Index

_

__contains__() (in module shephard.proteome.Proteome) __getitem__() (in module shephard.proteome.Proteome)

__iter__() (in module shephard.proteome.Proteome) __len__() (in module shephard.proteome.Proteome)

A

add_attribute() (in module shephard.domain.Domain) (in module shephard.protein.Protein) (in module shephard.proteome.Proteome) (in module shephard.site.Site) (in module shephard.track.Track) add_domain() (in module shephard.protein.Protein) add_domain_attributes_from_dictionary() (in module shephard.interfaces.si_domains) add_domain_attributes_from_file() (in module shephard.interfaces.si_domains) add_domains() (in module shephard.protein.Protein) add_domains_from_dictionary() (in module shephard.interfaces.si_domains) add_domains_from_file() (in module shephard.interfaces.si_domains) add_protein() (in module shephard.proteome.Proteome) add_protein_attributes_from_dictionary() (in module shephard.interfaces.si_protein_attributes) add_protein_attributes_from_file() (in module shephard.interfaces.si_protein_attributes) add_proteins() (in module shephard.proteome.Proteome) add_proteins_from_dictionary() (in module shephard.interfaces.si_proteins) add_proteins_from_file() (in module shephard.interfaces.si_proteins) add_site() (in module shephard.protein.Protein) add_sites_from_dictionary() (in module shephard.interfaces.si_sites)

add_sites_from_file() (in module shephard.interfaces.si_sites) add_track() (in module shephard.protein.Protein) add_tracks_from_dictionary() (in module shephard.interfaces.si_tracks) add_tracks_from_file() (in module shephard.interfaces.si_tracks) annotate_domains_with_dimensions() (in module shephard.apis.albatross_api) annotate_proteome_with_dimensions() (in module shephard.apis.albatross_api) annotate_proteome_with_disorder_track() (in module shephard.apis.metapredict_api) annotate_proteome_with_disorder_tracks_and_disordered_domains() (in module shephard.apis.metapredict_api) annotate_proteome_with_disordered_domains() (in module shephard.apis.metapredict_api) attribute() (in module shephard.domain.Domain) (in module shephard.protein.Protein) (in module shephard.proteome.Proteome) (in module shephard.site.Site) (in module shephard.track.Track) attributes() (in module shephard.domain.Domain) (in module shephard.protein.Protein) (in module shephard.proteome.Proteome) (in module shephard.site.Site) (in module shephard.track.Track)

B

build_domains_from_track_values() (in module shephard.tools.domain_tools) build_mega_string() (in module shephard.tools.sequence_tools) build_missing_domains() (in module shephard.tools.domain_tools)

build_site_density_vector() (in module shephard.tools.site_tools) build_track() (in module shephard.protein.Protein) build_track_symbols_from_sequence() (in module shephard.protein.Protein) build_track_values_from_sequence() (in module shephard.protein.Protein)

C

check_sequence_is_valid() (in module shephard.protein.Protein)

check_unique_ID() (in module shephard.proteome.Proteome) convert_to_valid() (in module shephard.protein.Protein)

D

Domain (class in shephard.domain) domain() (in module shephard.protein.Protein) domain_names() (in module shephard.protein.Protein) domain_overlap() (in module shephard.tools.domain_tools) domain_overlap_by_position() (in module shephard.tools.domain_tools)

domain_overlap_fraction() (in module shephard.tools.domain_tools) domain_type() (in module shephard.domain.Domain) domain_types() (in module shephard.protein.Protein) domains() (in module shephard.protein.Protein) (in module shephard.proteome.Proteome)

E

end() (in module shephard.domain.Domain)

F

fasta_to_proteome() (in module shephard.apis.fasta)

find_string_positions() (in module shephard.tools.sequence_tools)

