Index

A

aa_property_percentage() (in module peptacular.sequence.properties) alpha_helix_percent() (in module peptacular.sequence.properties) annotate_ambiguity() (in module peptacular.sequence.basic)

append_mods() (in module peptacular.sequence.mod_builder) aromaticity() (in module peptacular.sequence.properties) as_tuple() (peptacular.annotation.mod.Mod method) average_buried_area() (in module peptacular.sequence.properties)

B

beta_sheet_percent() (in module peptacular.sequence.properties)

beta_turn_percent() (in module peptacular.sequence.properties) bulkiness() (in module peptacular.sequence.properties)

C

calc_property() (in module peptacular.sequence.properties) calc_window_property() (in module peptacular.sequence.properties) charge_at_ph() (in module peptacular.sequence.properties) clear_cache() (peptacular.isotope.IsotopeLookup method) cleavage_sites() (in module peptacular.sequence.digestion) codons() (in module peptacular.sequence.properties) coil_percent() (in module peptacular.sequence.properties) combinations() (in module peptacular.sequence.combinatoric)

combinations_with_replacement() (in module peptacular.sequence.combinatoric) comp() (in module peptacular.sequence.mass_funcs) condense_static_mods() (in module peptacular.sequence.mod_builder) condense_to_peptidoform() (in module peptacular.sequence.mod_builder) convert_casanovo_sequence() (in module peptacular.sequence.converters) convert_diann_sequence() (in module peptacular.sequence.converters) convert_ip2_sequence() (in module peptacular.sequence.converters) count_residues() (in module peptacular.sequence.basic) coverage() (in module peptacular.sequence.subseqs)

D

digest() (in module peptacular.sequence.digestion)

E

end (peptacular.spans.Span attribute)

estimate_isotopic_distribution() (in module peptacular.sequence.isotope) extend_mods() (in module peptacular.sequence.mod_builder)

F

fast_fragment() (in module peptacular.sequence.fragmentation) filter_mods() (in module peptacular.sequence.mod_builder) find_subsequence_indices() (in module peptacular.sequence.subseqs)

flexibility() (in module peptacular.sequence.properties) frag() (in module peptacular.sequence.fragmentation) fragment() (in module peptacular.sequence.fragmentation) from_ms2_pip() (in module peptacular.sequence.mod_builder)

G

generate_random() (in module peptacular.sequence.basic) get_cache_size() (peptacular.isotope.IsotopeLookup method) get_charge() (peptacular.annotation.mod.Mod method) (peptacular.annotation.mod.Mods method) get_composition() (peptacular.annotation.mod.Mod method) (peptacular.annotation.mod.Mods method)

get_composition_with_delta_mass_charge() (peptacular.annotation.mod.Mods method) get_isotope_pattern() (peptacular.isotope.IsotopeLookup method) get_mass() (peptacular.annotation.mod.Mod method) (peptacular.annotation.mod.Mods method) get_mass_charge() (peptacular.annotation.mod.Mods method) get_mods() (in module peptacular.sequence.mod_builder)

H

hplc() (in module peptacular.sequence.properties)

hydrophilicity() (in module peptacular.sequence.properties) hydrophobicity() (in module peptacular.sequence.properties)

I

Interval (class in peptacular.annotation.mod) is_ambiguous() (in module peptacular.sequence.basic) is_modified() (in module peptacular.sequence.basic)

is_subsequence() (in module peptacular.sequence.subseqs) IsotopeLookup (class in peptacular.isotope) isotopic_distribution() (in module peptacular.sequence.isotope) IsotopicData (class in peptacular.isotope)

J

join() (in module peptacular.sequence.transformations)

L

left_semi_digest() (in module peptacular.sequence.digestion)

M

mass() (in module peptacular.sequence.mass_funcs) missed_cleavages (peptacular.spans.Span attribute) Mod (class in peptacular.annotation.mod) modification_coverage() (in module peptacular.sequence.subseqs) modify() (in module peptacular.sequence.mod_builder) Mods (class in peptacular.annotation.mod) mods (peptacular.annotation.mod.Mods property) module peptacular peptacular.sequence.basic peptacular.sequence.combinatoric peptacular.sequence.converters peptacular.sequence.digestion peptacular.sequence.fragmentation peptacular.sequence.isotope peptacular.sequence.mass_funcs peptacular.sequence.mod_builder peptacular.sequence.properties peptacular.sequence.subseqs peptacular.sequence.transformations

mutability() (in module peptacular.sequence.properties) mz() (in module peptacular.sequence.mass_funcs)

N

nonspecific_digest() (in module peptacular.sequence.digestion)

P

parse() (in module peptacular.sequence.basic) parse_chimeric() (in module peptacular.sequence.basic) parse_items() (peptacular.annotation.mod.Mods method) parse_tuples() (peptacular.annotation.mod.Mods method) peptacular module peptacular.sequence.basic module peptacular.sequence.combinatoric module peptacular.sequence.converters module peptacular.sequence.digestion module peptacular.sequence.fragmentation module peptacular.sequence.isotope module

peptacular.sequence.mass_funcs module peptacular.sequence.mod_builder module peptacular.sequence.properties module peptacular.sequence.subseqs module peptacular.sequence.transformations module percent_coverage() (in module peptacular.sequence.subseqs) percent_residues() (in module peptacular.sequence.basic) permutations() (in module peptacular.sequence.combinatoric) pi() (in module peptacular.sequence.properties) polarity() (in module peptacular.sequence.properties) pop_mods() (in module peptacular.sequence.mod_builder) product() (in module peptacular.sequence.combinatoric) property_partitions() (in module peptacular.sequence.properties)

R

recognition_factors() (in module peptacular.sequence.properties) refractivity() (in module peptacular.sequence.properties)

remove_mods() (in module peptacular.sequence.mod_builder) reverse() (in module peptacular.sequence.transformations) right_semi_digest() (in module peptacular.sequence.digestion)

S

secondary_structure() (in module peptacular.sequence.properties) semi_digest() (in module peptacular.sequence.digestion) sequence_length() (in module peptacular.sequence.basic) serialize() (in module peptacular.sequence.basic) (peptacular.annotation.mod.Mods method) serialize_chimeric() (in module peptacular.sequence.basic) set_mods() (in module peptacular.sequence.mod_builder) shift() (in module peptacular.sequence.transformations) shuffle() (in module peptacular.sequence.transformations)

simple_cleavage_sites() (in module peptacular.sequence.digestion) simple_digest() (in module peptacular.sequence.digestion) sort() (in module peptacular.sequence.transformations) Span (class in peptacular.spans) span_to_sequence() (in module peptacular.sequence.transformations) split() (in module peptacular.sequence.transformations) start (peptacular.spans.Span attribute) strip_mods() (in module peptacular.sequence.mod_builder) surface_accessibility() (in module peptacular.sequence.properties)

T

to_ms2_pip() (in module peptacular.sequence.mod_builder)

transmembrane_tendency() (in module peptacular.sequence.properties)

V

validate() (in module peptacular.sequence.basic)