Index

A

A (paftacular.constants.BackboneCleavageType attribute) (paftacular.constants.IonSeries attribute) Adduct (class in paftacular.comps) adducts (paftacular.annotation.CommonAnnotationParams attribute) (paftacular.annotation.PafAnnotation attribute) amino_acid (paftacular.comps.ImmoniumIon attribute) analyte_reference (paftacular.annotation.CommonAnnotationParams attribute) (paftacular.annotation.PafAnnotation attribute)

AnnotationName (class in paftacular.constants) annotations (paftacular.parser.ParseResult attribute) average_mass (paftacular.comps.MassProvider property) AX (paftacular.constants.InternalSeries attribute) AY (paftacular.constants.InternalSeries attribute) AZ (paftacular.constants.InternalSeries attribute)

B

B (paftacular.constants.BackboneCleavageType attribute) (paftacular.constants.IonSeries attribute) BackboneCleavageType (class in paftacular.constants) base_formula (paftacular.comps.Adduct attribute) (paftacular.comps.NeutralLoss attribute)

base_mass (paftacular.comps.NeutralLoss attribute) base_reference (paftacular.comps.NeutralLoss attribute) BX (paftacular.constants.InternalSeries attribute) BY (paftacular.constants.InternalSeries attribute) BZ (paftacular.constants.InternalSeries attribute)

C

C (paftacular.constants.BackboneCleavageType attribute) (paftacular.constants.IonSeries attribute) charge (paftacular.annotation.CommonAnnotationParams attribute) (paftacular.annotation.PafAnnotation attribute) ChemicalFormula (class in paftacular.comps) cleavage_correction (paftacular.comps.InternalFragment property) CommonAnnotationParams (class in paftacular.annotation) comp() (paftacular.annotation.PafAnnotation method) composition (paftacular.comps.ChemicalFormula property) (paftacular.comps.CompositionProvider property) (paftacular.comps.ImmoniumIon property) (paftacular.comps.InternalFragment property) (paftacular.comps.IsotopeSpecification property) (paftacular.comps.NamedCompound property) (paftacular.comps.PeptideIon property) (paftacular.comps.PrecursorIon property) (paftacular.comps.ReferenceIon property) (paftacular.comps.ScalableComposition property) (paftacular.comps.SMILESCompound property) (paftacular.comps.UnknownIon property)

composition_to_formula_string() (in module paftacular.comps) composition_to_proforma_formula_string() (in module paftacular.comps) CompositionProvider (class in paftacular.comps) confidence (paftacular.annotation.CommonAnnotationParams attribute) (paftacular.annotation.PafAnnotation attribute) count (paftacular.comps.Adduct attribute) (paftacular.comps.IsotopeSpecification attribute) (paftacular.comps.NeutralLoss attribute) (paftacular.comps.ScalableComposition attribute) cterm_ion_type (paftacular.comps.InternalFragment attribute) CX (paftacular.constants.InternalSeries attribute) CY (paftacular.constants.InternalSeries attribute) CZ (paftacular.constants.InternalSeries attribute)

D

D (paftacular.constants.IonSeries attribute)

DA (paftacular.constants.IonSeries attribute) DB (paftacular.constants.IonSeries attribute)

E

element (paftacular.comps.IsotopeSpecification attribute)

end_position (paftacular.comps.InternalFragment attribute) error (paftacular.parser.ParseResult attribute)

F

format_number() (in module paftacular.util) formula (paftacular.comps.Adduct property) (paftacular.comps.ChemicalFormula attribute) (paftacular.comps.ImmoniumIon property) (paftacular.comps.InternalFragment property) (paftacular.comps.NeutralLoss property) (paftacular.comps.PeptideIon property) (paftacular.comps.PrecursorIon property) (paftacular.comps.ReferenceIon property) (paftacular.comps.SMILESCompound property)