G

get_domains_by_position() (in module shephard.protein.Protein) get_domains_by_position_and_type() (in module shephard.protein.Protein) get_domains_by_range() (in module shephard.protein.Protein) get_domains_by_type() (in module shephard.protein.Protein) (in module shephard.proteome.Proteome) get_local_sequence_context() (in module shephard.site.Site) get_sequence_context() (in module shephard.protein.Protein) get_sequence_region() (in module shephard.protein.Protein) get_sites_by_position() (in module shephard.protein.Protein) get_sites_by_range() (in module shephard.protein.Protein)

get_sites_by_type() (in module shephard.domain.Domain) (in module shephard.protein.Protein) (in module shephard.proteome.Proteome) get_sites_by_type_and_range() (in module shephard.protein.Protein) get_track_symbols() (in module shephard.domain.Domain) (in module shephard.protein.Protein) (in module shephard.site.Site) get_track_values() (in module shephard.domain.Domain) (in module shephard.protein.Protein) (in module shephard.site.Site)

I

inside_domain() (in module shephard.domain.Domain)

M

module shephard.proteome

N

name() (in module shephard.protein.Protein) (in module shephard.track.Track)

P

position() (in module shephard.site.Site) Protein (class in shephard.protein) protein() (in module shephard.domain.Domain) (in module shephard.proteome.Proteome) (in module shephard.site.Site) (in module shephard.track.Track)

proteins() (in module shephard.proteome.Proteome) Proteome (class in shephard.proteome) proteome() (in module shephard.protein.Protein) proteome_to_fasta() (in module shephard.apis.fasta)

R

remove_attribute() (in module shephard.domain.Domain) (in module shephard.protein.Protein) (in module shephard.proteome.Proteome) (in module shephard.site.Site) (in module shephard.track.Track)

remove_protein() (in module shephard.proteome.Proteome) remove_proteins() (in module shephard.proteome.Proteome) remove_site() (in module shephard.protein.Protein) remove_track() (in module shephard.protein.Protein) residue() (in module shephard.protein.Protein) (in module shephard.site.Site)

S

sequence() (in module shephard.domain.Domain) (in module shephard.protein.Protein) shephard.proteome module Site (class in shephard.site) site() (in module shephard.domain.Domain) (in module shephard.protein.Protein) site_positions() (in module shephard.protein.Protein) site_type() (in module shephard.site.Site)

site_types() (in module shephard.protein.Protein) sites() (in module shephard.domain.Domain) (in module shephard.protein.Protein) (in module shephard.proteome.Proteome) start() (in module shephard.domain.Domain) symbol() (in module shephard.site.Site) (in module shephard.track.Track) symbols() (in module shephard.track.Track) symbols_region() (in module shephard.track.Track)

T

Track (class in shephard.track) track() (in module shephard.protein.Protein) track_names() (in module shephard.protein.Protein)

track_names_to_track_type() (in module shephard.proteome.Proteome) track_type() (in module shephard.track.Track) tracks() (in module shephard.protein.Protein)

U

uniprot_fasta_to_proteome() (in module shephard.apis.uniprot) uniprot_proteome_to_fasta() (in module shephard.apis.uniprot) unique_domain_types() (in module shephard.proteome.Proteome)

unique_ID() (in module shephard.protein.Protein) unique_site_types() (in module shephard.proteome.Proteome) unique_track_names() (in module shephard.proteome.Proteome)

V

value() (in module shephard.site.Site) (in module shephard.track.Track)

values() (in module shephard.track.Track) values_region() (in module shephard.track.Track)

W

write_all_symbols_tracks_single_file() (in module shephard.interfaces.si_tracks) write_all_tracks_separate_files() (in module shephard.interfaces.si_tracks) write_all_values_tracks_single_file() (in module shephard.interfaces.si_tracks) write_domains() (in module shephard.interfaces.si_domains) write_domains_from_list() (in module shephard.interfaces.si_domains)

write_protein_attributes() (in module shephard.interfaces.si_protein_attributes) write_proteins() (in module shephard.interfaces.si_proteins) write_sites() (in module shephard.interfaces.si_sites) write_sites_from_list() (in module shephard.interfaces.si_sites) write_tracks() (in module shephard.interfaces.si_tracks) write_tracks_from_list() (in module shephard.interfaces.si_tracks)