schrodinger.application.peptide_workflow.beam_adapter module¶

Contains beam transforms to use in the beam pipeline when running PeptideWorkflowBeam.

class schrodinger.application.peptide_workflow.beam_adapter.PeptideReplicate(seed: int, st: Structure)¶

Bases: object

Holds necessary information for a peptide during the workflow.

Parameters:

seed – Random seed for reproducibility.
st – The peptide structure copy as read in from the input_file from a PeptideConfig.

seed: int¶

st: Structure¶

__init__(seed: int, st: Structure) → None¶

class schrodinger.application.peptide_workflow.beam_adapter.PeptideWorkflowSettings(steps: int, num_simulations: int, rmsd_cutoff: float, num_poses_per_peptide: int, monte_options: MonteOptions)¶

Bases: object

Holds peptide workflow settings applicable to all modes.

Parameters:

steps – The number of monte carlo steps
num_simulations – The number of simulations to run. This variable is just used for logging purposes
rmsd_cutoff – RMSD cutoff for similar peptides
num_poses_per_peptide – Max number of poses to keep during deduplication post processing
monte_options – The monte carlo options

steps: int¶

num_simulations: int¶

rmsd_cutoff: float¶

num_poses_per_peptide: int¶

monte_options: MonteOptions¶

__init__(steps: int, num_simulations: int, rmsd_cutoff: float, num_poses_per_peptide: int, monte_options: MonteOptions) → None¶

class schrodinger.application.peptide_workflow.beam_adapter.SuperimposeSettings(steps: int, num_simulations: int, rmsd_cutoff: float, num_poses_per_peptide: int, monte_options: MonteOptions, ff_clash_tolerance: float, ff_dielectric_constant: float)¶

Bases: PeptideWorkflowSettings

Holds peptide workflow settings for running with the OPLS minimizer

Parameters:

ff_clash_tolerance – force field clash tolerance constant
ff_dielectric_constant – force field dielectric constant

ff_clash_tolerance: float¶

ff_dielectric_constant: float¶

classmethod fromArgs(args)¶

__init__(steps: int, num_simulations: int, rmsd_cutoff: float, num_poses_per_peptide: int, monte_options: MonteOptions, ff_clash_tolerance: float, ff_dielectric_constant: float) → None¶

class schrodinger.application.peptide_workflow.beam_adapter.GlideSettings(steps: int, num_simulations: int, rmsd_cutoff: float, num_poses_per_peptide: int, monte_options: MonteOptions, grid: GridArchive, glide_minimizer_options: dict, randomize_input_in_gridbox: bool)¶

Bases: PeptideWorkflowSettings

Holds peptide workflow settings for running with the Glide minimizer

Parameters:

grid – A glide grid archive with grid information
glide_minimizer_options – Options for the glide minimizer
randomize_input_in_gridbox – To randomize the input in the grid box

grid: GridArchive¶

glide_minimizer_options: dict¶

randomize_input_in_gridbox: bool¶

classmethod fromArgs(args)¶

__init__(steps: int, num_simulations: int, rmsd_cutoff: float, num_poses_per_peptide: int, monte_options: MonteOptions, grid: GridArchive, glide_minimizer_options: dict, randomize_input_in_gridbox: bool) → None¶

class schrodinger.application.peptide_workflow.beam_adapter.PrimeSettings(steps: int, num_simulations: int, rmsd_cutoff: float, num_poses_per_peptide: int, monte_options: MonteOptions, recept_asl: str, recept_st: str)¶

Bases: PeptideWorkflowSettings

Holds peptide workflow settings for running with the Prime minimizer.

Parameters:

recept_asl – Receptor ASL to minimize with Prime
recept_st – Receptor filename

recept_asl: str¶

recept_st: str¶

classmethod fromArgs(args)¶

__init__(steps: int, num_simulations: int, rmsd_cutoff: float, num_poses_per_peptide: int, monte_options: MonteOptions, recept_asl: str, recept_st: str) → None¶

schrodinger.application.peptide_workflow.beam_adapter.get_workflow_settings(args)¶

Get the workflow settings for the correct mode defined by the args.

