Index

A

acq_method (pygecko.gc_tools.injection.injection.Injection attribute), [1] acq_time (pygecko.gc_tools.injection.fid_injection.FID_Injection attribute), [1] Agilent_FID_Parser (class in pygecko.parsers.agilent_fid_parser) Agilent_MS_Parser (class in pygecko.parsers.agilent_ms_parser) alkanes (pygecko.gc_tools.analysis.retention_indices.RI_Calibration attribute), [1] Analysis (class in pygecko.analysis.analysis) Analysis_Settings (class in pygecko.gc_tools.analysis.analysis_settings) analysis_settings (pygecko.gc_tools.injection.fid_injection.FID_Injection attribute) (pygecko.gc_tools.injection.injection.Injection attribute) (pygecko.gc_tools.injection.ms_injection.MS_Injection attribute), [1]

Analyte (class in pygecko.gc_tools.analyte) analyte (pygecko.gc_tools.peak.fid_peak.FID_Peak attribute), [1] (pygecko.gc_tools.peak.ms_peak.MS_Peak attribute) (pygecko.gc_tools.peak.peak.Peak attribute), [1] area (pygecko.gc_tools.peak.fid_peak.FID_Peak attribute), [1] (pygecko.gc_tools.peak.ms_peak.MS_Peak attribute) (pygecko.gc_tools.peak.peak.Peak attribute), [1] array (pygecko.reaction.layout.Combinatorial_Layout attribute), [1] (pygecko.reaction.layout.Product_Layout attribute), [1] assign_ris() (pygecko.gc_tools.analysis.retention_indices.RI_Calibration method)

B

baseline_correction() (pygecko.gc_tools.injection.fid_injection.FID_Injection method) (pygecko.gc_tools.peak.peak_detection_fid.Peak_Detection_FID static method) boarder_threshold (pygecko.gc_tools.analysis.analysis_settings.Analysis_Settings attribute), [1] boarder_window (pygecko.gc_tools.analysis.analysis_settings.Analysis_Settings attribute), [1]

boarders (pygecko.gc_tools.peak.fid_peak.FID_Peak attribute), [1], [2] (pygecko.gc_tools.peak.ms_peak.MS_Peak attribute) (pygecko.gc_tools.peak.peak.Peak attribute), [1] build_dataset() (pygecko.reaction.reaction_parser.Reaction_Parser class method)

C

calc_plate_conv() (pygecko.analysis.analysis.Analysis static method) calc_plate_yield() (pygecko.analysis.analysis.Analysis static method) calculate_ri() (pygecko.gc_tools.analysis.retention_indices.RI_Calibration method) calculate_ri_fit() (pygecko.gc_tools.analysis.retention_indices.RI_Calibration method) calibration (pygecko.gc_tools.analysis.retention_indices.RI_Calibration attribute), [1] check_interval() (pygecko.gc_tools.utilities.Utilities static method) chromatogram (pygecko.gc_tools.injection.fid_injection.FID_Injection attribute), [1] (pygecko.gc_tools.injection.injection.Injection attribute) (pygecko.gc_tools.injection.ms_injection.MS_Injection attribute), [1]

Combinatorial_Layout (class in pygecko.reaction.layout) compare_mass_spectra() (pygecko.visualization.visuals.Visualization static method) convert_time_to_scan() (pygecko.gc_tools.utilities.Utilities static method) create_conditions_table() (pygecko.data_handling.reports.PDF_Report method) create_dataset_from_layout() (pygecko.reaction.reaction_parser.Reaction_Parser class method) create_discrete_cmap() (in module pygecko.visualization.utilities)

D

data_method (pygecko.gc_tools.injection.fid_injection.FID_Injection attribute) detector (pygecko.gc_tools.injection.fid_injection.FID_Injection attribute), [1] (pygecko.gc_tools.injection.injection.Injection attribute) (pygecko.gc_tools.injection.ms_injection.MS_Injection attribute), [1] (pygecko.gc_tools.sequence.fid_sequence.FID_Sequence attribute) (pygecko.gc_tools.sequence.gc_sequence.GC_Sequence attribute) (pygecko.gc_tools.sequence.ms_sequence.MS_Sequence attribute)

