schrodinger.protein.tasks.align_to_opm_st module¶

class schrodinger.protein.tasks.align_to_opm_st.OPMTask(*args, _param_type=<object object>, **kwargs)¶

Bases: BaseHitAlignTask

Task to align a structure to that of the matching OPM structure, ID’d by a hit in the OPM blast database.

After finding a sequence with high enough identity, the OPM structure (not the RCSB) structure is downloaded and then used for structural alignment.

Note: This inherits from BaseHitAlignTask, but does not implement transferAnnotationToQuerySeq. This is fine, as that function is not called anywhere inside the class, and is not needed here.

MINIMUM_IDENTITY = 0.9¶

LOW_IDENTITY_ERROR = 'Could not find OPM sequence with identity > 90%'¶

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

Bases: CompoundParam

st: Structure¶: A parameter of the class.

query_sequence: ProteinSequence¶: A parameter of the class.

custom_database_path: str¶: A parameter of the class.

consider_aln_gaps: bool¶: A parameter of the class.

consider_aln_gapsChanged¶: A pyqtSignal emitted by instances of the class.

consider_aln_gapsReplaced¶: A pyqtSignal emitted by instances 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.

stChanged¶: A pyqtSignal emitted by instances of the class.

stReplaced¶: A pyqtSignal emitted by instances of the class.

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

Bases: CompoundParam

st: Structure¶: A parameter of the class.

alignment: Alignment¶: A parameter of the class.

alignmentChanged¶: A pyqtSignal emitted by instances of the class.

alignmentReplaced¶: 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()¶

initializeValue()¶: @overrides: parameters.CompoundParam

getHits()¶

Get all the sequence hits to align to.

Subclasses must implement this.

alignToOPMfile(st, opm_fn, opm_chain) → Alignment¶

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: 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.