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_protein_with_uniprot() (in module shephard.apis.uniprot) 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) annotate_proteome_with_uniprot() (in module shephard.apis.uniprot) 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 (Domain property) (Protein property) (Proteome property) (Site property) (Track property)

B

binerize() (in module shephard.tools.track_tools) build_domain() (in module shephard.protein.Protein) 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_from_domains() (in module shephard.tools.track_tools) build_track_symbols_from_sequence() (in module shephard.protein.Protein) build_track_values_from_sequence() (in module shephard.protein.Protein)

C

cast_attributes() (in module shephard.tools.attribute_tools) 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_name (Domain property) domain_names (Protein property) domain_overlap() (in module shephard.domain.Domain) (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 (Domain property) domain_types (Protein property) domains (Protein property) (Proteome property)

E

end (Domain property)

F

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

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

G

get_domains() (in module shephard.site.Site) 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_site_density_in_domain_normalized_by_protein() (in module shephard.tools.experimental) get_site_density_percentile_normalized_by_protein() (in module shephard.tools.experimental) 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_symbol() (in module shephard.site.Site) get_track_symbols() (in module shephard.domain.Domain) (in module shephard.protein.Protein) (in module shephard.site.Site) get_track_value() (in module shephard.site.Site) get_track_values() (in module shephard.domain.Domain) (in module shephard.protein.Protein) (in module shephard.site.Site) get_tracks_by_name() (in module shephard.proteome.Proteome)

I

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

is_valid_uniprot_accession() (in module shephard.apis.uniprot)

N

name (Protein property) (Track property)

P

position (Site property) Protein (class in shephard.protein) protein (Domain property) (Site property) (Track property)

protein() (in module shephard.proteome.Proteome) proteins (Proteome property) Proteome (class in shephard.proteome) proteome (Protein property) 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_domain() (in module shephard.protein.Protein)

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 (Site property) residue() (in module shephard.protein.Protein)

S

sequence (Domain property) (Protein property) shephard_fasta_to_proteome() (in module shephard.apis.fasta) Site (class in shephard.site) site() (in module shephard.domain.Domain) (in module shephard.protein.Protein) site_positions (Domain property) (Protein property) site_type (Site property)

site_types (Protein property) sites (Domain property) (Protein property) (Proteome property) start (Domain property) symbol (Site property) symbol() (in module shephard.track.Track) symbols (Track property) symbols_region() (in module shephard.track.Track)

T

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

track_names_to_track_type (Proteome property) track_type (Track property) tracks (Protein property) (Proteome property)

U

uniprot_accession_from_line() (in module shephard.apis.uniprot) uniprot_annotation_groups() (in module shephard.apis.uniprot) uniprot_fasta_to_proteome() (in module shephard.apis.uniprot) uniprot_proteome_to_fasta() (in module shephard.apis.uniprot) unique_domain_types (Proteome property)

unique_ID (Protein property) unique_site_types (Proteome property) unique_track_names (Proteome property) update_domain_name() (in module shephard.domain.Domain) update_site_symbol() (in module shephard.site.Site) update_site_value() (in module shephard.site.Site)

V

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

values (Track property) 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_protein_attributes_from_dictionary() (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)