schrodinger.protein.tasks.optimize_alignment module

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

Bases: schrodinger.tasks.tasks.BlockingFunctionTask

Task to optimize the alignment between a target and template sequence by moving gaps out of secondary structure elements. See move_gaps_from_sse.py for additional documentation.

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

Bases: schrodinger.models.parameters.CompoundParam

template_seq: schrodinger.protein.sequence.ProteinSequence

A parameter of the class.

target_seq: schrodinger.protein.sequence.ProteinSequence

A parameter of the class.

ligand_asl: str

A parameter of the class.

residue_asl: str

A parameter of the class.

radius: float

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.

radiusChanged

A pyqtSignal emitted by instances of the class.

radiusReplaced

A pyqtSignal emitted by instances of the class.

residue_aslChanged

A pyqtSignal emitted by instances of the class.

residue_aslReplaced

A pyqtSignal emitted by instances of the class.

target_seqChanged

A pyqtSignal emitted by instances of the class.

target_seqReplaced

A pyqtSignal emitted by instances of the class.

template_seqChanged

A pyqtSignal emitted by instances of the class.

template_seqReplaced

A pyqtSignal emitted by instances of the class.

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

Bases: schrodinger.models.parameters.CompoundParam

template_seq: schrodinger.protein.sequence.ProteinSequence

A parameter of the class.

target_seq: schrodinger.protein.sequence.ProteinSequence

A parameter of the class.

target_seqChanged

A pyqtSignal emitted by instances of the class.

target_seqReplaced

A pyqtSignal emitted by instances of the class.

template_seqChanged

A pyqtSignal emitted by instances of the class.

template_seqReplaced

A pyqtSignal emitted by instances of the class.

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.

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.