E

extract_scans_from_mzml() (in module pygecko.parsers.file_readers)

extract_scans_from_mzxml() (in module pygecko.parsers.file_readers) extract_scans_from_raw_data() (pygecko.parsers.ms_base_parser.MS_Base_Parser static method)

F

FID_Base_Parser (class in pygecko.parsers.fid_base_parser) FID_Injection (class in pygecko.gc_tools.injection.fid_injection) FID_Peak (class in pygecko.gc_tools.peak.fid_peak) FID_Sequence (class in pygecko.gc_tools.sequence.fid_sequence) find_directories_with_extension() (in module pygecko.parsers.utilities) find_empty_ranges() (pygecko.gc_tools.utilities.Utilities static method)

find_peak() (pygecko.gc_tools.analysis.spectral_matching.Spectral_Match class method) fit_calibration_curve() (pygecko.analysis.analysis.Analysis static method) flag_peak() (pygecko.gc_tools.injection.injection.Injection method) Flags (class in pygecko.visualization.utilities) flags (pygecko.gc_tools.peak.fid_peak.FID_Peak attribute), [1] (pygecko.gc_tools.peak.ms_peak.MS_Peak attribute) (pygecko.gc_tools.peak.peak.Peak attribute), [1]

G

GC_Sequence (class in pygecko.gc_tools.sequence.gc_sequence) get_injection_by_pos() (pygecko.gc_tools.sequence.gc_sequence.GC_Sequence method)

get_num_substrates() (in module pygecko.reaction.utilities) get_plate_position() (pygecko.gc_tools.injection.injection.Injection method) gradient (pygecko.gc_tools.analysis.retention_indices.RI_Calibration attribute), [1]

H

height (pygecko.gc_tools.analysis.analysis_settings.Analysis_Settings attribute), [1] (pygecko.gc_tools.peak.fid_peak.FID_Peak attribute), [1] (pygecko.gc_tools.peak.ms_peak.MS_Peak attribute) (pygecko.gc_tools.peak.peak.Peak attribute), [1]

HiddenPrints (class in pygecko.parsers.utilities)

I

indices_range (pygecko.gc_tools.analysis.analysis_settings.Analysis_Settings attribute), [1] initialize_injection() (pygecko.parsers.ms_base_parser.MS_Base_Parser static method) Injection (class in pygecko.gc_tools.injection.injection) injections (pygecko.gc_tools.sequence.fid_sequence.FID_Sequence attribute) (pygecko.gc_tools.sequence.gc_sequence.GC_Sequence attribute), [1] (pygecko.gc_tools.sequence.ms_sequence.MS_Sequence attribute) injector_pos (pygecko.gc_tools.injection.fid_injection.FID_Injection attribute), [1] instrument_name (pygecko.gc_tools.injection.injection.Injection attribute), [1] (pygecko.gc_tools.sequence.fid_sequence.FID_Sequence attribute) (pygecko.gc_tools.sequence.gc_sequence.GC_Sequence attribute), [1] (pygecko.gc_tools.sequence.ms_sequence.MS_Sequence attribute)

integrate() (pygecko.gc_tools.injection.fid_injection.FID_Injection method) intercept (pygecko.gc_tools.analysis.retention_indices.RI_Calibration attribute), [1] internal_standard (pygecko.gc_tools.injection.injection.Injection attribute), [1] (pygecko.gc_tools.sequence.fid_sequence.FID_Sequence attribute) (pygecko.gc_tools.sequence.gc_sequence.GC_Sequence attribute), [1] (pygecko.gc_tools.sequence.ms_sequence.MS_Sequence attribute)

