Index

A

a (Ellipsoid attribute) a_curve (CsProxy attribute) (NullFlowChange attribute) a_curve2 (NullFlowChange attribute) add_annotate3D() (in module molass.PlotUtils.Annotation3D) add_arrow3D() (in module molass.PlotUtils.Arrow3D) add_center_plane() (in module molass.DensitySpace.VoxelSpace) add_unit() (ProgressSet method)

adjust_components_consistently() (in module molass.LowRank.ConsistentAdjuster) align_zero_y() (in module molass.PlotUtils.TwinAxesUtils) all_done() (ProgressUnit method) Annotation3D (class in molass.PlotUtils.Annotation3D) area (Component attribute) Arrow3D (class in molass.PlotUtils.Arrow3D) as_list() (PairedRange method) atsas_is_available (Controller attribute)

B

b (Ellipsoid attribute) Baseline2D (class in molass.Baseline.Baseline2D) baseline_method (SsMatrixData attribute) beamline_info (SecSaxsData attribute)

BeamlineInfo (class in molass.DataUtils.Beamline) best_params (V2Result attribute) bookpath (Controller attribute) bridge_recognize_peaks() (in module molass.Peaks.RecognizerSpecific) bubble_check_impl() (in module molass.DataUtils.AnomalyHandlers)

C

c (Ellipsoid attribute) caseid (FlowChangeJudgeInfo attribute) ccurve (Component attribute), [1] center (Ellipsoid attribute) (NewGrain attribute) (Particle attribute) (SolidGrain attribute) (Sphere attribute) center_x (Linesegment attribute) center_y (Linesegment attribute) check_egh_bounds() (in module molass.ScipyUtils.BoundsChecker) check_peaklike_segment() (in module molass.Geometric.Peaklike) check_pywin32_postinstall() (in module molass.PackageUtils.PyWin32Utils) cleanup() (Controller method) close() (PlotResult method) combination_pairs() (in module molass.Mapping.PeakMatcher) comparison_plot() (in module molass.PlotUtils.Comparison) completed_units (ProgressSet attribute) Component (class in molass.LowRank.Component) ComponentCurve (class in molass.LowRank.ComponentCurve) compute_3d_xyz() (in module molass.PlotUtils.MatrixPlot) compute_area() (Component method) compute_areas() (in module molass.LowRank.CurveDecomposer) compute_bounce_vector() (SolidGrain method) compute_boundary_walls() (in module molass.SEC.StationaryMove) compute_dfef_curve() (in module molass.Baseline.UvDiffEffect) compute_egh_area_fast() (in module molass.LowRank.ProportionalDecomposer) compute_egh_y() (EghMoment method) compute_flowchange_likelihoods() (in module molass.FlowChange.FlowChangeLikely) compute_inpore_nextpos() (SolidGrain method) compute_integral_baseline() (in module molass.Baseline.IntegralBaseline) compute_like_values() (in module molass.FlowChange.FlowChangeParams) compute_lowrank_matrices() (in module molass.LowRank.LowRankInfo) compute_lpm_baseline() (in module molass.Baseline.LpmBaseline) compute_mapping_by_full_coverage() (in module molass.Mapping.SimpleMapper) compute_mapping_coverage() (in module molass.Mapping.SimpleMapper) compute_meanstd() (in module molass.Stats.Moment) compute_poreentries() (NewGrain method) (SolidGrain method) compute_propagated_error() (in module molass.LowRank.ErrorPropagate) compute_range() (Component method) compute_ratio_curve() (MappingInfo method) compute_reflected_point() (in module molass.SEC.StationaryMove) compute_rg() (VoxelSpace method) (XrComponent method)

compute_rg_impl() (in module molass.DensitySpace.VoxelSpace) compute_rgcurve() (XrData method) compute_rgcurve_atsas() (XrData method) compute_rgcurve_info() (in module molass.Guinier.RgCurveUtils) compute_rgcurve_info_atsas() (in module molass.Guinier.RgCurveUtils) compute_saxs() (in module molass.SAXS.Simulator) compute_scd() (in module molass.InterParticle.ConcDepend) compute_scds() (Decomposition method) compute_uvdiff_baseline() (in module molass.Baseline.UvdiffBaseline) compute_whole_similarity() (CsProxy method) compute_yscale() (in module molass.FlowChange.FlowChangeLikely) conc_tracker (Controller attribute) configure_for_test() (in module molass.Testing) (in module molass.Testing.PlotControl) construct_rgcurve_from_list() (in module molass.Guinier.RgCurve) contour_plot() (in module molass.PlotUtils.MatrixPlot) control_matplotlib_plot() (in module molass.Testing) (in module molass.Testing.PlotControl) (PlotController method) Controller (class in molass.Reports.Controller) convert_to_guinier_result_array() (in module molass.Reports.V1LrfReport) convert_to_list_pairedranges() (in module molass.LowRank.PairedRange) convert_to_trimmed_prerecog() (in module molass.DataUtils.ForwardCompat) copy() (SecSaxsData method) (SsMatrixData method) (TrimmingInfo method) copy_with_new_components() (Decomposition method) corrected_copy() (Curve method) (SecSaxsData method) create_axes() (in module molass.PlotUtils.DecompositionPlot) create_diff_spline() (in module molass.Baseline.UvDiffEffect) create_icurve() (in module molass.DataObjects.Curve) create_jcurve() (in module molass.DataObjects.Curve) create_model() (in module molass.SEC.ModelFactory) cs (NullFlowChange attribute) (PreRecogProxy attribute) CsProxy (class in molass.FlowChange.NullFlowChange) Curve (class in molass.DataObjects.Curve) CurveDecomposer (class in molass.LowRank.CurveDecomposer) CurveProxy (class in molass.DataUtils.ForwardCompat) curves (EghMoment attribute) (FlowChangeInfo attribute) custom_slice_string() (in module molass.Trimming.TrimmingInfo)

