Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | X | Y | Z A Ac (mass_automation.utils.Element attribute) Add (class in mass_automation.formula.augmentations) add_new_peak() (in module mass_automation.formula.check_formula) add_to_index() (mass_automation.experiment.Experiment method) Ag (mass_automation.utils.Element attribute) agglosamples() (in module mass_automation.sample_identification.plot) Al (mass_automation.utils.Element attribute) Am (mass_automation.utils.Element attribute) Ar (mass_automation.utils.Element attribute) As (mass_automation.utils.Element attribute) At (mass_automation.utils.Element attribute) Au (mass_automation.utils.Element attribute) AugmentationWrapper (class in mass_automation.formula.augmentations) B B (mass_automation.utils.Element attribute) Ba (mass_automation.utils.Element attribute) Be (mass_automation.utils.Element attribute) best_peak() (in module mass_automation.formula.check_formula) Bh (mass_automation.utils.Element attribute) Bi (mass_automation.utils.Element attribute) BinaryProbaModelWrapper (class in mass_automation.uncertainty) Bk (mass_automation.utils.Element attribute) Br (mass_automation.utils.Element attribute) brute_force_search() (in module mass_automation.formula.determination) C C (mass_automation.utils.Element attribute) Ca (mass_automation.utils.Element attribute) calc_features() (mass_automation.deisotoping.process.Deisotoper method) (mass_automation.deisotoping.process.LinearDeisotoper method) (mass_automation.deisotoping.process.MlDeisotoper method) Cd (mass_automation.utils.Element attribute) Ce (mass_automation.utils.Element attribute) Cf (mass_automation.utils.Element attribute) charge (mass_automation.formula.Formula attribute) check_in_index() (mass_automation.experiment.Experiment method) check_presence() (in module mass_automation.formula.check_formula) Cl (mass_automation.utils.Element attribute) Cm (mass_automation.utils.Element attribute) Cn (mass_automation.utils.Element attribute) Co (mass_automation.utils.Element attribute) compute_entropy() (in module mass_automation.uncertainty) compute_mean_entropy() (in module mass_automation.uncertainty) configure_optimizers() (mass_automation.formula.model.LSTM method) (mass_automation.formula.model.MLP method) Cr (mass_automation.utils.Element attribute) Cs (mass_automation.utils.Element attribute) Cu (mass_automation.utils.Element attribute) D Db (mass_automation.utils.Element attribute) deisotoped (mass_automation.experiment.Spectrum attribute) Deisotoper (class in mass_automation.deisotoping.process) del_isotopologues() (in module mass_automation.formula.check_formula) dict_formula (mass_automation.formula.Formula attribute) DroppingAug (class in mass_automation.formula.augmentations) Ds (mass_automation.utils.Element attribute) dumpf() (mass_automation.deisotoping.process.FeatureLogger method) Dy (mass_automation.utils.Element attribute) E Element (class in mass_automation.utils) EnsembleWrapper (class in mass_automation.uncertainty) Er (mass_automation.utils.Element attribute) Es (mass_automation.utils.Element attribute) Eu (mass_automation.utils.Element attribute) Experiment (class in mass_automation.experiment) F F (mass_automation.utils.Element attribute) Fe (mass_automation.utils.Element attribute) FeatureLogger (class in mass_automation.deisotoping.process) features (mass_automation.deisotoping.process.FeatureLogger attribute) find_name() (mass_automation.experiment.Experiment method) find_peaks() (mass_automation.deisotoping.process.Deisotoper method) find_spec_peaks() (in module mass_automation.deisotoping.process) Fl (mass_automation.utils.Element attribute) Fm (mass_automation.utils.Element attribute) format (mass_automation.experiment.Experiment attribute) Formula (class in mass_automation.formula) formula (mass_automation.formula.Formula attribute) formula2element() (in module mass_automation.formula.data) formula2element_amount() (in module mass_automation.formula.data) formula2vector() (in module mass_automation.formula.data) forward() (mass_automation.formula.model.LinearWithHidden method) (mass_automation.formula.model.LSTM method) (mass_automation.formula.model.MLP method) (mass_automation.formula.model.WeightedMSELoss method) Fr (mass_automation.utils.Element attribute) G Ga (mass_automation.utils.Element attribute) Gd (mass_automation.utils.Element attribute) Ge (mass_automation.utils.Element attribute) generate_fake_representation() (in module