shephard
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Contents:
Overview
Getting Started
Proteome
Protein
Domain
Site
Track
SHEPHARD files
Interfaces
Tools
apis
Code convention
shephard
Index
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Index
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A
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B
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C
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D
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E
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F
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G
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I
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M
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N
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P
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R
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S
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T
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U
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V
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W
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__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_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)
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