D

datafiles (SecSaxsData attribute) debug_plot() (in module molass.Decompose.Proportional) (Moment method) decompose_from_partner() (in module molass.Decompose.Partner) decompose_icurve_impl() (in module molass.LowRank.CurveDecomposer) decompose_icurve_positioned() (in module molass.LowRank.PositionedDecomposer) decompose_icurve_proportionally() (in module molass.LowRank.ProportionalDecomposer) decompose_proportionally() (in module molass.Decompose.Proportional) Decomposition (class in molass.LowRank.Decomposition) decomposition (PreProcessing attribute) default_filter() (in module molass.DataUtils.FolderWalker) default_iswanted() (in module molass.DataUtils.FolderWalker) demo() (in module molass.SAXS.DmaxEstimation) DenssDetector (class in molass.SAXS.DenssDetector)

DetectorInfo (class in molass.SAXS.DenssTools) (class in molass.SAXS.DetectorInfo) diff_spline (Curve attribute) do_3d_projection() (Arrow3D method) draw() (Annotation3D method) (Arrow3D method) (NewGrain method) (Particle method) (SolidGrain method) draw_entries() (SolidGrain method) draw_saxs() (in module molass.SAXS.Simulator) draw_slice_states_impl() (in module molass.SEC.ColumnSliceStates) draw_voxles_as_dots_impl() (in module molass.DensitySpace.VoxelSpace) draw_wedges() (in module molass.SEC.ColumnElements)

E

E (SsMatrixData attribute) e0 (in module molass.SEC.Models.Simple) EDM (class in molass.SEC.Models.EDM) EdmColumn (class in molass.SEC.Models.EdmComponentCurve) EdmComponentCurve (class in molass.SEC.Models.EdmComponentCurve) egh() (in module molass.SEC.Models.Simple) egh_pdf() (in module molass.SEC.Models.Simple) egh_std() (in module molass.SEC.Models.Simple) egh_var() (in module molass.SEC.Models.Simple) EghMoment (class in molass.Stats.EghMoment) Ellipsoid (class in molass.Shapes.Ellipsoid) ellipsoid_of_revolution() (in module molass.SAXS.Models.Formfactors) elm_recs (PairedRange attribute) ElutioCurvProxy (class in molass.Legacy.BackCompatUtils) enters_stationary() (Particle method) entries (NewGrain attribute) (SolidGrain attribute) env_info (Controller attribute) error_cleanup() (Controller method)

estimate_baseline_params() (in module molass.Baseline.SimpleBaseline) estimate_dmax() (in module molass.SAXS.DmaxEstimation) estimate_edm_init_params() (in module molass.SEC.Models.EdmEstimator) estimate_initial_params() (in module molass.Decompose.Proportional) estimate_lpm_percent() (in module molass.Baseline.LpmBaseline) estimate_mapping() (SecSaxsData method) estimate_mapping_for_matching_peaks() (in module molass.Mapping.SimpleMapper) estimate_mapping_impl() (in module molass.Mapping.SimpleMapper) estimate_sdm_column_params() (in module molass.SEC.Models.SdmEstimator) estimate_slope_reliability() (in module molass.Mapping.SimpleMapper) estimate_uvbaseline_params() (in module molass.Baseline.UvBaseline) estimate_uvdiffeffect_params() (in module molass.Baseline.UvDiffEffect) evaluate_matching() (in module molass.Mapping.PeakMatcher) excel_client (Controller attribute) excel_is_available (Controller attribute) excel_version (Controller attribute) exclude_bubble_impl() (in module molass.DataUtils.AnomalyHandlers) export() (SecSaxsData method) export_ssd_impl() (in module molass.DataUtils.ExportSsd) extract_params_assumming_egh() (in module molass.Bridge.V2Result)

F

find_nearest_point() (in module molass.FlowChange.FlowChangeLikely) find_nearest_wall() (in module molass.SEC.StationaryMove) fit_data() (in module molass.SAXS.DenssUtils) fit_data_bc() (in module molass.SAXS.DenssUtils) fit_data_impl() (in module molass.SAXS.DenssUtils) flowchange (PreRecogProxy attribute)

flowchange_exclude_slice() (in module molass.FlowChange.FlowChange) flowchange_exclude_slice_impl() (in module molass.FlowChange.FlowChange) flowchange_likelihood() (in module molass.FlowChange.FlowChangeLikely) FlowChangeInfo (class in molass.FlowChange.FlowChangeInfo) FlowChangeJudge (class in molass.FlowChange.FlowChangeJudge) FlowChangeJudgeInfo (class in molass.FlowChange.FlowChangeInfo) folder (V2Result attribute)

