Reaction & Reagent Database - Retrieve Reaction Reagents

Category Paths

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

  • Role-based/Cheminformatician/Medicinal Chemistry Support

  • Role-based/Cheminformatician/Corporate Collection Support

Description

This floe will extract the reagents from the Reaction & Reagent Database for a specific reagent ID to a dataset.

Since reagent counts can be quite large, be conservative in the number of reagents requested as very large datasets cannot be viewed in the Analyze page.

The Molecule ID Field should generally match the source of the input molecules for the Reaction & Reagent Database file. In the case of ZINC as the reagent source, zinc_id is the structure ID field.

Promoted Parameters

Title in user interface (promoted name)

Outputs

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

  • Type: dataset_out

  • Default: Reaction_reagents

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 Selection

Reagent Classification (reagclass): 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: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 Classification (customreagclass): A reagent selection from the reaction database

  • Type: string

Return prepared reagents (sans leaving groups) (prepreagent): if ON, apply the half reaction transform to the returned reagents

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Field Output Options

Molecule ID Field (molid): Field name for the output molecule IDs.

  • Required

  • Type: field_parameter::string

  • Default: ID

Output Molecule (molfield): Field name for the output molecules.

  • Required

  • Type: field_parameter::mol

  • Default: Mol

Add Reagent Annotation (annotate): if ON, adds a string field indicating the reagent class for the reagents

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Smiles Field (smiles): Field name for the output classified structure SMILES.

  • Type: field_parameter::string

Half Reaction Transformation (halfrxn): An optional field containing the half reaction transformation for the specified reagent if defined in the database

  • Type: field_parameter::string

Advanced Options

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

  • Type: integer

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

  • Type: integer

  • Default: 0

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

  • Type: integer

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

Classifier Disk Space (classifierdisk): The amount of disk space limit available for the reaction classifier activities. It may need to be increased for large R&R Databases.

  • Required

  • Type: decimal

  • Default: 32240

Verbosity (verbosity): Sets the output logging verbosity.

  • Type: string

  • Default: warning

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