mass_automation.formula.data) get_chromatogram() (mass_automation.experiment.Experiment method) get_monoisotopic() (mass_automation.formula.RealIsotopicDistribution method) get_names() (mass_automation.experiment.Experiment method) get_peak_candidates() (in module mass_automation.formula.check_formula) get_representation() (mass_automation.formula.RealIsotopicDistribution method) get_slice() (mass_automation.experiment.Spectrum method) H H (mass_automation.utils.Element attribute) He (mass_automation.utils.Element attribute) Hf (mass_automation.utils.Element attribute) Hg (mass_automation.utils.Element attribute) Ho (mass_automation.utils.Element attribute) Hs (mass_automation.utils.Element attribute) I I (mass_automation.utils.Element attribute) In (mass_automation.utils.Element attribute) ints (mass_automation.experiment.Spectrum attribute) Ir (mass_automation.utils.Element attribute) isodistribution() (mass_automation.formula.Formula method) isotopic_distributions (mass_automation.experiment.Spectrum attribute) K K (mass_automation.utils.Element attribute) Kr (mass_automation.utils.Element attribute) L La (mass_automation.utils.Element attribute) Li (mass_automation.utils.Element attribute) LinearDeisotoper (class in mass_automation.deisotoping.process) LinearWithHidden (class in mass_automation.formula.model) load() (mass_automation.deisotoping.process.Deisotoper method) log_elementwise() (in module mass_automation.formula.model) lorentzian() (in module mass_automation.utils) Lr (mass_automation.utils.Element attribute) LSTM (class in mass_automation.formula.model) Lu (mass_automation.utils.Element attribute) Lv (mass_automation.utils.Element attribute) M make_prediction() (mass_automation.deisotoping.process.Deisotoper method) (mass_automation.deisotoping.process.LinearDeisotoper method) (mass_automation.deisotoping.process.MlDeisotoper method) mass_automation module mass_automation.deisotoping module mass_automation.deisotoping.process module mass_automation.experiment module mass_automation.formula module mass_automation.formula.augmentations module mass_automation.formula.check_formula module mass_automation.formula.data module mass_automation.formula.determination module mass_automation.formula.model module mass_automation.formula.plot module mass_automation.sample_identification module mass_automation.sample_identification.plot module mass_automation.uncertainty module mass_automation.utils module masses (mass_automation.experiment.Spectrum attribute) Mc (mass_automation.utils.Element attribute) Md (mass_automation.utils.Element attribute) Mg (mass_automation.utils.Element attribute) MlDeisotoper (class in mass_automation.deisotoping.process) MLP (class in mass_automation.formula.model) Mn (mass_automation.utils.Element attribute) Mo (mass_automation.utils.Element attribute) model (mass_automation.deisotoping.process.Deisotoper attribute) module mass_automation mass_automation.deisotoping mass_automation.deisotoping.process mass_automation.experiment mass_automation.formula mass_automation.formula.augmentations mass_automation.formula.check_formula mass_automation.formula.data mass_automation.formula.determination mass_automation.formula.model mass_automation.formula.plot mass_automation.sample_identification mass_automation.sample_identification.plot mass_automation.uncertainty mass_automation.utils monoisotopic_mass (mass_automation.formula.Formula attribute) Mt (mass_automation.utils.Element attribute) N N (mass_automation.utils.Element attribute) n_elements (mass_automation.utils.Element attribute) n_points (mass_automation.experiment.Experiment attribute) (mass_automation.experiment.Spectrum attribute) n_scans (mass_automation.experiment.Experiment attribute) (mass_automation.experiment.Spectrum attribute) Na (mass_automation.utils.Element attribute) Nb (mass_automation.utils.Element attribute) Nd (mass_automation.utils.Element attribute) Ne (mass_automation.utils.Element attribute) Nh (mass_automation.utils.Element attribute) Ni (mass_automation.utils.Element attribute) No (mass_automation.utils.Element attribute) Np (mass_automation.utils.Element attribute) O O (mass_automation.utils.Element attribute) Og (mass_automation.utils.Element attribute) OriginalFormulaDataset (class in mass_automation.formula.data) Os (mass_automation.utils.Element attribute) P P (mass_automation.utils.Element attribute) Pa (mass_automation.utils.Element attribute) PadSequence (class in