G

gaussian() (in module molass.SEC.Models.Simple) gaussian_density_for_demo() (in module molass.DensitySpace.Densities) get() (Surface method) get_animation() (in module molass.SEC.ColumnSimulation) get_argparser() (in module molass.SAXS.DenssUtils) get_baseline2d() (SsMatrixData method) get_baseline_func() (in module molass.Baseline.BaselineUtils) get_baseline_method() (SecSaxsData method) (SsMatrixData method) get_beamline_name() (SecSaxsData method) get_beamlineinfo_from_folder() (in module molass.DataUtils.Beamline) get_beamlineinfo_from_settings() (in module molass.DataUtils.Beamline) get_best_params() (V2Result method) get_cd_color_info() (Decomposition method) get_concfactor() (BeamlineInfo method) (SecSaxsData method) get_condition() (Ellipsoid method) (Sphere method) get_curve() (SaxsInfo method) get_datafolder() (in module molass.FlowChange.FlowChangeParams) get_denoised_data() (in module molass.LowRank.LowRankInfo) get_denss_detector() (in module molass.SAXS.DenssDetector) get_denss_log_items() (in module molass.SAXS.DenssUtils) get_denssfolder() (in module molass.SAXS.DenssUtils) get_detector_info() (in module molass.SAXS.DetectorInfo) get_detector_info_from_density() (in module molass.SAXS.DenssTools) get_diff_spline() (Curve method) get_dmax_with_datgnom() (in module molass.SAXS.DenssUtils) get_entry_including() (SolidGrain method) get_flowchange_points() (UvData method) get_fromto_list() (PairedRange method) get_groupable_peaks() (in module molass.Mapping.Grouping) get_groupable_peaks_impl() (in module molass.Mapping.Grouping) get_guinier_object() (XrComponent method) get_guinier_objects() (Decomposition method) get_ibaseline() (UvData method) (XrData method) get_icurve() (Component method) (SsMatrixData method) (UvData method) (XrData method) get_init_params() (V2Result method) get_ipickvalue() (XrData method) get_ipickvalues() (UvData method) get_jcurve() (Component method) (SsMatrixData method) get_jcurve_array() (Component method) (XrData method) get_labeltext_from_line() (in module molass.PlotUtils.Annotation3D) get_linear_surface() (in module molass.Baseline.Basesurface) get_local_settings() (in module molass.Local) get_lpm_percent() (Moment method) get_mapped_curve() (MappingInfo method) get_mapped_index() (MappingInfo method) get_mapped_info() (CsProxy method) get_mapped_x() (MappingInfo method) get_mapping() (SecSaxsData method) get_max_i() (Curve method) get_max_x() (Curve method) get_max_xy() (Curve method) get_max_y() (Curve method) get_meanstd() (Moment method) get_meshgrid() (in module molass.DensitySpace.VoxelSpace) get_minimizer_result() (PeakSimilarity method) get_molass_options() (in module molass.Global.Options) get_moment() (ComponentCurve method) (Curve method) (SsMatrixData method) get_next_position_impl() (in module molass.SEC.StationaryMove)

get_nsigma_points() (Moment method) get_num_components() (Decomposition method) get_num_components_assumming_egh() (in module molass.Bridge.V2Result) get_num_major_peaks() (Curve method) get_original_ssd() (V2Result method) get_outfolder() (in module molass.SAXS.DenssUtils) get_pairedranges() (Decomposition method) get_params() (ComponentCurve method) (EdmColumn method) (SdmColumn method) get_peak_positions() (in module molass.Peaks.Recognizer) get_peak_top_x() (ComponentCurve method) (EdmComponentCurve method) (SdmComponentCurve method) (UvComponentCurve method) get_peaks() (Curve method) get_pickvalue() (in module molass.SurveyUtils.UvPickvalue) get_point_from_angle() (SolidGrain method) get_primarypeak_i() (ElutioCurvProxy method) get_proportional_slices() (in module molass.Decompose.Proportional) get_proportions() (Decomposition method) get_ready_for_numba() (in module molass.PackageUtils.NumbaUtils) get_real_flow_changes() (NullFlowChange method) get_rg() (Ellipsoid method) (Sphere method) get_rgs() (Decomposition method) get_safeslice() (in module molass.FlowChange.FlowChangeLikely) get_segments() (in module molass.Geometric.Linesegment) get_similarity() (NullFlowChange method) get_spline() (Curve method) get_start_index() (in module molass.DataUtils.ForwardCompat) get_std() (Linesegment method) get_stdratio() (PeakSimilarity method) get_trimmed_curve() (in module molass.DataUtils.ForwardCompat) get_trimmed_mapping() (TrimmingInfo method) get_trimmed_ssd() (V2Result method) get_trimming() (V2Result method) get_usable_qrange() (XrData method) get_usable_qrange_impl() (in module molass.Trimming.UsableQrange) get_usable_wrange() (UvData method) get_usable_wrange_impl() (in module molass.Trimming.UsableWrange) get_uv_baseline_func() (in module molass.Baseline.BaselineUtils) get_uv_components() (Decomposition method) get_uv_device_id() (SecSaxsData method) get_uv_matrices() (Decomposition method) get_uvcurves() (in module molass.DataUtils.UvLoader) get_uvdiff_baseline_info() (in module molass.Baseline.UvdiffBaseline) get_version() (in module molass), [1] get_volume() (Ellipsoid method) (Sphere method) get_xr_baseline_func() (in module molass.Baseline.BaselineUtils) get_xr_components() (Decomposition method) get_xr_matrices() (Decomposition method) get_xy() (ComponentCurve method) (Curve method) (EdmComponentCurve method) (SdmComponentCurve method) (UvComponentCurve method) get_y() (ComponentCurve method) (EdmComponentCurve method) (Linesegment method) (SdmComponentCurve method) (UvComponentCurve method) get_y_() (EghMoment method) (Moment method) grain_particle_test() (in module molass.SEC.ColumnElements) guess() (in module molass.SEC.Models.EdmEstimatorImpl) guess_multiple_impl() (in module molass.SEC.Models.EdmEstimatorImpl) guinier_plot() (in module molass.PlotUtils.V1GuinierPlot) guinier_porod() (in module molass.SAXS.Models.Simple)

