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.
make_dise_job
(dise_ctrl, *, infile, n_total)[source]¶ - 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 and output file name.
- Return type
-
schrodinger.application.vss.tasks.
make_glide_jobs
(cfg, ctrl)[source]¶ 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 and output file names or None.
- Return type
JobAndOutcomes
or NoneType
-
schrodinger.application.vss.tasks.
make_glide_al_jobs
(cfg, ctrl)[source]¶ - Parameters
cfg (
schrodinger.application.vss.config.Config
) – VSS runner configuration.ctrl (
schrodinger.application.vss.control.RunnerControl
) – Run specification.
- Returns
Glide AL job and output file names or None.
- Return type
JobAndOutcomes
or NoneType
-
schrodinger.application.vss.tasks.
get_shape_query
(cfg, ctrl)[source]¶ - Parameters
cfg (
schrodinger.application.vss.config.Config
) – VSS runner configuration.ctrl (
schrodinger.application.vss.control.RunnerControl
) – Run specification.
- 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
cfg (
schrodinger.application.vss.config.Config
) – VSS runner configuration.ctrl (
schrodinger.application.vss.control.RunnerControl
) – Run specification.
- 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
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)[source]¶ - Parameters
cfg (
schrodinger.application.vss.config.Config
) – VSS runner configuration.ctrl (
schrodinger.application.vss.control.RunnerControl
) – Run specification.
- 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
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)[source]¶ 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)[source]¶ Executes “virtual screening” pilot.
- Parameters
cfg (
schrodinger.application.vss.config.Config
) – VSS runner configuration.ctrl (
schrodinger.application.vss.control.RunnerControl
) – Run specification.