schrodinger.application.phase.shape_screen_reporter.tasks module

class schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.application.phase.shape_screen_reporter.tasks._AbstractShapeScreenReporterTaskMixin, schrodinger.tasks.jobtasks.CmdJobTask

Task to create a virtual screening database. Adds a label property to the newly created DB in a postprocessor.

MODE = 'create'

class Input(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

hits_file: schrodinger.tasks.tasks.TaskFile

A parameter of the class.

query_file: schrodinger.tasks.tasks.TaskFile

A parameter of the class.

props: List[str]

A parameter of the class.

label_prop: str

A parameter of the class.

hits_fileChanged

A pyqtSignal emitted by instances of the class.

hits_fileReplaced

A pyqtSignal emitted by instances of the class.

label_propChanged

A pyqtSignal emitted by instances of the class.

label_propReplaced

A pyqtSignal emitted by instances of the class.

propsChanged

A pyqtSignal emitted by instances of the class.

propsReplaced

A pyqtSignal emitted by instances of the class.

query_fileChanged

A pyqtSignal emitted by instances of the class.

query_fileReplaced

A pyqtSignal emitted by instances of the class.

getDBFile() → str

@overrides: _AbstractShapeScreenReporterTaskMixin

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: parameters.CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: parameters.CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.tasks.tasks.ComboSubprocessTask

Task to run filtering on a virtual screening database.

DEFAULT_TASKDIR_SETTING = 2

class Input(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

screening_db_file: schrodinger.tasks.tasks.TaskFile

A parameter of the class.

property_filters: List[Tuple]

A parameter of the class.

smarts_filters: List[str]

A parameter of the class.

sel_features: Set[str]

A parameter of the class.

sampling_fraction: float

A parameter of the class.

sample_by_scaffold: bool

A parameter of the class.

property_filtersChanged

A pyqtSignal emitted by instances of the class.

property_filtersReplaced

A pyqtSignal emitted by instances of the class.

sample_by_scaffoldChanged

A pyqtSignal emitted by instances of the class.

sample_by_scaffoldReplaced

A pyqtSignal emitted by instances of the class.

sampling_fractionChanged

A pyqtSignal emitted by instances of the class.

sampling_fractionReplaced

A pyqtSignal emitted by instances of the class.

screening_db_fileChanged

A pyqtSignal emitted by instances of the class.

screening_db_fileReplaced

A pyqtSignal emitted by instances of the class.

sel_featuresChanged

A pyqtSignal emitted by instances of the class.

sel_featuresReplaced

A pyqtSignal emitted by instances of the class.

smarts_filtersChanged

A pyqtSignal emitted by instances of the class.

smarts_filtersReplaced

A pyqtSignal emitted by instances of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

filtered_row_nums: List[int]

A parameter of the class.

filtered_row_numsChanged

A pyqtSignal emitted by instances of the class.

filtered_row_numsReplaced

A pyqtSignal emitted by instances of the class.

mainFunction()

Create the shape screening reporter and filter based on various criteria. Write the filtered structs to the hits file.

getDBFile() → str

@overrides: _AbstractShapeScreenReporterTaskMixin

getHitsFile() → Optional[str]

Return the path to the output hits file or None if the taskdir has not yet been created.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

input: parameters.CompoundParam

A parameter of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: parameters.CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyInput(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

Variables

• vsdb_file – The VSDB file from which to extract property values.

• property_names – The properties to extract from the VSDB.

• row_nums – The specific VSDB row numbers to query. If empty, property values will be extracted from all rows.

vsdb_file: schrodinger.tasks.tasks.TaskFile

A parameter of the class.

property_names: List[str]

A parameter of the class.

row_nums: List[int]

A parameter of the class.

property_namesChanged

A pyqtSignal emitted by instances of the class.

property_namesReplaced

A pyqtSignal emitted by instances of the class.

row_numsChanged

A pyqtSignal emitted by instances of the class.

row_numsReplaced

A pyqtSignal emitted by instances of the class.

vsdb_fileChanged

A pyqtSignal emitted by instances of the class.

vsdb_fileReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.tasks.tasks.ComboSubprocessTask

Task to extract structure-level properties that meet certain requirements.

DEFAULT_TASKDIR_SETTING = 2

MAX_UNIQUE_STR_PROPS = 10

INT_PROP_PREFIX = 'i'

FLOAT_PROP_PREFIX = 'r'

STR_PROP_PREFIX = 's'

input: schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyInput

A parameter of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

vals_by_prop: Dict[str, Tuple]

A parameter of the class.

vals_by_propChanged

A pyqtSignal emitted by instances of the class.

vals_by_propReplaced

A pyqtSignal emitted by instances of the class.

checkVsdbFile()

mainFunction()

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: parameters.CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.