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from inspect import cleandoc |
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from typing import Mapping |
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import typer |
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from mandos.entry.utils._arg_utils import ArgUtils, Opt |
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from mandos.model.apis.chembl_support.chembl_targets import ConfidenceLevel, TargetType |
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from mandos.model.apis.chembl_support.target_traversal import TargetTraversalStrategies |
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def _stringify(keys: Mapping[str, str]): |
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return ", ".join((k if v is None else f"{k} ({v.lower()})" for k, v in keys.items())) |
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class EntryArgs: |
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@staticmethod |
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def key(name: str) -> typer.Option: |
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return typer.Option( |
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name, |
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min=1, |
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max=120, |
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help=cleandoc( |
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r""" |
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A unique key to designate the search. |
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A <60-character name that describes the search and parameters. |
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Intermediate output filenames will use this value. |
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""" |
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), |
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) |
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check = Opt.flag( |
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r"Do not run searches; just check everything.", |
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hidden=True, |
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) |
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############################################################################################### |
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# CHEMBL # |
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############################################################################################### |
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traversal = typer.Option( |
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"@null", |
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"--traversal", |
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show_default=False, |
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help=cleandoc( |
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rf""" |
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Target traversal strategy name, file, or class. |
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This is an experimental option. See the docs. |
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Can be one of: |
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(A) A standard strategy name, starting with @; |
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(B) The path to a *.strat file; OR |
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(C) The fully qualified name of a TargetTraversal |
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Standard strategies: |
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{ArgUtils.list(TargetTraversalStrategies.standard_strategies(), sep="; ")} |
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[default: @null] (leave targets as-is) |
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""" |
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), |
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) |
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target_types = typer.Option( |
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"@molecular", |
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"--targets", |
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help=cleandoc( |
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f""" |
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The accepted target types, comma-separated. |
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NOTE: This affects only the types are are accepted after traversal, |
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and the types must be included in the traversal. |
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This means that this must be AT LEAST as restrictive as the traversal strategy. |
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The ChEMBL-defined types are: |
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{ArgUtils.list(TargetType)} |
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These special names are also accepted: |
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{ArgUtils.definition_bullets(TargetType.special_type_names())} |
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""" |
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), |
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) |
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min_confidence = typer.Option( |
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3, |
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"--confidence", |
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min=0, |
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max=9, |
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show_default=False, |
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help=cleandoc( |
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rf""" |
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Minimum target confidence score, inclusive. |
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This is useful to modify in only some cases. |
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More important options are min_pchembl and taxa. |
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Values are: {ArgUtils.list(ConfidenceLevel)} |
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[default: 3] ("Target assigned is molecular non-protein target") |
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""" |
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), |
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) |
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min_pchembl = typer.Option( |
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0.0, |
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"--pchembl", |
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min=0.0, |
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help=cleandoc( |
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""" |
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Minimum pCHEMBL value, inclusive. |
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Set to 0 if "cutoff" is set. |
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""" |
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), |
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) |
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binds_cutoff = typer.Option( |
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7.0, |
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"--binding", |
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min=0.0, |
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show_default=False, |
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help=cleandoc( |
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""" |
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Cutoff of pCHEMBL at which "binds" is declared. |
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Applies only if the relation is >, >=, =, or ~. |
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[default: 7.0 (100 nanomolar)] |
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""" |
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), |
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) |
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min_threshold = typer.Option( |
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70, |
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"--min-threshold", |
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min=70, |
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help=cleandoc( |
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""" |
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Minimum pCHEMBL threshold used to limit the true examples when training the QSAR model. |
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Must be either 70, 80, or 90. |
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An "active" or "inactive" prediction is required for this threshold or higher. |
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""" |
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), |
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) |
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binding_search_name = typer.Option( |
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None, |
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help=cleandoc( |
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r""" |
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The fully qualified name of a class inheriting ``BindingSearch``. |
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If specified, all parameters above are passed to its constructor. |
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""" |
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), |
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) |
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chembl_trial = typer.Option( |
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0, |
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"--phase", |
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help=cleandoc( |
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r""" |
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Minimum clinical trial phase, inclusive. |
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Values are: 0, 1, 2, 3. |
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""" |
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), |
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min=0, |
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max=3, |
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) |
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atc_level = typer.Option("1,2,3,4", help="""List of ATC levels, comma-separated.""") |
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############################################################################################### |
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# PUBCHEM # |
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############################################################################################### |
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min_cooccurrence_score = typer.Option( |
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0.0, |
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help=r"Minimum enrichment score, inclusive. See the docs.", |
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min=0.0, |
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) |
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min_cooccurring_articles = typer.Option( |
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0, |
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help=r"Minimum number of articles for both the compound and object, inclusive.", |
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min=0, |
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) |
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match_name = Opt.flag( |
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r""" |
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Require that the name of the compound(s) exactly matches those on PubChem (case-insensitive). |
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""" |
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) |
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banned_sources = Opt.val( |
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r""" |
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Comma-separated list of sources to exclude. |
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""" |
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) |
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min_nanomolar = Opt.val( |
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r""" |
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Minimum tissue concentration in nanomolar required to include. |
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""", |
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default=1, |
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) |
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acute_effect_level = typer.Option( |
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2, |
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min=1, |
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max=2, |
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help=cleandoc( |
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r""" |
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The level in the ChemIDPlus hierarchy of effect names. |
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(E.g. 'behavioral' for level 1 and 'behavioral: excitement' for level 2.) |
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""" |
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), |
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) |
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KNOWN_USEFUL_KEYS: Mapping[str, str] = { |
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"weight": "Molecular Weight", |
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"xlogp3": None, |
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"hydrogen-bond-donors": "Hydrogen Bond Donor Count", |
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"hydrogen-bond-acceptors": "Hydrogen Bond Acceptor Count", |
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"rotatable-bonds": "Rotatable Bond Count", |
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"exact-mass": None, |
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"monoisotopic-mass": None, |
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"tpsa": "Topological Polar Surface Area", |
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"heavy-atoms": "Heavy Atom Count", |
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"charge": "Formal Charge", |
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"complexity": None, |
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} |
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KNOWN_USELESS_KEYS: Mapping[str, str] = { |
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"components": "Covalently-Bonded Unit Count", |
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"isotope-atoms": "Isotope Atom Count", |
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"defined-atom-stereocenter-count": None, |
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"undefined-atom-stereocenter-count": None, |
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"defined-bond-stereocenter-count": None, |
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"undefined-bond-stereocenter-count": None, |
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"compound-is-canonicalized": None, |
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} |
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pubchem_computed_keys = typer.Option( |
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"weight,xlogp3,tpsa,complexity,exact-mass,heavy-atom-count,charge", |
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help=cleandoc( |
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rf""" |
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The keys of the computed properties, comma-separated. |
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Keys are case-insensitive and mainly ignore punctuation. |
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Main keys: {_stringify(KNOWN_USEFUL_KEYS)} |
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Less-useful keys: {_stringify(KNOWN_USELESS_KEYS)} |
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""" |
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), |
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) |
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############################################################################################### |
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# G2P # |
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############################################################################################### |
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############################################################################################### |
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# HMDB # |
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############################################################################################### |
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############################################################################################### |
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# META # |
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############################################################################################### |
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__all__ = ["EntryArgs"] |
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dmyersturnbull /
mandos
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