FORMULA (paftacular.constants.AnnotationName attribute) formula() (paftacular.annotation.PafAnnotation method) formula_to_composition() (in module paftacular.comps) from_dict() (in module paftacular.serialization) (paftacular.annotation.PafAnnotation static method)

G

get_mass() (paftacular.annotation.PafAnnotation method) (paftacular.comps.CompositionProvider method) (paftacular.comps.ImmoniumIon method) (paftacular.comps.InternalFragment method) (paftacular.comps.IsotopeSpecification method) (paftacular.comps.MassProvider method) (paftacular.comps.NamedCompound method) (paftacular.comps.NeutralLoss method) (paftacular.comps.PeptideIon method) (paftacular.comps.PrecursorIon method) (paftacular.comps.ReferenceIon method) (paftacular.comps.UnknownIon method)

I

IMMONIUM (paftacular.constants.AnnotationName attribute) ImmoniumIon (class in paftacular.comps) index (paftacular.parser.ParseResult attribute) INTERNAL (paftacular.constants.AnnotationName attribute) InternalFragment (class in paftacular.comps) InternalSeries (class in paftacular.constants) ion_type (paftacular.annotation.PafAnnotation attribute)

IonSeries (class in paftacular.constants) is_auxiliary (paftacular.annotation.CommonAnnotationParams attribute) (paftacular.annotation.PafAnnotation attribute) is_average (paftacular.comps.IsotopeSpecification attribute) isotopes (paftacular.annotation.CommonAnnotationParams attribute) (paftacular.annotation.PafAnnotation attribute) IsotopeSpecification (class in paftacular.comps) iter_parse() (in module paftacular.parser)

L

label (paftacular.comps.UnknownIon attribute)

loss_type (paftacular.comps.NeutralLoss property)

M

make_formula() (paftacular.annotation.PafAnnotation static method) make_immonium() (paftacular.annotation.PafAnnotation static method) make_internal() (paftacular.annotation.PafAnnotation static method) make_named_compound() (paftacular.annotation.PafAnnotation static method) make_peptide() (paftacular.annotation.PafAnnotation static method) make_precursor() (paftacular.annotation.PafAnnotation static method) make_reference() (paftacular.annotation.PafAnnotation static method) make_smiles() (paftacular.annotation.PafAnnotation static method) make_unknown() (paftacular.annotation.PafAnnotation static method) mass_error (paftacular.annotation.CommonAnnotationParams attribute) (paftacular.annotation.PafAnnotation attribute) mass_error_unit (paftacular.annotation.CommonAnnotationParams attribute) MassError (class in paftacular.comps)

MassProvider (class in paftacular.comps) modification (paftacular.comps.ImmoniumIon attribute) module paftacular.annotation paftacular.comps paftacular.constants paftacular.conversion paftacular.errors paftacular.parser paftacular.resolution paftacular.serialization paftacular.util monoisotopic_mass (paftacular.comps.MassProvider property) mz() (paftacular.annotation.PafAnnotation method)

N

name (paftacular.comps.NamedCompound attribute) (paftacular.comps.ReferenceIon attribute) NAMED_COMPOUND (paftacular.constants.AnnotationName attribute) NamedCompound (class in paftacular.comps)

neutral_losses (paftacular.annotation.CommonAnnotationParams attribute) (paftacular.annotation.PafAnnotation attribute) NeutralLoss (class in paftacular.comps) nterm_ion_type (paftacular.comps.InternalFragment attribute)

O

ok (paftacular.parser.ParseResult property)

