schrodinger.protein.tasks.blast module

class schrodinger.protein.tasks.blast.BlastAlgorithm

Bases: schrodinger.models.jsonable.JsonableEnum

BLAST = 1

PSIBLAST = 2

class schrodinger.protein.tasks.blast.BlastDatabase

Bases: schrodinger.models.jsonable.JsonableEnum

PDB = 1

NR = 2

CUSTOM = 3

class schrodinger.protein.tasks.blast.SimilarityMatrix

Bases: schrodinger.models.jsonable.JsonableEnum

BLOSUM45 = 1

BLOSUM62 = 2

BLOSUM80 = 3

PAM30 = 4

PAM70 = 5

exception schrodinger.protein.tasks.blast.NoBlastHitsError

Bases: RuntimeError

Custom exception if no blast hits are returned

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

Bases: schrodinger.models.parameters.CompoundParam

progname: schrodinger.protein.tasks.blast.BlastAlgorithm

A parameter of the class.

location: str

A parameter of the class.

database_name: schrodinger.protein.tasks.blast.BlastDatabase

A parameter of the class.

custom_database_path: str

A parameter of the class.

word_size: int

A parameter of the class.

filter_query: bool

A parameter of the class.

gap_open_cost: int

A parameter of the class.

gap_extend_cost: int

A parameter of the class.

possible_gap_open: set

A parameter of the class.

allowed_gap_extend: set

A parameter of the class.

similarity_matrix: schrodinger.protein.tasks.blast.SimilarityMatrix

A parameter of the class.

num_iterations: int

A parameter of the class.

evalue_threshold: int

A parameter of the class.

inclusion_threshold: float

A parameter of the class.

allow_multiple_chains: bool

A parameter of the class.

download_structures: bool

A parameter of the class.

align_after_download: bool

A parameter of the class.

num_alignments: int

A parameter of the class.

DEFAULTS = {<SimilarityMatrix.BLOSUM45: 1>: (15, 2), <SimilarityMatrix.BLOSUM62: 2>: (9, 2), <SimilarityMatrix.BLOSUM80: 3>: (10, 1), <SimilarityMatrix.PAM30: 4>: (9, 1), <SimilarityMatrix.PAM70: 5>: (10, 1)}

EXT_OPEN_VALUES = {<SimilarityMatrix.BLOSUM45: 1>: {3: {10, 11, 12, 13}, 2: {12, 13, 14, 15}, 1: {16, 17, 18, 19}}, <SimilarityMatrix.BLOSUM62: 2>: {2: {6, 7, 8, 9, 10, 11}, 1: {9, 10, 11, 12, 13}}, <SimilarityMatrix.BLOSUM80: 3>: {2: {8, 6, 7}, 1: {9, 10, 11}}, <SimilarityMatrix.PAM30: 4>: {2: {5, 6, 7}, 1: {8, 9, 10}}, <SimilarityMatrix.PAM70: 5>: {2: {8, 6, 7}, 1: {9, 10, 11}}}

OPEN_EXT_VALUES = {<SimilarityMatrix.BLOSUM45: 1>: {10: {3}, 11: {3}, 12: {2, 3}, 13: {2, 3}, 14: {2}, 15: {2}, 16: {1}, 17: {1}, 18: {1}, 19: {1}}, <SimilarityMatrix.BLOSUM62: 2>: {6: {2}, 7: {2}, 8: {2}, 9: {1, 2}, 10: {1, 2}, 11: {1, 2}, 12: {1}, 13: {1}}, <SimilarityMatrix.BLOSUM80: 3>: {8: {2}, 6: {2}, 7: {2}, 9: {1}, 10: {1}, 11: {1}}, <SimilarityMatrix.PAM30: 4>: {5: {2}, 6: {2}, 7: {2}, 8: {1}, 9: {1}, 10: {1}}, <SimilarityMatrix.PAM70: 5>: {8: {2}, 6: {2}, 7: {2}, 9: {1}, 10: {1}, 11: {1}}}

initConcrete()

Override to customize initialization of concrete params.

initializeValue()

Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.

classmethod fromJsonImplementation(json_obj)

Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

getBlastSettings()

Returns BLAST settings as a dictionary.