H

has_special() (NullFlowChange method)

homogeneous_sphere() (in module molass.SAXS.Models.Formfactors)

I

icurve (Component attribute) (EghMoment attribute) (UsableQrange attribute) icurve_array (Component attribute) id_ (NewGrain attribute) (SolidGrain attribute) ij_from_slice() (in module molass.PlotUtils.TrimmingPlot) illustrate_dmax() (in module molass.SAXS.DmaxEstimation) import_best_params() (V2Result method) import_init_params() (V2Result method) import_trimming() (V2Result method) InadequateUseError InconsistentUseError indeces (RgCurve attribute) individual_axes() (Baseline2D method) individual_axes_impl() (in module molass.Baseline.Baseline2D) init_params (FlowChangeJudge attribute) (V2Result attribute)

inspect_ip_effect() (SecSaxsData method) inspect_uv_baseline() (in module molass.Baseline.UvBaseline) intensities (RgCurve attribute) intercept (CsProxy attribute) (Linesegment attribute) (MappingInfo attribute) inv() (Mapping method) IpEffectInfo (class in molass.InterParticle.IpEffectInspect) is_in_nsigma() (Moment method) is_interactive() (in module molass.Testing) (in module molass.Testing.PlotControl) (PlotController method) is_minor() (PairedRange method) islike_differential() (in module molass.FlowChange.Differential) iterlen() (in module molass.Baseline.BaselineUtils) iv (SsMatrixData attribute)

J

j (FlowChangeInfo attribute) jcurve (Component attribute) jcurve_array (Component attribute)

judge() (FlowChangeJudge method) judge_info (FlowChangeInfo attribute) judge_peaklike_segment() (in module molass.Geometric.Peaklike) jv (SsMatrixData attribute)

K

kratky_plot() (in module molass.PlotUtils.V1KratkyPlot) kwargs (Controller attribute) (FlowChangeJudgeInfo attribute) (PreProcessing attribute)

L

Linesegment (class in molass.Geometric.Linesegment) linregress_segments() (in module molass.Geometric.LinesegmentUtils) load_uv() (in module molass.DataUtils.UvLoader) load_xr() (in module molass.DataUtils.XrLoader) load_xr_with_options() (in module molass.DataUtils.XrLoader)

logger (Controller attribute) (ProgressUnit attribute) (SecSaxsData attribute) lpm_percent (Moment attribute) LpmBaseline (class in molass.Baseline.LpmBaseline)

