Generative Structure Indexing - MMP Transform Extractor
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 is the final step of indexing a custom dataset for the Matched Molecular Pair (MMP) method of the Generative Design Floes.
The input is the index (File) generated from the Generative Structure Indexing - MMP Molecule Indexer Floe. For the transformation extraction, indicate the desired chemistry context for the extracted transforms. The more chemistry context you request, the more targeted the chemistry transformation will be in the generated analogs. Typically, separate extraction runs would be performed for each of the desired transformation chemical contexts, with the output stored in the same output collection and then selected during the transformation application activities.
For a ~1 M structure index, each run of the floe extraction run can take approximately one hour, and much less for smaller index sets.
Promoted Parameters
Title in user interface (promoted name)
Inputs
MMP Index (mmp_index): The MMP index file to load.
Required
Type: file_in
Outputs
Transform Collection (colname): Name of the output collection.
Required
Type: string
Transform Extract Outputs
Chemistry Context (xform_context):
How many bonds of chemistry context to include in the transformations, larger contexts produce more explicit chemical transformations, smaller context values produce very broad and less specific chemical transformations. The more specific the chemical context specified, the fewer number of examples that may be present as matched molecular pairs from the index.
Type: string
Default: default
Choices: [‘default’, ‘allbonds’, ‘bond0’, ‘bond1’, ‘bond2’, ‘bond3’]
Min MMP count (xform_minmmp): Only return transforms having >= this number of Matched Molecular Pairs examples in the index, or 0 to indicate unconstrained.
Type: integer
Default: 6
Max MMP count (xform_maxmmp): Only return transforms having <= this number of Matched Molecular Pairs examples in the index, or 0 to indicate unconstrained.
Type: integer
Default: 0
Advanced Options
MMP Example (xform_bestmmp): Optional field to provide an example MMP for each transform.
Type: string
Default: xform_bestmmp
Verbosity (verbosity): Logging verbosity level.
Type: string
Default: warning
Choices: [‘info’, ‘warning’, ‘error’, ‘debug’, ‘ddebug’]