Returns

Dictionary of BLAST settings.

Return type

dict

align_after_downloadChanged

A pyqtSignal emitted by instances of the class.

align_after_downloadReplaced

A pyqtSignal emitted by instances of the class.

allow_multiple_chainsChanged

A pyqtSignal emitted by instances of the class.

allow_multiple_chainsReplaced

A pyqtSignal emitted by instances of the class.

allowed_gap_extendChanged

A pyqtSignal emitted by instances of the class.

allowed_gap_extendReplaced

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.

database_nameChanged

A pyqtSignal emitted by instances of the class.

database_nameReplaced

A pyqtSignal emitted by instances of the class.

download_structuresChanged

A pyqtSignal emitted by instances of the class.

download_structuresReplaced

A pyqtSignal emitted by instances of the class.

evalue_thresholdChanged

A pyqtSignal emitted by instances of the class.

evalue_thresholdReplaced

A pyqtSignal emitted by instances of the class.

filter_queryChanged

A pyqtSignal emitted by instances of the class.

filter_queryReplaced

A pyqtSignal emitted by instances of the class.

gap_extend_costChanged

A pyqtSignal emitted by instances of the class.

gap_extend_costReplaced

A pyqtSignal emitted by instances of the class.

gap_open_costChanged

A pyqtSignal emitted by instances of the class.

gap_open_costReplaced

A pyqtSignal emitted by instances of the class.

inclusion_thresholdChanged

A pyqtSignal emitted by instances of the class.

inclusion_thresholdReplaced

A pyqtSignal emitted by instances of the class.

locationChanged

A pyqtSignal emitted by instances of the class.

locationReplaced

A pyqtSignal emitted by instances of the class.

num_alignmentsChanged

A pyqtSignal emitted by instances of the class.

num_alignmentsReplaced

A pyqtSignal emitted by instances of the class.

num_iterationsChanged

A pyqtSignal emitted by instances of the class.

num_iterationsReplaced

A pyqtSignal emitted by instances of the class.

possible_gap_openChanged

A pyqtSignal emitted by instances of the class.

possible_gap_openReplaced

A pyqtSignal emitted by instances of the class.

prognameChanged

A pyqtSignal emitted by instances of the class.

prognameReplaced

A pyqtSignal emitted by instances of the class.

similarity_matrixChanged

A pyqtSignal emitted by instances of the class.

similarity_matrixReplaced

A pyqtSignal emitted by instances of the class.

word_sizeChanged

A pyqtSignal emitted by instances of the class.

word_sizeReplaced

A pyqtSignal emitted by instances of the class.

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

Bases: schrodinger.tasks.jobtasks.ComboJobTask

This is a thin wrapper over BlastPlus object that implements job running and incorporation.

To enable DEBUG_MODE, set DEBUG_MODE to True at the bottom of this class. In DEBUG_MODE, no blast call will actually be made and the first top 10 hits of a BLAST search with 1cmy:a will be returned as the output.

DEFAULT_TASKDIR_SETTING = 2

PROGRAM_NAME = 'BLAST'

output: List[dict]

A parameter of the class.

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

Bases: schrodinger.models.parameters.CompoundParam

query_sequence: schrodinger.protein.sequence.ProteinSequence

A parameter of the class.

settings: schrodinger.protein.tasks.blast.BlastSettings

A parameter of the class.

genomes: List[str]

A parameter of the class.

getQueryName()

initConcrete()

Override to customize initialization of concrete params.

classmethod getJsonBlacklist()

@overrides: parameters.CompoundParam

Rather than encode the whole ProteinSequence object, we just save the necessary parts and rehydrate it in the backend.

classmethod fromJsonImplementation(json_obj)

Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

genomesChanged

A pyqtSignal emitted by instances of the class.

genomesReplaced

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.

settingsChanged

A pyqtSignal emitted by instances of the class.

settingsReplaced

A pyqtSignal emitted by instances of the class.

getExpectedRuntime()

Return the expected runtime of the task based on the current settings

Returns

Expected runtime in seconds

Return type

int

getQueryName()

checkLocalDatabase()

Return True if the local database exists and is correctly configured. Return False if the local database is missing or truncated.

mainFunction()

getBlastAlignment()

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.

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.