M

M (Moment attribute) (SsMatrixData attribute) make_and_slicepair() (in module molass.Trimming.TrimmingUtils) make_component_curves() (in module molass.LowRank.CoupledAdjuster) make_component_curves_with_proportions() (in module molass.LowRank.QuickImplement) make_decomposition_impl() (in module molass.LowRank.QuickImplement) make_guinier_plot() (in module molass.PlotUtils.DecompositionPlot) make_guinier_report() (in module molass.Reports.V1GuinierReport) make_gunier_row_values() (in module molass.Reports.Migrating) make_kratky_plot() (in module molass.PlotUtils.DecompositionPlot) make_lrf_report() (in module molass.Reports.V1LrfReport) make_mapped_trimming_info() (in module molass.Trimming.TrimmingUtils) make_paired_range() (Component method) make_plot() (in module molass.FlowChange.FlowChangePlot) make_summary_report() (in module molass.Reports.V1SummaryReport) make_temp_folder() (Controller method) make_test_targets() (in module molass.FlowChange.FlowChangeParams) make_trimming() (SecSaxsData method) make_trimming_impl() (in module molass.Trimming.TrimmingUtils) make_v1report() (in module molass.Reports.V1Report) make_v1report_ranges_impl() (in module molass.Reports.ReportRange) make_v1report_runner() (in module molass.Reports.V1Report) mapped_curve (Decomposition attribute) mapped_info (CsProxy attribute) Mapping (class in molass.Mapping.Mapping) mapping (Decomposition attribute) (SecSaxsData attribute) (TrimmingInfo attribute) (UvComponentCurve attribute) MappingInfo (class in molass.Mapping.MappingInfo) max_i (Curve attribute) max_x (Curve attribute) max_y (Curve attribute) mirrorImage() (in module molass.SEC.StationaryMove) module molass, [1] molass.Baseline molass.Baseline.Baseline2D molass.Baseline.BaselineUtils molass.Baseline.Basesurface molass.Baseline.IntegralBaseline molass.Baseline.LpmBaseline molass.Baseline.SimpleBaseline molass.Baseline.Surface molass.Baseline.UvBaseline molass.Baseline.UvdiffBaseline molass.Baseline.UvDiffEffect molass.Batch molass.Batch.V1Legacy molass.Batch.V1Result molass.Bridge molass.Bridge.V2Result molass.DataObjects molass.DataObjects.Curve molass.DataObjects.SecSaxsData molass.DataObjects.SsMatrixData molass.DataObjects.UvData molass.DataObjects.XrData molass.DataUtils molass.DataUtils.AnomalyHandlers molass.DataUtils.Beamline molass.DataUtils.ExportSsd molass.DataUtils.FolderWalker molass.DataUtils.ForwardCompat molass.DataUtils.Outliers molass.DataUtils.UvFileTrimming molass.DataUtils.UvLoader molass.DataUtils.XrLoader molass.DataUtils.ZipFolder molass.Decompose molass.Decompose.Partner molass.Decompose.Proportional molass.Decompose.VaryUtils molass.DensitySpace molass.DensitySpace.Densities molass.DensitySpace.VoxelSpace molass.Except molass.Except.ExceptionTypes molass.FlowChange molass.FlowChange.Differential molass.FlowChange.FlowChange molass.FlowChange.FlowChangeInfo molass.FlowChange.FlowChangeJudge molass.FlowChange.FlowChangeLikely molass.FlowChange.FlowChangeParams molass.FlowChange.FlowChangePlot molass.FlowChange.NullFlowChange molass.FlowChange.Possibility molass.Geometric molass.Geometric.Linesegment molass.Geometric.LinesegmentUtils molass.Geometric.Peaklike molass.Global molass.Global.Options molass.Guinier molass.Guinier.RgCurve molass.Guinier.RgCurveUtils molass.InterParticle molass.InterParticle.ConcDepend molass.InterParticle.IpEffectInspect molass.Legacy molass.Legacy.BackCompatUtils molass.Local molass.LowRank molass.LowRank.Component molass.LowRank.ComponentCurve molass.LowRank.ConsistentAdjuster molass.LowRank.CoupledAdjuster molass.LowRank.CurveDecomposer molass.LowRank.Decomposition molass.LowRank.ErrorPropagate molass.LowRank.LowRankInfo molass.LowRank.PairedRange molass.LowRank.PositionedDecomposer molass.LowRank.ProportionalDecomposer molass.LowRank.QuickImplement molass.Mapping molass.Mapping.Grouping molass.Mapping.Mapping molass.Mapping.MappingInfo molass.Mapping.PeakMatcher molass.Mapping.RatioCurve molass.Mapping.SimpleMapper molass.PackageUtils molass.PackageUtils.NumbaUtils molass.PackageUtils.PyWin32Utils molass.Peaks molass.Peaks.PeakSimilarity molass.Peaks.Recognizer molass.Peaks.RecognizerSpecific molass.PlotUtils molass.PlotUtils.Annotation3D molass.PlotUtils.Arrow3D molass.PlotUtils.Comparison molass.PlotUtils.DecompositionPlot molass.PlotUtils.MatrixPlot molass.PlotUtils.PlotResult molass.PlotUtils.SecSaxsDataPlot molass.PlotUtils.SsMatrixDataPlot molass.PlotUtils.TrimmingPlot molass.PlotUtils.TwinAxesUtils molass.PlotUtils.V1GuinierPlot molass.PlotUtils.V1KratkyPlot molass.PlotUtils.ViewArrows molass.Progress molass.Progress.ProgessUtils molass.Reports molass.Reports.Controller molass.Reports.Migrating molass.Reports.ReportRange molass.Reports.V1GuinierReport molass.Reports.V1LrfReport molass.Reports.V1Report molass.Reports.V1SummaryReport molass.SAXS molass.SAXS.DenssDetector molass.SAXS.DenssTools molass.SAXS.DenssUtils molass.SAXS.DetectorInfo molass.SAXS.DmaxEstimation molass.SAXS.FourierIllust molass.SAXS.Models molass.SAXS.Models.Formfactors molass.SAXS.Models.Simple molass.SAXS.MrcViewer molass.SAXS.Simulator molass.ScipyUtils molass.ScipyUtils.BoundsChecker molass.SEC molass.SEC.ColumnElements molass.SEC.ColumnSimulation molass.SEC.ColumnSliceStates molass.SEC.ColumnStructure molass.SEC.ModelFactory molass.SEC.Models molass.SEC.Models.EDM molass.SEC.Models.EdmComponentCurve molass.SEC.Models.EdmEstimator molass.SEC.Models.EdmEstimatorImpl molass.SEC.Models.EdmOptimizer molass.SEC.Models.SDM molass.SEC.Models.SdmComponentCurve molass.SEC.Models.SdmEstimator molass.SEC.Models.SdmOptimizer molass.SEC.Models.Simple molass.SEC.Models.UvComponentCurve molass.SEC.Models.UvOptimizer molass.SEC.StationaryMove molass.Shapes molass.Shapes.Ellipsoid molass.Shapes.Sphere molass.Stats molass.Stats.EghMoment molass.Stats.Moment molass.SurveyUtils molass.SurveyUtils.UvPickvalue molass.Testing molass.Testing.PlotControl molass.Trimming molass.Trimming.TrimmingInfo molass.Trimming.TrimmingUtils molass.Trimming.UsableQrange molass.Trimming.UsableWrange molass module, [1] molass.Baseline module molass.Baseline.Baseline2D module molass.Baseline.BaselineUtils module molass.Baseline.Basesurface module molass.Baseline.IntegralBaseline module molass.Baseline.LpmBaseline module molass.Baseline.SimpleBaseline module molass.Baseline.Surface module molass.Baseline.UvBaseline module molass.Baseline.UvdiffBaseline module molass.Baseline.UvDiffEffect module molass.Batch module molass.Batch.V1Legacy module molass.Batch.V1Result module molass.Bridge module molass.Bridge.V2Result module molass.DataObjects module molass.DataObjects.Curve module molass.DataObjects.SecSaxsData module molass.DataObjects.SsMatrixData module molass.DataObjects.UvData module molass.DataObjects.XrData module molass.DataUtils module molass.DataUtils.AnomalyHandlers module molass.DataUtils.Beamline module molass.DataUtils.ExportSsd module molass.DataUtils.FolderWalker module molass.DataUtils.ForwardCompat module molass.DataUtils.Outliers module molass.DataUtils.UvFileTrimming module molass.DataUtils.UvLoader module molass.DataUtils.XrLoader module molass.DataUtils.ZipFolder module molass.Decompose module

