CHOMP - Generate BROOD Fragment Database

Category Paths

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

  • Product-based/BROOD

  • Role-based/Computational Chemist

  • Solution-based/Virtual-screening/DB Search

  • Task-based/Scaffold-Hopping

Description

CHOMP - BROOD Fragments database generation is a utility to the lead generation tool BROOD. CHOMP allows users to fragment molecules, filter the fragments, generate 3D conformations, organize and index the fragments for rapid searching, and write a Brood database.

The minimal inputs into CHOMP is a dataset, file, or collection of 2D or 3D molecules.

Output from the CHOMP floe is a tarball that can be used as the database for the BROOD floe.

It is recommended to run the CHOMP floe in two steps, especially for larger molecular datasets. In the first step, run the CHOMP floe with the OMEGA flag turned OFF to generate the 2D Fragments Collection. In the second step, rerun the CHOMP floe with the OMEGA flag turned ON by loading the 2D Fragments Collection and turning ON the User Fragments switch to generate the 3D BROOD Fragments database.

The default values for system cube parameters like memory and disk space have been set to handle up to ~10 million fragments. For larger jobs, these cube parameters would need to be scaled up.

If you plan on running the CHOMP floe on larger datasets, we strongly recommend that you contact customer support for guidelines specific to your job.

Promoted Parameters

Title in user interface (promoted name)

Input parameters

Input dataset (in_dataset): Input dataset containing molecules or user fragments

  • Type: data_source

Input file (in_file): Input file containing molecules or user fragments

  • Type: file_in

Input collection (in_collection): Input collection containing molecules or user fragments

  • Type: collection_source

User Fragments (userFrags): This flag specifies whether the above input represents pre-generated fragments from the user

  • Required

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Input 3D conformers (readConfs): Specify a 3D structure file from which the database generation algorithm will sample conformers

  • Type: data_source

userUnique (userUnique): Provide a compressed database file for duplicate removal. The fragments in the specified database will be determined as unique and skipped in the new database

  • Type: file_in

Output parameters

Output database (out_file_name): Output Brood database file name

  • Type: file_out

  • Default: brood_database

Output 2D Fragments Collection (out_fragments_collection): Output collection containing 2D fragments

  • Required

  • Type: collection_sink

  • Default: Fragment collection

Failed Dataset (failed): Output dataset of failed calculations

  • Required

  • Type: dataset_out

  • Default: Failed Output for CHOMP - Generate BROOD Fragment Database

CHOMP parameters

omega (omega): This flag controls whether the conformer generation using the OMEGA conformers is applied to the fragments

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Filter (filter): Flag indicating if the default filter should be applied to fragments

  • Type: string

  • Default: true

  • Choices: [‘true’, ‘false’]

minFrequency (minFrequency): This flag indicates the minimum

number of source molecules that are required in order for the fragment to be retained. This parameter is normalized as a percentile where 99 indicates the most common fragments and 0 indicates the least common fragments.

  • Type: integer

  • Default: 0

Max Degree (maxDegree): Maximum number of

attachment points for fragments generated by Chomp

  • Type: integer

  • Default: 3

Min Degree (minDegree): Minimum number of

attachment points for fragments generated by Chomp

  • Type: integer

  • Default: 1

Max Molecular Weight (maxMolWt): Maximum molecular

weight of any fragment generated by Chomp

  • Type: decimal

  • Default: 350.0

Max Heavy Atoms (maxHvy): Maximum number of heavy

atoms allowed in fragments generated by Chomp

  • Type: integer

  • Default: 15

Min Heavy Atoms (minHvy): Minimum number of heavy

atoms allowed in fragments generated by Chomp

  • Type: integer

  • Default: 0

Max Chiral Centers (maxChiral): Maximum number of

chiral centers (both atom and bond centers) in a fragment.

  • Type: integer

  • Default: 3