Parameters:: args (argparse.Namespace) – job settings
Return type:: GlideSettings|PrimeSettings|SuperimposeSettings
Returns:: a settings dataclass

class schrodinger.application.peptide_workflow.beam_adapter.ReadPeptideStructures(label: Optional[str] = None)¶

Bases: _LocalOnlyPTransform, ReadPeptideStructures

Beam transform to create peptide structures with their output file and number of replicates as structure properties.

class schrodinger.application.peptide_workflow.beam_adapter.PeptideWorkflowMonteCarlo(settings, random_seed)¶

Bases: PTransform

Beam transform to run the monte carlo based peptide docking.

Parameters:

settings (GlideSettings|PrimeSettings|SuperimposeSettings) – settings to use with the specific mode
random_seed (int) – the initial random seed to use

Return type:

tuple[str, list[Structure]]

Returns:

a tuple of output file and list of structure poses to write

__init__(settings, random_seed)¶

expand(peptide_structure)¶

schrodinger.application.peptide_workflow.beam_adapter.duplicate_and_enumerate_replicate(peptide_structure: Structure, seed: int)¶

Reads input files to create peptide structures and binds them with a randomly generated seed in a PeptideReplicate object.

Parameters:

peptide_structure – Config for the peptide containing input file, output file, jobname and replicates.
seed – Random seed.

Return type:

list[PeptideReplicate]

Returns:

A list of PeptideReplicate objects.

class schrodinger.application.peptide_workflow.beam_adapter.CreateReplicates(seed)¶

Bases: PTransform

Create Peptide elements based on PeptideConfig elements which were created during argument parsing.

__init__(seed)¶

expand(peptide_structure)¶

class schrodinger.application.peptide_workflow.beam_adapter.PostProcessPeptides(settings)¶

Bases: PTransform

Beam transform to map a PCollection of tuple[str, [structures]] to post_process to deduplicate the list of structures.

Parameters:: setting (GlideSettings|PrimeSettings|SuperimposeSettings) – a settings dataclass
Return type:: tuple[str, list[Structure]]
Returns:: A PCollection of tuples containing the output file and list of output structure poses

__init__(settings)¶

expand(simulation_result)¶

schrodinger.application.peptide_workflow.beam_adapter.run_single_peptide_workflow(peptide_obj, mover, minimizer, random_seed, monte_options, steps)¶

Run the Peptide Workflow with a single peptide structure.

Parameters:

peptide_obj – A peptide.Peptide object
mover (PeptideMovements) – movement sampler to be used
minimizer (PeptideMinimizer) – minimizer to be used
random_seed (int) – random seed to create random generator
monte_options (MonteOptions) – contains constants for monte
steps (int) – max steps to run for the simulation

Return type:

Structure

Returns:

Yields an output pose

class schrodinger.application.peptide_workflow.beam_adapter.RunMonte(settings)¶

Bases: PTransform

Beam transform to transform a PCollection of PeptideReplicate to a PCollection of tuples bundling the output file and the output structure together. There are 3 monte carlo methods each with a unique minimizer which are run by different DoFn based classes.

The transform reads the grid or receptor as bytes when a grid or receptor supplied by the user.

Parameters:: settings (GlideSettings | PrimeSettings | SuperimposeSettings) – Settings for which workflow method to use
Return type:: PCollection(Structure)
Returns:: A colleciton of output structures (poses)

__init__(settings)¶

expand(peptide_replicate)¶

schrodinger.application.peptide_workflow.beam_adapter.write_sts(simulation_result)¶

Write out the structures associated with each output file. Removes the internal properties s_peptide_outputfile and i_peptide_num_replicates.

Parameters:: simulation_result (tuple of str and list of structures) – A tuple that contains the output file and list of structures