mass_automation.formula.data) PadSequenceConstant (class in mass_automation.formula.data) path (mass_automation.experiment.Experiment attribute) Pb (mass_automation.utils.Element attribute) Pd (mass_automation.utils.Element attribute) peak_pick() (in module mass_automation.experiment) plot_compare() (in module mass_automation.formula.plot) plot_pca() (in module mass_automation.sample_identification.plot) Pm (mass_automation.utils.Element attribute) Po (mass_automation.utils.Element attribute) Pr (mass_automation.utils.Element attribute) predict() (mass_automation.uncertainty.BinaryProbaModelWrapper method) (mass_automation.uncertainty.EnsembleWrapper method) predict_all() (mass_automation.uncertainty.EnsembleWrapper method) predict_w_uncertainty() (mass_automation.uncertainty.EnsembleWrapper method) Pt (mass_automation.utils.Element attribute) Pu (mass_automation.utils.Element attribute) R Ra (mass_automation.utils.Element attribute) RandomNoise (class in mass_automation.formula.augmentations) Rb (mass_automation.utils.Element attribute) Re (mass_automation.utils.Element attribute) RealIsotopicDistribution (class in mass_automation.formula) Rf (mass_automation.utils.Element attribute) Rg (mass_automation.utils.Element attribute) Rh (mass_automation.utils.Element attribute) Rn (mass_automation.utils.Element attribute) Ru (mass_automation.utils.Element attribute) run() (mass_automation.deisotoping.process.Deisotoper method) S S (mass_automation.utils.Element attribute) save_state() (mass_automation.experiment.Spectrum method) Sb (mass_automation.utils.Element attribute) Sc (mass_automation.utils.Element attribute) Scale (class in mass_automation.formula.augmentations) Se (mass_automation.utils.Element attribute) Sg (mass_automation.utils.Element attribute) Shift (class in mass_automation.formula.augmentations) Si (mass_automation.utils.Element attribute) Sm (mass_automation.utils.Element attribute) Sn (mass_automation.utils.Element attribute) spectra_ints (mass_automation.experiment.Experiment attribute) spectra_mass (mass_automation.experiment.Experiment attribute) Spectrum (class in mass_automation.experiment) Sr (mass_automation.utils.Element attribute) str_formula (mass_automation.formula.Formula attribute) summarize() (mass_automation.experiment.Experiment method) T Ta (mass_automation.utils.Element attribute) targets (mass_automation.deisotoping.process.FeatureLogger attribute) Tb (mass_automation.utils.Element attribute) Tc (mass_automation.utils.Element attribute) Te (mass_automation.utils.Element attribute) test_epoch_end() (mass_automation.formula.model.LSTM method) (mass_automation.formula.model.MLP method) test_step() (mass_automation.formula.model.LSTM method) (mass_automation.formula.model.MLP method) Th (mass_automation.utils.Element attribute) Ti (mass_automation.utils.Element attribute) Tl (mass_automation.utils.Element attribute) Tm (mass_automation.utils.Element attribute) to_chrom_align_net() (mass_automation.experiment.Experiment method) to_msi_warp() (mass_automation.experiment.Spectrum method) to_sima() (mass_automation.experiment.Experiment method) train_epoch_end() (mass_automation.formula.model.LSTM method) (mass_automation.formula.model.MLP method) training (mass_automation.formula.model.LinearWithHidden attribute) (mass_automation.formula.model.LSTM attribute) (mass_automation.formula.model.MLP attribute) (mass_automation.formula.model.WeightedMSELoss attribute) training_step() (mass_automation.formula.model.LSTM method) (mass_automation.formula.model.MLP method) Ts (mass_automation.utils.Element attribute) U U (mass_automation.utils.Element attribute) V V (mass_automation.utils.Element attribute) validation_epoch_end() (mass_automation.formula.model.LSTM method) (mass_automation.formula.model.MLP method) validation_step() (mass_automation.formula.model.LSTM method) (mass_automation.formula.model.MLP method) vector() (mass_automation.formula.Formula method) vectorize() (mass_automation.experiment.Spectrum method) vectorize_by_convolution() (mass_automation.experiment.Spectrum method) W W (mass_automation.utils.Element attribute) WeightedMSELoss (class in mass_automation.formula.model) write() (mass_automation.deisotoping.process.FeatureLogger method) X Xe (mass_automation.utils.Element attribute) Y Y (mass_automation.utils.Element attribute) Yb (mass_automation.utils.Element attribute) Z Zn (mass_automation.utils.Element attribute) Zr (mass_automation.utils.Element attribute)