molass.Decompose.Partner module molass.Decompose.Proportional module molass.Decompose.VaryUtils module molass.DensitySpace module molass.DensitySpace.Densities module molass.DensitySpace.VoxelSpace module molass.Except module molass.Except.ExceptionTypes module molass.FlowChange module molass.FlowChange.Differential module molass.FlowChange.FlowChange module molass.FlowChange.FlowChangeInfo module molass.FlowChange.FlowChangeJudge module molass.FlowChange.FlowChangeLikely module molass.FlowChange.FlowChangeParams module molass.FlowChange.FlowChangePlot module molass.FlowChange.NullFlowChange module molass.FlowChange.Possibility module molass.Geometric module molass.Geometric.Linesegment module molass.Geometric.LinesegmentUtils module molass.Geometric.Peaklike module molass.Global module molass.Global.Options module molass.Guinier module molass.Guinier.RgCurve module molass.Guinier.RgCurveUtils module molass.InterParticle module molass.InterParticle.ConcDepend module molass.InterParticle.IpEffectInspect module molass.Legacy module molass.Legacy.BackCompatUtils module molass.Local module molass.LowRank module molass.LowRank.Component module molass.LowRank.ComponentCurve module molass.LowRank.ConsistentAdjuster module molass.LowRank.CoupledAdjuster module molass.LowRank.CurveDecomposer module molass.LowRank.Decomposition module molass.LowRank.ErrorPropagate module molass.LowRank.LowRankInfo module molass.LowRank.PairedRange module molass.LowRank.PositionedDecomposer module molass.LowRank.ProportionalDecomposer module molass.LowRank.QuickImplement module molass.Mapping module molass.Mapping.Grouping module molass.Mapping.Mapping module molass.Mapping.MappingInfo module molass.Mapping.PeakMatcher module molass.Mapping.RatioCurve module molass.Mapping.SimpleMapper module molass.PackageUtils module molass.PackageUtils.NumbaUtils module molass.PackageUtils.PyWin32Utils module molass.Peaks module molass.Peaks.PeakSimilarity module molass.Peaks.Recognizer module molass.Peaks.RecognizerSpecific module molass.PlotUtils module molass.PlotUtils.Annotation3D module molass.PlotUtils.Arrow3D module molass.PlotUtils.Comparison module molass.PlotUtils.DecompositionPlot module molass.PlotUtils.MatrixPlot module molass.PlotUtils.PlotResult module molass.PlotUtils.SecSaxsDataPlot module molass.PlotUtils.SsMatrixDataPlot module molass.PlotUtils.TrimmingPlot module molass.PlotUtils.TwinAxesUtils module molass.PlotUtils.V1GuinierPlot module molass.PlotUtils.V1KratkyPlot module molass.PlotUtils.ViewArrows module molass.Progress module molass.Progress.ProgessUtils module molass.Reports module molass.Reports.Controller module molass.Reports.Migrating module molass.Reports.ReportRange module molass.Reports.V1GuinierReport module molass.Reports.V1LrfReport module molass.Reports.V1Report module molass.Reports.V1SummaryReport module molass.SAXS module molass.SAXS.DenssDetector module molass.SAXS.DenssTools module molass.SAXS.DenssUtils module molass.SAXS.DetectorInfo module molass.SAXS.DmaxEstimation module molass.SAXS.FourierIllust module molass.SAXS.Models module molass.SAXS.Models.Formfactors module molass.SAXS.Models.Simple module molass.SAXS.MrcViewer module molass.SAXS.Simulator module molass.ScipyUtils module molass.ScipyUtils.BoundsChecker module molass.SEC module molass.SEC.ColumnElements module molass.SEC.ColumnSimulation module molass.SEC.ColumnSliceStates module molass.SEC.ColumnStructure module molass.SEC.ModelFactory module molass.SEC.Models module molass.SEC.Models.EDM module molass.SEC.Models.EdmComponentCurve module molass.SEC.Models.EdmEstimator module molass.SEC.Models.EdmEstimatorImpl module molass.SEC.Models.EdmOptimizer module molass.SEC.Models.SDM module molass.SEC.Models.SdmComponentCurve module molass.SEC.Models.SdmEstimator module molass.SEC.Models.SdmOptimizer module molass.SEC.Models.Simple module molass.SEC.Models.UvComponentCurve module molass.SEC.Models.UvOptimizer module molass.SEC.StationaryMove module molass.Shapes module molass.Shapes.Ellipsoid module molass.Shapes.Sphere module molass.Stats module molass.Stats.EghMoment module molass.Stats.Moment module molass.SurveyUtils module molass.SurveyUtils.UvPickvalue module molass.Testing module molass.Testing.PlotControl module molass.Trimming module molass.Trimming.TrimmingInfo module molass.Trimming.TrimmingUtils module molass.Trimming.UsableQrange module molass.Trimming.UsableWrange module molass_integral_impl() (in module molass.Baseline.BaselineUtils) molass_lpm_impl() (in module molass.Baseline.BaselineUtils) molass_uvdiff_impl() (in module molass.Baseline.BaselineUtils) Moment (class in molass.Stats.Moment) moment (ComponentCurve attribute) (Curve attribute) (SsMatrixData attribute) more_multicore (Controller attribute)

N

new_grain_unit_test() (in module molass.SEC.ColumnElements) NewGrain (class in molass.SEC.ColumnElements) NotSpecifedError nquad_vec() (in module molass.SAXS.Models.Formfactors) NullFlowChange (class in molass.FlowChange.NullFlowChange) num_components (Decomposition attribute)

num_done (ProgressUnit attribute) num_peaks (EghMoment attribute) num_pores (NewGrain attribute) num_steps (PreProcessing attribute) (ProgressSet attribute) (ProgressUnit attribute)

O

objective (PeakSimilarity attribute) optimize_decomposition() (EDM method) (SDM method) optimize_edm_xr_decomposition() (in module molass.SEC.Models.EdmOptimizer)

optimize_sdm_uv_decomposition() (in module molass.SEC.Models.SdmOptimizer) optimize_sdm_xr_decomposition() (in module molass.SEC.Models.SdmOptimizer) optimize_uv_decomposition() (in module molass.SEC.Models.UvOptimizer) optimize_with_model() (Decomposition method)

P

paired_ranges (Decomposition attribute) PairedRange (class in molass.LowRank.PairedRange) pairedranges (PreProcessing attribute) params (ComponentCurve attribute) (EdmColumn attribute) (EdmComponentCurve attribute) (SdmColumn attribute) (SdmComponentCurve attribute) (UvBaseline attribute) (UvDiffEffect attribute) Particle (class in molass.SEC.ColumnElements) peak_index (Component attribute) (PairedRange attribute) peak_info (CurveProxy attribute) peaks (Curve attribute) PeakSimilarity (class in molass.Peaks.PeakSimilarity) plot_3d() (SecSaxsData method) plot_3d_impl() (in module molass.PlotUtils.SecSaxsDataPlot) plot_3d_sa_impl() (in module molass.PlotUtils.SsMatrixDataPlot) plot_as_dots() (VoxelSpace method) plot_column_structure() (in module molass.SEC.ColumnStructure) plot_compact() (SecSaxsData method) plot_compact_impl() (in module molass.PlotUtils.SecSaxsDataPlot) plot_components() (Decomposition method) plot_components_impl() (in module molass.PlotUtils.DecompositionPlot) plot_elution_curve() (in module molass.PlotUtils.DecompositionPlot)

plot_flowchange() (in module molass.FlowChange.FlowChangeParams) plot_input() (in module molass.SAXS.DmaxEstimation) plot_saxs_illust() (in module molass.SAXS.FourierIllust) plot_segments() (in module molass.Geometric.Linesegment) plot_trimming() (SecSaxsData method) plot_trimming_impl() (in module molass.PlotUtils.TrimmingPlot) plot_varied_decompositions() (SecSaxsData method) plot_view_arrows() (in module molass.PlotUtils.ViewArrows) plot_with_density() (VoxelSpace method) PlotController (class in molass.Testing.PlotControl) PlotResult (class in molass.PlotUtils.PlotResult) poredist (SolidGrain attribute) poreradius (NewGrain attribute) (SolidGrain attribute) possibly_has_flowchange_points() (in module molass.FlowChange.Possibility) pre_rg (UsableQrange attribute) prepare_averaged_data() (Controller method) prepare_controller_for_lrf() (in module molass.Reports.V1LrfReport) preproc (Controller attribute) PreProcessing (class in molass.Reports.V1Report) PreRecogProxy (class in molass.DataUtils.ForwardCompat) ProgressSet (class in molass.Progress.ProgessUtils) ProgressUnit (class in molass.Progress.ProgessUtils) pybaselines_asls_impl() (in module molass.Baseline.BaselineUtils) pybaselines_imor_impl() (in module molass.Baseline.BaselineUtils) pybaselines_mormol_impl() (in module molass.Baseline.BaselineUtils)

Q

queue_ (ProgressSet attribute) (ProgressUnit attribute)

quick_decomposition() (SecSaxsData method) qv (XrData attribute)

R

radius (NewGrain attribute) (Particle attribute) (SolidGrain attribute) (Sphere attribute) ranges (PairedRange attribute) RatioCurve (class in molass.Mapping.RatioCurve) reduce_segments() (in module molass.Geometric.LinesegmentUtils) remove_bubbles_impl() (in module molass.DataUtils.AnomalyHandlers) remove_irregular_points() (NullFlowChange method) remove_outliers() (in module molass.DataUtils.Outliers) restore_params() (FlowChangeJudge method) restore_segments() (in module molass.Geometric.LinesegmentUtils)

result_wb (Controller attribute) results (PeakSimilarity attribute) (RgCurve attribute) RgCurve (class in molass.Guinier.RgCurve) rgcurves (PreProcessing attribute) rgvalues (RgCurve attribute) rho (VoxelSpace attribute) run() (PreProcessing method) run_denss() (in module molass.SAXS.DenssTools) run_denss_impl() (in module molass.SAXS.DenssUtils) run_denss_impl_dummy() (in module molass.SAXS.DenssUtils) run_fullyautomatic_v1() (in module molass.Batch.V1Legacy) run_pdb2mrc() (in module molass.SAXS.DenssUtils)

