Prepared Reagent Filter (filter_preag_file): If prepared reagent filtering is active AND a filter file is provided, the prepared reagents will be filtered using the designated custom filter.

  • Type: file_in

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

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Custom Product Filter (prod_filter_file): Filter file to use for custom product filtering.

  • Type: file_in

Product Filter (prod_filter_type): The named molecule filter type to apply to the generated products unless a custom product filter file is provided.

  • Type: string

  • Default: BlockBuster

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

Mol Filter Summary Report (filter_summary): If ON, will generate a summary report of the rules that filtered molecules.

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Focused Library Property Generation

Compute Product Properties (mol_props): Which molecule properties to calculate for the products generated.

  • Type: string

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

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

Advanced Reagent Joining Options

Core ID (coreid): If core provided has no title, use this.

  • Type: string

Annotate Reagents (reagannotate): Annotate the output records with the joined reagent classification.

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Sample Seed (reagseed): Use the specified seed for any sampling activities.

  • Type: integer

Sample Reagents (reagsample): Sample this percentage of the total reagent available, limited by the (optional) Maximum Reagents total.

  • Type: integer

  • Default: 100

H-Cap Attachment Sites (hcapping): After the reagent join, if any attachment site(s) remain, convert them all to hydrogens.

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Smart Join (smartjoin): Do some minimal chemistry validation on the reagent join to avoid undesirable chemistry, which can interfere with general joins.

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Retain Input Dataset Fields (keepfields): If ON, copies the input data record retaining existing data fields. If OFF, discards all but the structure (which will change) and sends it downstream for processing.

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Classifier Memory Limit (classifiermem): The memory limit for the reaction classifier. It may need to be increased for large R&R Databases.

  • Required

  • Type: decimal

  • Default: 10240

Verbosity (verbosity): Sets the output logging verbosity.

  • Type: string

  • Default: warning

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