schrodinger.application.vss.tasks module

class schrodinger.application.vss.tasks.JobAndOutcomes

Bases: tuple

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

__contains__

Return key in self.

__init__

Initialize self. See help(type(self)) for accurate signature.

__len__

Return len(self).

count()

Return number of occurrences of value.

index()

Return first index of value.

Raises ValueError if the value is not present.

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:
Returns:

DiSE job and output file name.
Return type:

(schrodinger.job.queue.JobControlJob, str)
schrodinger.application.vss.tasks.make_glide_jobs(cfg, ctrl)

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

Parameters:
Returns:

Glide job and output file names or None.
Return type:

JobAndOutcomes or NoneType
schrodinger.application.vss.tasks.make_glide_al_jobs(cfg, ctrl)
Parameters:
Returns:

Glide AL job and output 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:
Returns:

Shape query filename (maestro) and job handle.
Return type:

(str, schrodinger.job.queue.JobControlJob or NoneType)
schrodinger.application.vss.tasks.make_shape_jobs(cfg, ctrl)
Parameters:
Returns:

Shape job and output 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:
Returns:

CSV SMILES file with “truth” column.
Return type:

csvsmiles.CsvSmilesFile
schrodinger.application.vss.tasks.make_ligand_ml_jobs(cfg, ctrl)
Parameters:
Returns:

Ligand ML job and output 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:
schrodinger.application.vss.tasks.run_production(cfg, ctrl)

Executes “virtual screening” tasks.

Parameters:
schrodinger.application.vss.tasks.run_pilot(cfg, ctrl)

Executes “virtual screening” pilot.

Parameters: