schrodinger.protein.gpcr.tasks module

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

Bases: BaseHitAlignTask

Task to run ‘protein.tasks.blast.BlastTask’ task against a custom database.

MINIMUM_IDENTITY = 0.7

LOW_IDENTITY_ERROR = 'Could not find sequence with identity > 70%'

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

Bases: CompoundParam

query_sequence: ProteinSequence

A parameter of the class.

custom_database_path: str

A parameter of the class.

sqlite_path: str

A parameter of the class.

custom_database_pathChanged

A pyqtSignal emitted by instances of the class.

custom_database_pathReplaced

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.

sqlite_pathChanged

A pyqtSignal emitted by instances of the class.

sqlite_pathReplaced

A pyqtSignal emitted by instances of the class.

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

Bases: CompoundParam

alignment: ProteinAlignment

A parameter of the class.

gpcr_anno = None

alignmentChanged

A pyqtSignal emitted by instances of the class.

alignmentReplaced

A pyqtSignal emitted by instances of the class.

initializeValue()

@overrides: parameters.CompoundParam

getHits() → List[ProteinSequence]

Run the blast task and convert all hits to protein sequences.

getBestAlignment(hits: List[ProteinSequence], ref_seq: ProteinSequence) → ProteinAlignment

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

Overrides to implement custom behavior to attempt to remove lysozyme from the sequence if the identity is too low.

Raises:

ValueError – when there is no sequence with 70% or more identity

Parameters:

• hits – list of all blast output sequences

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

Returns:

the best alignment

transferAnnotationToQuerySeq()

Transfer the GPCR annotation from the blast hit to the query sequence.

getGPCRAnnotationMap(gpcr_anno)

Generate a map of residues in input sequence to the corresponding gpcr annotation that is transferred from the blast hit.

extendBrokenAnnotations()

Extend GPCR values across broken regions for the input 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: 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.