schrodinger.application.vss.tasks module¶

class schrodinger.application.vss.tasks.JobAndOutcomes(job, outcomes)¶

Bases: tuple

JobAndOutcomes(job, outcomes): job handle & output filenames

job¶: job handle

outcomes¶: notable output filenames

schrodinger.application.vss.tasks.get_jobname(ctrl, default='vs')¶

schrodinger.application.vss.tasks.make_job(cmd)¶

schrodinger.application.vss.tasks.make_dise_job(dise_ctrl, *, infile, n_total)¶

Parameters

dise_ctrl (schrodinger.application.vss.control.DiseControl) – DiSE parameters.
n_total (int) – Total number of ordered compounds to be DiSE-ed.
infile (str) – Ordered compounds.

Returns

DiSE job, output file name, and log file name.

Return type

(schrodinger.job.queue.JobControlJob, str, str)

schrodinger.application.vss.tasks.make_glide_jobs(cfg, ctrl)¶

Run glide for actives/decoys only (not “databases”).

Parameters

cfg (schrodinger.application.vss.config.Config) – VSS runner configuration.
ctrl (schrodinger.application.vss.control.RunnerControl) – Run specification.

Returns

Glide job, output and log file names or None.

Return type

JobAndOutcomes or NoneType

schrodinger.application.vss.tasks.make_glide_al_jobs(cfg, ctrl)¶

Parameters

cfg (schrodinger.application.vss.config.Config) – VSS runner configuration.
ctrl (schrodinger.application.vss.control.RunnerControl) – Run specification.

Returns

Glide AL job, output and log file names or None.

Return type

JobAndOutcomes or NoneType

schrodinger.application.vss.tasks.get_ligprep_command(cfg, infile, outfile, jobname=None)¶

schrodinger.application.vss.tasks.get_shape_query(cfg, ctrl)¶

Parameters

cfg (schrodinger.application.vss.config.Config) – VSS runner configuration.
ctrl (schrodinger.application.vss.control.RunnerControl) – Run specification.

Returns

Shape query filename (maestro), job handle, and log filenames.

Return type

(str, schrodinger.job.queue.JobControlJob or NoneType, list[str] or NoneType)

schrodinger.application.vss.tasks.make_shape_jobs(cfg, ctrl)¶

Parameters

cfg (schrodinger.application.vss.config.Config) – VSS runner configuration.
ctrl (schrodinger.application.vss.control.RunnerControl) – Run specification.

Returns

Shape job, output and log file names or None.

Return type

JobAndOutcomes or NoneType

schrodinger.application.vss.tasks.make_ligand_ml_training_set(cfg, ctrl)¶

Concatenates actives and decoys into single file (“training set” to be used for Ligand ML).

Parameters

cfg (schrodinger.application.vss.config.Config) – VSS runner configuration.
ctrl (schrodinger.application.vss.control.RunnerControl) – Run specification.

Returns

CSV SMILES file with “truth” column.

Return type

csvsmiles.CsvSmilesFile

schrodinger.application.vss.tasks.make_ligand_ml_jobs(cfg, ctrl)¶

Parameters

cfg (schrodinger.application.vss.config.Config) – VSS runner configuration.
ctrl (schrodinger.application.vss.control.RunnerControl) – Run specification.

Returns

Ligand ML job, output and log file names or None.

Return type

JobAndOutcomes or NoneType

schrodinger.application.vss.tasks.get_new_filename(root, ext)¶: Returns either root + ext (if no such file exists) or a non-existing variation of it.

schrodinger.application.vss.tasks.ensure_decoys(cfg, ctrl)¶

Sample decoys from a pool if not provided via control.

Parameters

cfg (schrodinger.application.vss.config.Config) – VSS runner configuration.
ctrl (schrodinger.application.vss.control.RunnerControl) – Run specification.

schrodinger.application.vss.tasks.run_production(cfg, ctrl)¶

Executes “virtual screening” tasks.

Parameters

cfg (schrodinger.application.vss.config.Config) – VSS runner configuration.
ctrl (schrodinger.application.vss.control.RunnerControl) – Run specification.

schrodinger.application.vss.tasks.run_pilot(cfg, ctrl)¶

Executes “virtual screening” pilot.

Parameters

cfg (schrodinger.application.vss.config.Config) – VSS runner configuration.
ctrl (schrodinger.application.vss.control.RunnerControl) – Run specification.