L

layout (pygecko.reaction.layout.Combinatorial_Layout attribute), [1] (pygecko.reaction.layout.Product_Layout attribute), [1] list_files_and_directories() (in module pygecko.parsers.utilities) load_injection() (in module pygecko.gc_tools.injection.injection) (pygecko.parsers.agilent_fid_parser.Agilent_FID_Parser class method) (pygecko.parsers.agilent_ms_parser.Agilent_MS_Parser class method) (pygecko.parsers.fid_base_parser.FID_Base_Parser static method) (pygecko.parsers.ms_base_parser.MS_Base_Parser static method)

load_ri_calibration() (pygecko.parsers.agilent_fid_parser.Agilent_FID_Parser class method) (pygecko.parsers.agilent_ms_parser.Agilent_MS_Parser class method) (pygecko.parsers.fid_base_parser.FID_Base_Parser static method) (pygecko.parsers.ms_base_parser.MS_Base_Parser static method) load_sequence() (in module pygecko.gc_tools.sequence.gc_sequence) (pygecko.parsers.agilent_fid_parser.Agilent_FID_Parser class method) (pygecko.parsers.agilent_ms_parser.Agilent_MS_Parser class method) (pygecko.parsers.fid_base_parser.FID_Base_Parser static method) (pygecko.parsers.ms_base_parser.MS_Base_Parser static method)

M

mass_spectrum (pygecko.gc_tools.peak.ms_peak.MS_Peak attribute), [1] match_mol() (pygecko.gc_tools.injection.ms_injection.MS_Injection method) match_mz() (pygecko.gc_tools.injection.ms_injection.MS_Injection method) match_mz_plate() (pygecko.analysis.analysis.Analysis static method) match_peaks() (pygecko.gc_tools.analysis.spectral_matching.Spectral_Match class method) match_ri() (pygecko.gc_tools.injection.injection.Injection method) max_half_window (pygecko.gc_tools.analysis.analysis_settings.Analysis_Settings attribute), [1] max_isotopic_diff (pygecko.gc_tools.analysis.analysis_settings.Analysis_Settings attribute), [1] meta_data (pygecko.reaction.layout.Combinatorial_Layout attribute), [1] min_rel_intensity (pygecko.gc_tools.analysis.analysis_settings.Analysis_Settings attribute), [1] module pygecko pygecko.analysis pygecko.analysis.analysis pygecko.data_handling pygecko.data_handling.reports pygecko.gc_tools pygecko.gc_tools.analysis pygecko.gc_tools.analysis.analysis_settings pygecko.gc_tools.analysis.quantification pygecko.gc_tools.analysis.retention_indices pygecko.gc_tools.analysis.spectral_matching pygecko.gc_tools.analyte pygecko.gc_tools.injection pygecko.gc_tools.injection.fid_injection pygecko.gc_tools.injection.injection pygecko.gc_tools.injection.ms_injection pygecko.gc_tools.peak pygecko.gc_tools.peak.fid_peak pygecko.gc_tools.peak.ms_peak pygecko.gc_tools.peak.peak pygecko.gc_tools.peak.peak_detection_fid pygecko.gc_tools.peak.peak_detection_ms pygecko.gc_tools.sequence pygecko.gc_tools.sequence.fid_sequence pygecko.gc_tools.sequence.gc_sequence pygecko.gc_tools.sequence.ms_sequence pygecko.gc_tools.utilities pygecko.parsers pygecko.parsers.agilent_fid_parser pygecko.parsers.agilent_ms_parser pygecko.parsers.fid_base_parser pygecko.parsers.file_readers pygecko.parsers.ms_base_parser pygecko.parsers.msconvert_wraper pygecko.parsers.utilities pygecko.reaction pygecko.reaction.layout pygecko.reaction.reaction_parser pygecko.reaction.transformation pygecko.reaction.utilities pygecko.visualization pygecko.visualization.utilities pygecko.visualization.visuals

mol (pygecko.gc_tools.analyte.Analyte attribute), [1] MS_Base_Parser (class in pygecko.parsers.ms_base_parser) MS_Injection (class in pygecko.gc_tools.injection.ms_injection) MS_Peak (class in pygecko.gc_tools.peak.ms_peak) ms_score (pygecko.gc_tools.analysis.spectral_matching.Spectral_Match attribute), [1] MS_Sequence (class in pygecko.gc_tools.sequence.ms_sequence) msconvert() (in module pygecko.parsers.msconvert_wraper) mz (pygecko.gc_tools.analyte.Analyte attribute)

