schrodinger.protein.tasks.hit_align module

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

Bases: schrodinger.tasks.tasks.ComboSubprocessTask

Task to align custom BLAST hits against a sequence and apply annotations.

This is an abstract class that must be subclassed.

output: schrodinger.protein.alignment.ProteinAlignment

A parameter of the class.

MINIMUM_IDENTITY = 0.0

LOW_IDENTITY_ERROR = 'Could not find sequence with any identity match'

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

Bases: schrodinger.models.parameters.CompoundParam

query_sequence: schrodinger.protein.sequence.ProteinSequence

A parameter of the class.

query_sequenceChanged

A pyqtSignal emitted by instances of the class.

query_sequenceReplaced

A pyqtSignal emitted by instances of the class.

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

Bases: schrodinger.models.parameters.CompoundParam

alignment: schrodinger.protein.alignment.ProteinAlignment

A parameter of the class.

alignmentChanged

A pyqtSignal emitted by instances of the class.

alignmentReplaced

A pyqtSignal emitted by instances of the class.

mainFunction()

getHits() → List[schrodinger.protein.sequence.ProteinSequence]

Get all the sequence hits to align to.

Subclasses must implement this.

transferAnnotationToQuerySeq()

Transfer the annotation from the best hit to the query sequence.

Subclasses must implement this.

getBestAlignment(hits: List[schrodinger.protein.sequence.ProteinSequence], ref_seq: schrodinger.protein.sequence.ProteinSequence) → schrodinger.protein.alignment.ProteinAlignment

Get the alignment that consists of query sequence (as ref seq) and the sequence that has the highest identity with the reference sequence.

Raises

ValueError – when there is no sequence greater than MINIMUM_IDENTITY

Parameters

• hits – list of all blast output sequences

• ref_seq – a copy of the query sequence, potentially to be modified

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.

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.hit_align.CustomFamilyTask(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.protein.tasks.hit_align.BaseHitAlignTask

Task to transfer custom family annotations to a sequence against custom family annotated sequences.

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

Bases: schrodinger.models.parameters.CompoundParam

query_sequence: schrodinger.protein.sequence.ProteinSequence

A parameter of the class.

custom_aln: schrodinger.protein.alignment.ProteinAlignment

A parameter of the class.

custom_alnChanged

A pyqtSignal emitted by instances of the class.

custom_alnReplaced

A pyqtSignal emitted by instances of the class.

query_sequenceChanged

A pyqtSignal emitted by instances of the class.

query_sequenceReplaced

A pyqtSignal emitted by instances of the class.

getHits() → List[schrodinger.protein.sequence.ProteinSequence]

Get all sequences from the custom family.

transferAnnotationToQuerySeq()

Transfer the custom family annotations from the best matching custom alignment sequence to the query sequence.

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: schrodinger.protein.alignment.ProteinAlignment

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.