S

safe_log10() (in module molass.Decompose.Proportional) (in module molass.LowRank.CurveDecomposer) savefig() (PlotResult method) SaxsInfo (class in molass.SAXS.Simulator) scale (UvComponentCurve attribute) scores (RgCurve attribute) SDM (class in molass.SEC.Models.SDM) SdmColumn (class in molass.SEC.Models.SdmComponentCurve) SdmComponentCurve (class in molass.SEC.Models.SdmComponentCurve) SecSaxsData (class in molass.DataObjects.SecSaxsData) select_components() (in module molass.LowRank.CoupledAdjuster) select_matching_peaks() (in module molass.Mapping.PeakMatcher) set() (Annotation3D method) (Arrow3D method) set_baseline_method() (SecSaxsData method) (SsMatrixData method) set_limits_from_interval() (in module molass.PlotUtils.V1GuinierPlot) set_max() (Curve method) set_molass_options() (in module molass.Global.Options) sg (XrComponent attribute) show_mrc() (in module molass.SAXS.MrcViewer) show_or_save() (in module molass.Testing) (in module molass.Testing.PlotControl) (PlotController method) simple_plot_3d() (in module molass.PlotUtils.MatrixPlot) slice_to_values() (in module molass.Trimming.TrimmingUtils)

slope (CsProxy attribute) (Linesegment attribute) (MappingInfo attribute) smooth_copy() (Curve method) SolidGrain (class in molass.SEC.ColumnElements) Sphere (class in molass.Shapes.Sphere) sphere_volume() (in module molass.SAXS.Models.Formfactors) spherical_shell() (in module molass.SAXS.Models.Formfactors) spline (Curve attribute) (CurveProxy attribute) (Surface attribute) ssd (Controller attribute) (Decomposition attribute) (PreProcessing attribute) SsMatrixData (class in molass.DataObjects.SsMatrixData) start (UsableQrange attribute) stationary_move() (Particle method) std (Moment attribute) std_err (Linesegment attribute) step_done() (ProgressUnit method) stop (UsableQrange attribute) stop() (Controller method) stop_check() (Controller method) suppress_numerical_warnings() (in module molass.Testing) (in module molass.Testing.PlotControl) (PlotController method) Surface (class in molass.Baseline.Surface)

T

tell_error() (ProgressUnit method) teller (Controller attribute) temp_folder (Controller attribute) test_params() (in module molass.FlowChange.FlowChangeParams) time_initialized (SecSaxsData attribute) time_required (SecSaxsData attribute) time_required_total (SecSaxsData attribute) to_int_tuple() (in module molass), [1]

to_negative_segments() (in module molass.Geometric.Linesegment) tri_axial_ellipsoid() (in module molass.SAXS.Models.Formfactors) trim_uvfile() (in module molass.DataUtils.UvFileTrimming) trimmed (SecSaxsData attribute) trimmed_copy() (SecSaxsData method) trimming (V2Result attribute) TrimmingInfo (class in molass.Trimming.TrimmingInfo) type (Curve attribute)

U

unit_status (ProgressSet attribute) update_params() (FlowChangeJudge method) update_xr_ranks() (Decomposition method) UsableQrange (class in molass.Trimming.UsableQrange) uv (Decomposition attribute) (SecSaxsData attribute) uv_ccurves (Decomposition attribute) uv_curve (MappingInfo attribute) uv_icurve (Decomposition attribute)

uv_moment (MappingInfo attribute) uv_peaks (MappingInfo attribute) uv_ranks (Decomposition attribute) uv_slices (TrimmingInfo attribute) UvBaseline (class in molass.Baseline.UvBaseline) UvComponent (class in molass.LowRank.Component) UvComponentCurve (class in molass.SEC.Models.UvComponentCurve) UvData (class in molass.DataObjects.UvData) UvDiffEffect (class in molass.Baseline.UvDiffEffect)

V

V1Result (class in molass.Batch.V1Result) V2Result (class in molass.Bridge.V2Result)

Version (class in molass), [1] VoxelSpace (class in molass.DensitySpace.VoxelSpace)

W

walk_folders() (in module molass.DataUtils.FolderWalker)

work_folder (Controller attribute) wv (UvData attribute)

X

x (ComponentCurve attribute) (Curve attribute) (CurveProxy attribute) (EdmComponentCurve attribute) (ElutioCurvProxy attribute) (Linesegment attribute) (LpmBaseline attribute) (RatioCurve attribute) (SdmComponentCurve attribute) (UvBaseline attribute) (UvComponentCurve attribute) x_curve (CsProxy attribute) (NullFlowChange attribute)

xr (Decomposition attribute) (SecSaxsData attribute) xr_ccurve (UvComponentCurve attribute) xr_ccurves (Decomposition attribute) xr_curve (MappingInfo attribute) xr_icurve (Decomposition attribute) xr_moment (MappingInfo attribute) xr_peaks (MappingInfo attribute) xr_ranks (Decomposition attribute) xr_remove_bubbles() (in module molass.DataUtils.XrLoader) xr_slices (TrimmingInfo attribute) XrComponent (class in molass.LowRank.Component) XrData (class in molass.DataObjects.XrData)

Y

y (Curve attribute) (CurveProxy attribute) (ElutioCurvProxy attribute) (Linesegment attribute) (LpmBaseline attribute) (Moment attribute) (RatioCurve attribute) (UvBaseline attribute) (UvDiffEffect attribute)

y_ (Moment attribute)

Z

Z (Surface attribute)

zip_folder() (in module molass.DataUtils.ZipFolder)