from .constants import constants

from . import composition
from .composition import Composition, formula, ChemicalCompositionError

from . import base
from .base import (
    MoleculeBase, PeptideSequenceBase, ModificationBase,
    ResidueBase, SequencePosition)

from . import parser
from .parser import (sequence_tokenizer, strip_modifications)

from . import residue
from .residue import (
    AminoAcidResidue, register_degenerate, register_residue)

from .terminal_group import TerminalGroup

from . import sequence
from .sequence import (
    PeptideSequence, NamedSequence, ProteinSequence,
    AnnotatedSequence,
    find_glycosaminoglycan_sequons, find_n_glycosylation_sequons,
    find_o_glycosylation_sequons, )

from . import modification
from .modification import (
    Modification, ModificationRule, ModificationTarget,
    ModificationTable, RestrictedModificationTable,
    AnonymousModificationRule, AminoAcidSubstitution,
    ModificationCategory, SequenceLocation, Glycosylation,
    CoreGlycosylation, NGlycanCoreGlycosylation, OGlycanCoreGlycosylation,
    GlycosaminoglycanLinkerGlycosylation, OGlcNAcylation, GlycanFragment,
    ModificationStringParseError, ModificationNameResolutionError)

from . import fragment
from .fragment import (
    ChemicalShift, FragmentBase, PeptideFragment,
    SimpleFragment, StubFragment, IonSeries)

from . import fragmentation_strategy
from .fragmentation_strategy import (
    FragmentationStrategyBase, CADFragmentationStrategy, HCDFragmentationStrategy,
    EXDFragmentationStrategy, StubGlycopeptideStrategy)

from . import glycan
from .glycan import (
    TypedGlycan, TypedGlycanComposition, GlycosylationType,
    GlycanCompositionProxy, GlycosylationManager, )


__all__ = [
    "constants",

    "base",
    "MoleculeBase", "PeptideSequenceBase", "ModificationBase",
    "ResidueBase", "SequencePosition",

    "parser",
    "sequence_tokenizer", "strip_modifications",

    "residue",
    "AminoAcidResidue", "register_degenerate", "register_residue",

    "sequence",
    "PeptideSequence", "NamedSequence", "ProteinSequence",
    "AnnotatedSequence", "TerminalGroup", "find_glycosaminoglycan_sequons",
    "find_o_glycosylation_sequons", "find_n_glycosylation_sequons",

    "modification",
    "Modification", "ModificationRule", "ModificationTarget",
    "ModificationTable", "RestrictedModificationTable",
    "AnonymousModificationRule", "AminoAcidSubstitution",
    "ModificationCategory", "SequenceLocation", "Glycosylation",
    "CoreGlycosylation", "NGlycanCoreGlycosylation", "OGlycanCoreGlycosylation",
    "GlycosaminoglycanLinkerGlycosylation", "OGlcNAcylation", "GlycanFragment",
    "ModificationStringParseError", "ModificationNameResolutionError",

    "composition", "Composition", "formula", "ChemicalCompositionError",

    "fragment",
    "ChemicalShift", "FragmentBase", "PeptideFragment",
    "SimpleFragment", "StubFragment", "IonSeries",

    "fragmentation_strategy",
    "FragmentationStrategyBase", "CADFragmentationStrategy", "HCDFragmentationStrategy",
    "EXDFragmentationStrategy", "StubGlycopeptideStrategy",

    "glycan",
    "TypedGlycan", "TypedGlycanComposition", "GlycosylationType",
    "GlycanCompositionProxy", "GlycosylationManager",

]
