schrodinger.seam.transforms package

Seam Transform Catalog

See also:

• Beam transform catalog

• Seam YAML transform catalog

Transform	Description
ReadStructuresFromFile	Read a file (or files) containing structures and return a PCollection of Structure objects.
WriteStructuresToFile	Write a PCollection of Structure objects to a file.
ReadMolsFromFile	Read a file (or files) containing molecules.
WriteMolsToFile	Write a PCollection of Mol objects to a file.
FixedSample	Split a PCollection into two PCollections: a random sample of the input PCollection and the remaining elements.
Top	Split a PCollection into two PCollections: the largest n elements of the input PCollection and the remaining elements.
RandomSample	Create a PCollection made up of a random sample of the input PCollection.
Throttle	Wrap a PTransform with a RandomSample pre-filter to limit the number of elements processed, based on a compute budget.
Smallest	Create a PCollection containing the smallest element(s) of the input PCollection.
IPythonInspect	Starts an IPython shell to interactively inspect the contents of a PCollection.
ParetoRank	Associate inputs with the Pareto front for parameter minimization.

Scientific Transforms

General

Transform	Description
LigPrep	Prepare ligands using LigPrep, turning 2D `Mol`s into 3D structures. LigPrep works by expanding tautomeric and ionization states, ring conformations, and stereoisomers consistent with the input mol to fully capture the relevant states of the molecule in 3D. For each input mol, multiple output structures may be generated.

Conformer Generation

Transforms for generating 3d structures in a variety of conformations and poses.

Transform	Description
Dock	Dock ligands into a receptor using Glide.
FastConfGen	Generate conformers using Fast3D.
ShapeScreen	Generate conformers aligned to shape(s).

Structure Minimization

Transforms for minimizing structures with various methods.

Transform	Description
FFMinimize	Minimize a structure using a force field minimization. Supports independent structures, homogeneous conformers, or custom grouping.
SetMinimizationEnergy	Extract energy from MinimizationResult and set it as a property on the structure.
CollectConformers	Group structures by a conformer key function into lists.
RunMLFFMinimize	Run MLFF minimization and yield an MLFFMinimizeResult for each input, regardless of success or failure.
MLFFMinimize	Minimize a structure using an MLFF model. Backward-compatible wrapper around RunMLFFMinimize with dropped output for failed structures.

Protein Preparation and Refinement

Transforms for preparing and refining protein structures.

Transform	Description
ProteinPrep	Clean up and prepare a protein using PrepWizard.
Refine	Refine a protein receptor using Prime.

Chemical Space Exploration

Transforms for taking molecules and enumerating new molecules based on them.

Transform	Description
Decorate	Decorates a PCollection of Mol objects using RGroup objects.
Fragment	Generate molecular fragments from input Mol objects.
Synthesize	Combinatorial retrosynthesis of Mol objects.

Filtering

Transforms for filtering collections of molecules based on various criteria.

Transform	Description
PropertySpaceFilter	Filters a PCollection of Structure or Mol objects based on physicochemical property ranges.
SubstructureFilter	Filters a PCollection of Structure or Mol objects based on substructure matches.

Machine Learning

Transforms for training and applying ML models to molecular data.

Transform	Description
TrainModel	Train an ML model to predict numeric properties from molecular structure fingerprints.
PredictProperties	Predict properties on structures using a trained ML model. Accepts a direct MLModel instance or a PCollection side input.
RunRetroSynth	Run retrosynthesis predictions on structures via the LiveDesign ML API, returning a RetroSynthResult per input structure.
AnnotateRetroSynth	Annotate structures with retrosynthesis properties (synthesis score, difficulty, etc.) via the LiveDesign ML API.

FEP

Transforms for running FEP+ calculations via web services or job server.

Transform	Description
RunFEP	Run FEP+ calculations on a perturbation graph using either Web Services or a local job server. Supports both FEPWebServicesSettings and FEPJobServerSettings execution modes.
FEPMapper	Generate an FEP perturbation map (graph) from receptor structures, reference ligands, and candidate ligands.
WriteFEPResults	Write FEP calculation results (graphs and fmpdb files) to an output directory.

Submodules

• schrodinger.seam.transforms.combiners module
• schrodinger.seam.transforms.core module
• schrodinger.seam.transforms.grouping module
• schrodinger.seam.transforms.outcomes module
• schrodinger.seam.transforms.partitioners module
• schrodinger.seam.transforms.resources module
• schrodinger.seam.transforms.samplers module
• schrodinger.seam.transforms.window module