schrodinger.protein.tasks.kinase module

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

Bases: schrodinger.tasks.tasks.ComboSubprocessTask

DEFAULT_TASKDIR_SETTING = 2

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

Bases: schrodinger.models.parameters.CompoundParam

seq: schrodinger.protein.sequence.ProteinSequence

A parameter of the class.

seqChanged

A pyqtSignal emitted by instances of the class.

seqReplaced

A pyqtSignal emitted by instances of the class.

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

Bases: schrodinger.models.parameters.CompoundParam

annotation: list

A parameter of the class.

annotationChanged

A pyqtSignal emitted by instances of the class.

annotationReplaced

A pyqtSignal emitted by instances of the class.

BACKEND_SINGLE_LETTER_CODE_TO_KINASE_FEATURE = {'A': KinaseFeatureLabel.ALPHA_C, 'C': KinaseFeatureLabel.CATALYTIC_LOOP, 'D': KinaseFeatureLabel.DFG, 'G': KinaseFeatureLabel.GLYCINE_RICH_LOOP, 'H': KinaseFeatureLabel.HINGE, 'K': KinaseFeatureLabel.GATE_KEEPER, 'L': KinaseFeatureLabel.LINKER, 'R': KinaseFeatureLabel.HRD, 'T': KinaseFeatureLabel.ACTIVATION_LOOP, '~': KinaseFeatureLabel.NO_FEATURE}

mainFunction()

getKinaseFeatures()

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.protein.tasks.kinase.KinaseConservationTask(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.tasks.jobtasks.CmdJobTask

Task to run kinase binding site conservation analysis on the specified sequence and ligand.

DEFAULT_TASKDIR_SETTING = 2

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

Bases: schrodinger.models.parameters.CompoundParam

seq: schrodinger.protein.sequence.ProteinSequence

A parameter of the class.

ligand_asl: str

A parameter of the class.

ligand_aslChanged

A pyqtSignal emitted by instances of the class.

ligand_aslReplaced

A pyqtSignal emitted by instances of the class.

seqChanged

A pyqtSignal emitted by instances of the class.

seqReplaced

A pyqtSignal emitted by instances of the class.

out_fname = 'receptor_conservation.csv'

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

parseOutput()

See parse_kinase_conservation for documentation.

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.

schrodinger.protein.tasks.kinase.parse_kinase_conservation(outfile: str, seq: schrodinger.protein.sequence.ProteinSequence)

Read the output file and associate the output with the correct residues.

Return type

dict[residue.Residue, annotation.KinaseConservation]

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

Bases: schrodinger.protein.tasks.kinase.KinaseFeatureTask

Task to compute both kinase features and kinase conservation

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

Bases: schrodinger.models.parameters.CompoundParam

seq: schrodinger.protein.sequence.ProteinSequence

A parameter of the class.

st: schrodinger.structure._structure.Structure

A parameter of the class.

entry_id: int

A parameter of the class.

ligand_asl: str

A parameter of the class.

entry_idChanged

A pyqtSignal emitted by instances of the class.

entry_idReplaced

A pyqtSignal emitted by instances of the class.

ligand_aslChanged

A pyqtSignal emitted by instances of the class.

ligand_aslReplaced

A pyqtSignal emitted by instances of the class.

seqChanged

A pyqtSignal emitted by instances of the class.

seqReplaced

A pyqtSignal emitted by instances of the class.

stChanged

A pyqtSignal emitted by instances of the class.

stReplaced

A pyqtSignal emitted by instances of the class.

mainFunction()

Compute kinase features if necessary, then compute kinase conservation if the sequence is a kinase

parseConservationOutput()

See parse_kinase_conservation for documentation.

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.