MMP Molecule Indexer¶
Category Paths
Follow one of these paths in the Orion user interface, to find the floe.
Solution-based/Hit to Lead/Generative Design/Match Molecular Pairs (MMP)
Task-based/Virtual Screening - Structure-Based
Role-based/Cheminformatician/Medicinal Chemistry Support
Role-based/Cheminformatician/Corporate Collection Support
Description
This Floe is intended to provide the capability to index a user-provided set of structures for use in the Generative Design Floes for the Matched Molecular Pair (MMP) method.
The input to the Floe is a (File) input and a (File) output is generated. When uploading a structure set for indexing, use the Advanced options in the upload process to suppress ETL (especially for large input structure sets). Large datasets are in the <1M range - larger datasets are not recommended at this time.
Once an MMP index has been created, there is another Floe to extract the desired MMP transformations to use in the Generative Design Floe.
Promoted Parameters
Title in user interface (promoted name)
Inputs
Input File (input_file): Orion file resource containing the molecules to be indexed
Required
Type: file_in
Outputs
Output MMP Index (output_mmpindex): Orion file resource for the output MMP index file
Required
Type: file_out
Matched Molecular Pair Indexing Options
MolField (idxmol): Field containing the molecules to be indexed
Type: field_parameter::mol
Sequence id (molid): Field containing the input molecule sequence identifier
Required
Type: field_parameter
Default: molid
Data Handling (moldata): Desired handling of data on the input molecules
Required
Type: string
Default: keep
Choices: [‘keep’, ‘clear’, ‘any’, ‘all’]
Fragmentation Cuts (fragcuts): Selects the type(s) of fragmentation cuts for the indexing activity
Type: string
Default: [‘all’]
Choices: [‘all’, ‘single’, ‘double’, ‘triple’]
Min Indexed Fragment Size (fragGe): Set the minimum range of the indexable fragment filter as a percentage of the input structure
Type: decimal
Default: 85.0
Max Indexed Fragment Size (fragLe): Set the maximum range of the indexable fragment filter as a percentage of the input structure
Type: decimal
Default: 100.0
Advanced Options
Strip salts (strip_salts): Whether to strip salts from the input structures
Required
Type: boolean
Default: False
Choices: [True, False]
Strip stereochemistry (strip_stereo): Whether to strip stereochemistry from the input structures
Required
Type: boolean
Default: False
Choices: [True, False]
Finalize MMP Index (finalize_index): Whether to finalize the index file or allow it to have additional molecules added at some later time
Required
Type: boolean
Default: True
Choices: [True, False]
Log level (verbosity): Desired level of logging verbosity
Type: string
Default: warning
Choices: [‘info’, ‘warning’, ‘error’, ‘debug’, ‘ddebug’]
Indexing Resource Options
Max Parallel Indexers (idx_max_parallel): Limit the number of parallel indexing instances to this limit
Type: integer
Default: 1000
Disk Limit (mmp_disk_space): Maximum disk space for the serialized MMP index
Type: decimal
Default: 30000
Memory Limit (Frag) (mmp_frag_memory): Maximum memory limit for molecule fragmentation
Type: decimal
Default: 10000
Memory Limit (Merge) (mmp_merge_memory): Maximum memory limit for MMP index merge
Type: decimal
Default: 50000