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@@ 145-183 (lines=39) @@
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return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
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class ChemblQsarPredictions(Entry[TargetPredictionSearch]): |
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@classmethod |
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def run( |
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cls, |
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path: Path = CommonArgs.compounds, |
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key: str = EntryArgs.key("chembl:predictions"), |
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to: Optional[Path] = CommonArgs.to_single, |
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taxa: str = CommonArgs.taxa, |
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traversal: str = EntryArgs.traversal_strategy, |
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target_types: str = EntryArgs.target_types, |
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min_threshold: float = EntryArgs.min_threshold, |
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as_of: Optional[str] = CommonArgs.as_of, |
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check: bool = EntryArgs.check, |
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log: Optional[Path] = CommonArgs.log_path, |
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quiet: bool = CommonArgs.quiet, |
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verbose: bool = CommonArgs.verbose, |
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no_setup: bool = CommonArgs.no_setup, |
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) -> Searcher: |
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""" |
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Predicted target binding from ChEMBL. |
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https://mandos-chem.readthedocs.io/en/latest/binding.html |
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OBJECT: ChEMBL preferred target name |
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PREDICATE: Either "binding:yes", "binding:no", or "binding:unknown". |
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WEIGHT: The sqrt pchembl multiplied by a normalized odds ratio from the confidence set |
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""" |
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built = TargetPredictionSearch( |
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key=key, |
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api=Apis.Chembl, |
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scrape=Apis.ChemblScrape, |
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taxa=EntryUtils.get_taxa(taxa), |
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traversal=traversal, |
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target_types=EntryUtils.get_target_types(target_types), |
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min_threshold=min_threshold, |
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) |
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return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
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class EntryChemblTrials(Entry[IndicationSearch]): |
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@@ 107-142 (lines=36) @@
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return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
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class EntryChemblMechanism(Entry[MechanismSearch]): |
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@classmethod |
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def run( |
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cls, |
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path: Path = CommonArgs.compounds, |
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key: str = EntryArgs.key("chembl:mechanism"), |
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to: Optional[Path] = CommonArgs.to_single, |
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taxa: Optional[str] = CommonArgs.taxa, |
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traversal: str = EntryArgs.traversal_strategy, |
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target_types: str = EntryArgs.target_types, |
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min_confidence: Optional[int] = EntryArgs.min_confidence, |
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as_of: Optional[str] = CommonArgs.as_of, |
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check: bool = EntryArgs.check, |
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log: Optional[Path] = CommonArgs.log_path, |
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quiet: bool = CommonArgs.quiet, |
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verbose: bool = CommonArgs.verbose, |
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no_setup: bool = CommonArgs.no_setup, |
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) -> Searcher: |
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""" |
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Mechanism of action (MoA) data from ChEMBL. |
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OBJECT: ChEMBL preferred target name |
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PREDICATE: Target action; e.g. "agonist" or "positive allosteric modulator" |
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WEIGHT: 1.0 |
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""" |
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built = MechanismSearch( |
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key=key, |
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api=Apis.Chembl, |
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taxa=EntryUtils.get_taxa(taxa), |
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traversal_strategy=traversal, |
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allowed_target_types=EntryUtils.get_target_types(target_types), |
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min_confidence_score=min_confidence, |
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) |
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return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
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class ChemblQsarPredictions(Entry[TargetPredictionSearch]): |
dmyersturnbull /
mandos
