Index

_

_parse_evidence_and_format_fixed_labels() (in module adaptors)

A

add() (pyqms.Results method) add_chemical_formula() (pyqms.ChemicalComposition method) add_peptide() (pyqms.ChemicalComposition method)

appMass2element_list() (pyqms.UnimodMapper method) appMass2id_list() (pyqms.UnimodMapper method) appMass2name_list() (pyqms.UnimodMapper method)

C

calc_amount_function() (in module adaptors) calc_amounts_from_rt_info_file() (pyqms.Results method) ChemicalComposition (class in pyqms) clear() (pyqms.ChemicalComposition method) composition2id_list() (pyqms.UnimodMapper method)

composition2mass() (pyqms.UnimodMapper method) composition2name_list() (pyqms.UnimodMapper method) composition_at_pos (pyqms.ChemicalComposition attribute) composition_of_aa_at_pos (pyqms.ChemicalComposition attribute) composition_of_mod_at_pos (pyqms.ChemicalComposition attribute) curate_rt_windows() (pyqms.Results method)

D

determine_max_itensity() (pyqms.Results method)

E

extract_results() (pyqms.Results method)

H

hill_notation() (pyqms.ChemicalComposition method)

hill_notation_unimod() (pyqms.ChemicalComposition method)

I

id2composition() (pyqms.UnimodMapper method) id2mass() (pyqms.UnimodMapper method)

id2name() (pyqms.UnimodMapper method) IsotopologueLibrary (class in pyqms)

M

main() (in module access_result_class) (in module basic_quantification_example) (in module complete_BSA_quantification) (in module determine_mz_and_i_error) (in module generate_quant_summary_file) (in module get_example_BSA_file) (in module mic_2d_plot) (in module mic_3d_plot) (in module parse_ident_file_and_quantify) (in module parse_ident_file_and_quantify_with_carbamidomethylation) (in module plot_match_examples) (in module view_result_pkl_stats) (in module visualize_scoring_information) (in module write_BSA_mztab_results) (in module write_mztab_result) (in module write_raw_result_csv)

mass2composition_list() (pyqms.UnimodMapper method) mass2id_list() (pyqms.UnimodMapper method) mass2name_list() (pyqms.UnimodMapper method) match_all() (pyqms.IsotopologueLibrary method) match_isotopologue() (pyqms.IsotopologueLibrary method) max_score() (pyqms.Results method)

N

name2composition() (pyqms.UnimodMapper method) name2id() (pyqms.UnimodMapper method)

name2mass() (pyqms.UnimodMapper method) name2specificity_site_list() (pyqms.UnimodMapper method)

P

parse_evidence() (in module adaptors) plot_MIC_3D() (pyqms.Results method)

plot_MICs_2D() (pyqms.Results method) print_overview() (pyqms.IsotopologueLibrary method)

R

Results (class in pyqms)

S

score_matches() (pyqms.IsotopologueLibrary method)

subtract_chemical_formula() (pyqms.ChemicalComposition method) subtract_peptide() (pyqms.ChemicalComposition method)

U

UnimodMapper (class in pyqms)

use() (pyqms.ChemicalComposition method)

W

write_result_csv() (pyqms.Results method)

write_result_mztab() (pyqms.Results method) write_rt_info_file() (pyqms.Results method)