Index

A

A (paftacular.constants.AminoAcids attribute) (paftacular.constants.BackboneCleavageType attribute) (paftacular.constants.IonSeries attribute) Adduct (class in paftacular.comps) amino_acid (paftacular.comps.ImmoniumIon attribute) AminoAcids (class in paftacular.constants) AnnotationName (class in paftacular.constants)

as_dict() (paftacular.comps.Adduct method) (paftacular.comps.IsotopeSpecification method) (paftacular.comps.NeutralLoss method) 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.AminoAcids attribute) (paftacular.constants.BackboneCleavageType attribute) (paftacular.constants.IonSeries attribute) ChemicalFormula (class in paftacular.comps) 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) 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.AminoAcids attribute) (paftacular.constants.IonSeries attribute)

DA (paftacular.constants.IonSeries attribute) DB (paftacular.constants.IonSeries attribute) dict_composition (paftacular.comps.CompositionProvider property)

E

E (paftacular.constants.AminoAcids attribute)

element (paftacular.comps.IsotopeSpecification attribute) end_position (paftacular.comps.InternalFragment attribute)

F

F (paftacular.constants.AminoAcids attribute) 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_to_composition() (in module paftacular.comps)

G

G (paftacular.constants.AminoAcids attribute)

H

H (paftacular.constants.AminoAcids attribute)

I

I (paftacular.constants.AminoAcids attribute) IMMONIUM (paftacular.constants.AnnotationName attribute) ImmoniumIon (class in paftacular.comps) INTERNAL (paftacular.constants.AnnotationName attribute)

InternalFragment (class in paftacular.comps) InternalSeries (class in paftacular.constants) IonSeries (class in paftacular.constants) is_average (paftacular.comps.IsotopeSpecification attribute) IsotopeSpecification (class in paftacular.comps)

K

K (paftacular.constants.AminoAcids attribute)

L

L (paftacular.constants.AminoAcids attribute)

label (paftacular.comps.UnknownIon attribute) loss_type (paftacular.comps.NeutralLoss property)

M

M (paftacular.constants.AminoAcids attribute) mass() (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)

MassError (class in paftacular.comps) MassProvider (class in paftacular.comps) modification (paftacular.comps.ImmoniumIon attribute) module paftacular.comps paftacular.constants paftacular.parser paftacular.util monoisotopic_mass (paftacular.comps.MassProvider property) mzPAFParser (class in paftacular.parser)

N

N (paftacular.constants.AminoAcids attribute) name (paftacular.comps.NamedCompound attribute) (paftacular.comps.ReferenceIon attribute)

NAMED_COMPOUND (paftacular.constants.AnnotationName attribute) NamedCompound (class in paftacular.comps) NeutralLoss (class in paftacular.comps) nterm_ion_type (paftacular.comps.InternalFragment attribute)

P

P (paftacular.constants.AminoAcids attribute) paftacular.comps module paftacular.constants module paftacular.parser module paftacular.util module parse() (in module paftacular.parser) (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) (paftacular.parser.mzPAFParser method)

parse_formula() (in module paftacular.util) parse_multi() (in module paftacular.parser) (paftacular.parser.mzPAFParser method) parse_single() (in module paftacular.parser) 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)

Q

Q (paftacular.constants.AminoAcids attribute)

R

R (paftacular.constants.AminoAcids attribute) reference (paftacular.comps.NeutralLoss property) (paftacular.comps.ReferenceIon property)

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

S

S (paftacular.constants.AminoAcids attribute) ScalableComposition (class in paftacular.comps) sequence (paftacular.comps.InternalFragment attribute) (paftacular.comps.PeptideIon attribute) Serializable (class in paftacular.comps) serialize() (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

T (paftacular.constants.AminoAcids attribute)

U

UNANNOTATED (paftacular.constants.AnnotationName attribute)

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

V

V (paftacular.constants.AminoAcids attribute) (paftacular.constants.IonSeries attribute)

value (paftacular.comps.MassError attribute)

W

W (paftacular.constants.AminoAcids attribute) (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.AminoAcids attribute) (paftacular.constants.BackboneCleavageType attribute) (paftacular.constants.IonSeries attribute)

Z

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