Index

A

add_base_track() (IPTK.Classes.Annotator.Annotator method) add_coverage_track() (IPTK.Classes.Annotator.Annotator method) add_marked_positions_track() (IPTK.Classes.Annotator.Annotator method)

add_segmented_track() (IPTK.Classes.Annotator.Annotator method) add_stacked_track() (IPTK.Classes.Annotator.Annotator method) Annotator (class in IPTK.Classes.Annotator) append_to_calling_string() (in module IPTK.Utils.UtilityFunction)

B

build_sequence_table() (in module IPTK.Utils.UtilityFunction)

C

call_meme() (in module IPTK.IO.MEMEInterface)

check_peptide_made_of_std_20_aa() (in module IPTK.Utils.UtilityFunction) combine_summary() (in module IPTK.Utils.UtilityFunction)

F

Features (class in IPTK.Classes.Features)

G

generate_color_scale() (in module IPTK.Utils.UtilityFunction) generate_random_name() (in module IPTK.Utils.UtilityFunction) generate_random_protein_mapping() (in module IPTK.Utils.UtilityFunction) get_allele_group() (IPTK.Classes.HLAChain.HLAChain method) (IPTK.Classes.HLAMolecules.HLAMolecule method) get_alleles() (IPTK.Classes.HLASet.HLASet method) get_chain_class() (IPTK.Classes.HLAChain.HLAChain method) get_chains() (IPTK.Classes.Features.Features method) get_class() (IPTK.Classes.HLAChain.HLAChain method) (IPTK.Classes.HLAMolecules.HLAMolecule method) (IPTK.Classes.HLASet.HLASet method) get_disulfide_bonds() (IPTK.Classes.Features.Features method) get_domains() (IPTK.Classes.Features.Features method) get_experiment_summary() (in module IPTK.Utils.UtilityFunction) get_figure() (IPTK.Classes.Annotator.Annotator method) get_gene() (IPTK.Classes.HLAChain.HLAChain method) (IPTK.Classes.HLAMolecules.HLAMolecule method) get_hla_count() (IPTK.Classes.HLASet.HLASet method) get_idx_peptide_in_sequence_table() (in module IPTK.Utils.UtilityFunction) get_meme_help() (in module IPTK.IO.MEMEInterface)

get_meta_data() (IPTK.Classes.Proband.Proband method) get_name() (IPTK.Classes.HLAChain.HLAChain method) (IPTK.Classes.HLAMolecules.HLAMolecule method) (IPTK.Classes.Proband.Proband method) get_names() (IPTK.Classes.HLASet.HLASet method) get_number_chains() (IPTK.Classes.Features.Features method) get_number_disulfide_bonds() (IPTK.Classes.Features.Features method) get_number_domains() (IPTK.Classes.Features.Features method) get_number_glycosylation_sites() (IPTK.Classes.Features.Features method) get_number_modifications() (IPTK.Classes.Features.Features method) get_number_PTMs() (IPTK.Classes.Features.Features method) get_number_sequence_variants() (IPTK.Classes.Features.Features method) get_number_splice_variants() (IPTK.Classes.Features.Features method) get_protein_group() (IPTK.Classes.HLAChain.HLAChain method) (IPTK.Classes.HLAMolecules.HLAMolecule method) get_PTMs() (IPTK.Classes.Features.Features method) get_PTMs_glycosylation() (IPTK.Classes.Features.Features method) get_PTMs_modifications() (IPTK.Classes.Features.Features method) get_sequence_variants() (IPTK.Classes.Features.Features method) get_signal_peptide_index() (IPTK.Classes.Features.Features method) get_splice_variants() (IPTK.Classes.Features.Features method)

H

has_allele() (IPTK.Classes.HLASet.HLASet method) has_allele_group() (IPTK.Classes.HLASet.HLASet method) has_chains() (IPTK.Classes.Features.Features method) has_disulfide_bond() (IPTK.Classes.Features.Features method) has_domains() (IPTK.Classes.Features.Features method) has_gene() (IPTK.Classes.HLASet.HLASet method) has_glycosylation_site() (IPTK.Classes.Features.Features method) has_protein_group() (IPTK.Classes.HLASet.HLASet method)

has_PTMs() (IPTK.Classes.Features.Features method) has_sequence_variants() (IPTK.Classes.Features.Features method) has_signal_peptide() (IPTK.Classes.Features.Features method) has_site_modifications() (IPTK.Classes.Features.Features method) has_splice_variants() (IPTK.Classes.Features.Features method) HLAChain (class in IPTK.Classes.HLAChain) HLAMolecule (class in IPTK.Classes.HLAMolecules) HLASet (class in IPTK.Classes.HLASet)

I

IPTK module IPTK.Analysis module IPTK.Classes module IPTK.Classes.Annotator module IPTK.Classes.Features module IPTK.Classes.HLAChain module IPTK.Classes.HLAMolecules module IPTK.Classes.HLASet module

IPTK.Classes.Proband module IPTK.IO module IPTK.IO.MEMEInterface module IPTK.Utils module IPTK.Utils.Mapping module IPTK.Utils.Types module IPTK.Utils.UtilityFunction module IPTK.Visualization module is_meme_callable() (in module IPTK.IO.MEMEInterface)

L

load_3d_figure() (in module IPTK.Utils.UtilityFunction)

M

map_from_uniprot_gene() (in module IPTK.Utils.Mapping) map_from_uniprot_pdb() (in module IPTK.Utils.Mapping) module IPTK IPTK.Analysis IPTK.Classes IPTK.Classes.Annotator IPTK.Classes.Features IPTK.Classes.HLAChain IPTK.Classes.HLAMolecules IPTK.Classes.HLASet IPTK.Classes.Proband IPTK.IO IPTK.IO.MEMEInterface IPTK.Utils IPTK.Utils.Mapping IPTK.Utils.Types IPTK.Utils.UtilityFunction IPTK.Visualization

P

pad_mapped_proteins() (in module IPTK.Utils.UtilityFunction)

Proband (class in IPTK.Classes.Proband)

S

save_3d_figure() (in module IPTK.Utils.UtilityFunction) save_fig() (IPTK.Classes.Annotator.Annotator method)

simulate_protein_binary_represention() (in module IPTK.Utils.UtilityFunction) simulate_protein_representation() (in module IPTK.Utils.UtilityFunction) summary() (IPTK.Classes.Features.Features method)

U

update_info() (IPTK.Classes.Proband.Proband method)