schrodinger.application.vss.tasks module

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

Bases: tuple

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

__contains__(key, /)

Return key in self.

__len__()

Return len(self).

count(value, /)

Return number of occurrences of value.

index(value, start=0, stop=9223372036854775807, /)

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')[source]
schrodinger.application.vss.tasks.make_job(cmd)[source]
schrodinger.application.vss.tasks.make_dise_job(dise_ctrl, *, infile, n_total)[source]
Parameters
Returns

DiSE job and output file name.

Return type

(schrodinger.job.queue.JobControlJob, str)

schrodinger.application.vss.tasks.make_glide_jobs(cfg, ctrl)[source]

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)[source]
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)[source]
schrodinger.application.vss.tasks.get_shape_query(cfg, ctrl)[source]
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)[source]
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)[source]

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)[source]
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)[source]

Returns either root + ext (if no such file exists) or a non-existing variation of it.

schrodinger.application.vss.tasks.ensure_decoys(cfg, ctrl)[source]

Sample decoys from a pool if not provided via control.

Parameters
schrodinger.application.vss.tasks.run_production(cfg, ctrl)[source]

Executes “virtual screening” tasks.

Parameters
schrodinger.application.vss.tasks.run_pilot(cfg, ctrl)[source]

Executes “virtual screening” pilot.

Parameters