P

PafAnnotation (class in paftacular.annotation) PafParseError paftacular.annotation module paftacular.comps module paftacular.constants module paftacular.conversion module paftacular.errors module paftacular.IonType (in module paftacular.comps) paftacular.parser module paftacular.resolution module paftacular.serialization module paftacular.util module PaftacularError PafUnknownReferenceError PafUnsupportedCalculationError parse() (in module paftacular.parser) (paftacular.annotation.PafAnnotation static method) (paftacular.comps.Adduct static method) (paftacular.comps.ChemicalFormula static method) (paftacular.comps.ImmoniumIon static method) (paftacular.comps.InternalFragment static method) (paftacular.comps.IsotopeSpecification static method) (paftacular.comps.MassError static method) (paftacular.comps.NamedCompound static method) (paftacular.comps.NeutralLoss static method) (paftacular.comps.PeptideIon static method) (paftacular.comps.PrecursorIon static method) (paftacular.comps.ReferenceIon static method) (paftacular.comps.SMILESCompound static method) (paftacular.comps.UnknownIon static method)

parse_formula() (in module paftacular.util) parse_multi() (in module paftacular.parser) ParseResult (class in paftacular.parser) peptacular_ion_type (paftacular.annotation.PafAnnotation property) PeptideIon (class in paftacular.comps) position (paftacular.comps.PeptideIon attribute) PRECURSOR (paftacular.constants.AnnotationName attribute) PrecursorIon (class in paftacular.comps) proforma_formula (paftacular.comps.Adduct property) (paftacular.comps.ChemicalFormula property) (paftacular.comps.NeutralLoss property) (paftacular.comps.SMILESCompound property) proforma_formula() (paftacular.annotation.PafAnnotation method)

R

reference (paftacular.comps.NeutralLoss property) (paftacular.comps.ReferenceIon property) REFERENCE (paftacular.constants.AnnotationName attribute) ReferenceIon (class in paftacular.comps)

reraise_as_paftacular() (in module paftacular.errors) resolve() (in module paftacular.resolution) (paftacular.annotation.PafAnnotation method) resolved_sequence (paftacular.annotation.PafAnnotation attribute)

S

ScalableComposition (class in paftacular.comps) sequence (paftacular.annotation.PafAnnotation property) (paftacular.comps.InternalFragment attribute) (paftacular.comps.PeptideIon attribute) Serializable (class in paftacular.comps) serialize() (paftacular.annotation.PafAnnotation method) (paftacular.comps.Adduct method) (paftacular.comps.ChemicalFormula method) (paftacular.comps.ImmoniumIon method) (paftacular.comps.InternalFragment method) (paftacular.comps.IsotopeSpecification method) (paftacular.comps.MassError method) (paftacular.comps.NamedCompound method) (paftacular.comps.NeutralLoss method) (paftacular.comps.PeptideIon method) (paftacular.comps.PrecursorIon method) (paftacular.comps.ReferenceIon method) (paftacular.comps.Serializable method) (paftacular.comps.SMILESCompound method) (paftacular.comps.UnknownIon method)

series (paftacular.comps.PeptideIon attribute) SERIES (paftacular.constants.AnnotationName attribute) smiles (paftacular.comps.SMILESCompound attribute) SMILES (paftacular.constants.AnnotationName attribute) SMILESCompound (class in paftacular.comps) start_position (paftacular.comps.InternalFragment attribute)

T

text (paftacular.parser.ParseResult attribute) to_dict() (in module paftacular.serialization) (paftacular.annotation.PafAnnotation method)

to_enum() (in module paftacular.util) to_mzpaf() (in module paftacular.conversion)

U

UNANNOTATED (paftacular.constants.AnnotationName attribute)

unit (paftacular.comps.MassError attribute) UnknownIon (class in paftacular.comps)

V

V (paftacular.constants.IonSeries attribute) validate_integer() (in module paftacular.util)

validate_number() (in module paftacular.util) value (paftacular.comps.MassError attribute)

W

W (paftacular.constants.IonSeries attribute)

WA (paftacular.constants.IonSeries attribute) WB (paftacular.constants.IonSeries attribute)

X

X (paftacular.constants.BackboneCleavageType attribute) (paftacular.constants.IonSeries attribute)

Y

Y (paftacular.constants.BackboneCleavageType attribute) (paftacular.constants.IonSeries attribute)

Z

Z (paftacular.constants.BackboneCleavageType attribute) (paftacular.constants.IonSeries attribute)