unidec.LipiDec.Infusion package¶
Submodules¶
unidec.LipiDec.Infusion.Formulas module¶
- unidec.LipiDec.Infusion.Formulas.get_count(comp, element)¶
unidec.LipiDec.Infusion.LipiDecEng module¶
- class unidec.LipiDec.Infusion.LipiDecEng.LipiDec(data, topdf)¶
Bases:
object- apply_ratio(ratio)¶
- cleanup_db(mode='positive', ignore_list=None, include_list=None, drop_duplicates=True)¶
- correct_peaks()¶
- detect_coalescence(isomasses, isoints, isomatches, row, index=2)¶
- find_alternates()¶
- find_good_species()¶
- find_initial_matches()¶
- find_isotope_matches(minmatches=2)¶
- find_matches(tolerance=None)¶
- find_missing_peaks()¶
- get_peaks()¶
- make_spectrum()¶
- plot_hits(ax)¶
- run_decon()¶
- sort_df()¶
- class unidec.LipiDec.Infusion.LipiDecEng.LipiDecRunner(datapath, libpath, dir, datarange=None)¶
Bases:
object- make_plot(show=True, plottype='log')¶
- run(ignore_list=None, outdir=None, include_list=None)¶
- unidec.LipiDec.Infusion.LipiDecEng.matcher(array, target, tolerance, fwhms)¶
unidec.LipiDec.Infusion.LipiDec_DataBaseGenerator module¶
- unidec.LipiDec.Infusion.LipiDec_DataBaseGenerator.adduct_mass(name)¶
Calculate the mass shift of an adduct from the name :param name: The name from the adduct database :return: Monoisotopic Mass
- unidec.LipiDec.Infusion.LipiDec_DataBaseGenerator.construct_mol(smiles, subs)¶
- unidec.LipiDec.Infusion.LipiDec_DataBaseGenerator.find_basemods(struct)¶
- unidec.LipiDec.Infusion.LipiDec_DataBaseGenerator.get_subs(att, subs, cond, mods)¶
- unidec.LipiDec.Infusion.LipiDec_DataBaseGenerator.make_adduct_db(adducts)¶
- unidec.LipiDec.Infusion.LipiDec_DataBaseGenerator.make_subs_list(lclass, subs)¶
Get the list of substituents for a given class :param lclass: Lipid Class XML object :param subs: Substituents XML object :return: DataFrame with substituent info, numpy array of similar info
- unidec.LipiDec.Infusion.LipiDec_DataBaseGenerator.massfromsmiles(smiles, subs)¶
- unidec.LipiDec.Infusion.LipiDec_DataBaseGenerator.massfromstruct(struct, subs, basemods=None)¶
- unidec.LipiDec.Infusion.LipiDec_DataBaseGenerator.sum_comp_only(df)¶