schrodinger.protein.tasks.descriptors module

class schrodinger.protein.tasks.descriptors.StructureDescriptorsTask(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.tasks.jobtasks.CmdJobTask

Given a list of structures, generate descriptors for them using the calc_protein_descriptors.py backend.

Example usage:

task = StructureDescriptorsTask()
task.input.sts = list(structure.StructureReader('1cmy.pdb'))
task.start()

DEFAULT_TASKDIR_SETTING = 1

PROP_SOURCE = 3

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

Bases: schrodinger.models.parameters.CompoundParam

seqs: List[schrodinger.protein.sequence.AbstractSequence]

A parameter of the class.

seqsChanged

A pyqtSignal emitted by instances of the class.

seqsReplaced

A pyqtSignal emitted by instances of the class.

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

Bases: schrodinger.tasks.jobtasks._CmdJobTaskOutput

Variables

descriptors (scollections.IdDict) – A dictionary mapping the (ID of the) original sequence to a dictionary which maps names of descriptors to their values

descriptors: schrodinger.utils.scollections.IdDict

A parameter of the class.

descriptorsChanged

A pyqtSignal emitted by instances of the class.

descriptorsReplaced

A pyqtSignal emitted by instances of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

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.protein.tasks.descriptors.SequenceDescriptorsTask(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.tasks.jobtasks.CmdJobTask

Given a list of sequences, generate descriptors for them using the calc_sequence_descriptors.py backend.

Example usage:

task = SequenceDescriptorsTask()
task.input.sts = list(alignment.ProteinAlignment(['VVVV', 'AAA', 'TT']))
task.start()

DEFAULT_TASKDIR_SETTING = 2

PROP_SOURCE = 2

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

Bases: schrodinger.models.parameters.CompoundParam

Parameters

• seqs – Sequence to calculate descriptors for.

• specified_descriptors – What descriptors to calculate for seqs. If empty, all possible descriptors will be calculated.

seqs: List[schrodinger.protein.sequence.AbstractSequence]

A parameter of the class.

requested_descriptors: List[str]

A parameter of the class.

requested_descriptorsChanged

A pyqtSignal emitted by instances of the class.

requested_descriptorsReplaced

A pyqtSignal emitted by instances of the class.

seqsChanged

A pyqtSignal emitted by instances of the class.

seqsReplaced

A pyqtSignal emitted by instances of the class.

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

Bases: schrodinger.tasks.jobtasks._CmdJobTaskOutput

Variables

descriptors (scollections.IdDict) – A dictionary mapping the (ID of the) original sequence to a dictionary which maps names of descriptors to their values

descriptors: schrodinger.utils.scollections.IdDict

A parameter of the class.

descriptorsChanged

A pyqtSignal emitted by instances of the class.

descriptorsReplaced

A pyqtSignal emitted by instances of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

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.