N

name (pygecko.gc_tools.analyte.Analyte attribute), [1]

O

overlap (pygecko.visualization.utilities.Flags attribute)

P

PDF_Report (class in pygecko.data_handling.reports) Peak (class in pygecko.gc_tools.peak.peak) Peak_Detection_FID (class in pygecko.gc_tools.peak.peak_detection_fid) Peak_Detection_MS (class in pygecko.gc_tools.peak.peak_detection_ms) peaks (pygecko.gc_tools.analysis.spectral_matching.Spectral_Match attribute), [1] (pygecko.gc_tools.injection.fid_injection.FID_Injection attribute), [1] (pygecko.gc_tools.injection.injection.Injection attribute), [1] (pygecko.gc_tools.injection.ms_injection.MS_Injection attribute), [1] pick_peaks() (pygecko.gc_tools.injection.fid_injection.FID_Injection method) (pygecko.gc_tools.injection.ms_injection.MS_Injection method) (pygecko.gc_tools.peak.peak_detection_fid.Peak_Detection_FID static method) (pygecko.gc_tools.peak.peak_detection_ms.Peak_Detection_MS static method) (pygecko.gc_tools.sequence.gc_sequence.GC_Sequence method) plate_pos (pygecko.gc_tools.injection.injection.Injection attribute) pop() (pygecko.gc_tools.analysis.analysis_settings.Analysis_Settings method) processed_chromatogram (pygecko.gc_tools.injection.fid_injection.FID_Injection attribute), [1] Product_Layout (class in pygecko.reaction.layout) prominence_fid (pygecko.gc_tools.analysis.analysis_settings.Analysis_Settings attribute), [1] prominence_ms (pygecko.gc_tools.analysis.analysis_settings.Analysis_Settings attribute), [1] pygecko module pygecko.analysis module pygecko.analysis.analysis module pygecko.data_handling module pygecko.data_handling.reports module pygecko.gc_tools module pygecko.gc_tools.analysis module pygecko.gc_tools.analysis.analysis_settings module pygecko.gc_tools.analysis.quantification module pygecko.gc_tools.analysis.retention_indices module pygecko.gc_tools.analysis.spectral_matching module pygecko.gc_tools.analyte module pygecko.gc_tools.injection module pygecko.gc_tools.injection.fid_injection module pygecko.gc_tools.injection.injection module pygecko.gc_tools.injection.ms_injection module pygecko.gc_tools.peak module

pygecko.gc_tools.peak.fid_peak module pygecko.gc_tools.peak.ms_peak module pygecko.gc_tools.peak.peak module pygecko.gc_tools.peak.peak_detection_fid module pygecko.gc_tools.peak.peak_detection_ms module pygecko.gc_tools.sequence module pygecko.gc_tools.sequence.fid_sequence module pygecko.gc_tools.sequence.gc_sequence module pygecko.gc_tools.sequence.ms_sequence module pygecko.gc_tools.utilities module pygecko.parsers module pygecko.parsers.agilent_fid_parser module pygecko.parsers.agilent_ms_parser module pygecko.parsers.fid_base_parser module pygecko.parsers.file_readers module pygecko.parsers.ms_base_parser module pygecko.parsers.msconvert_wraper module pygecko.parsers.utilities module pygecko.reaction module pygecko.reaction.layout module pygecko.reaction.reaction_parser module pygecko.reaction.transformation module pygecko.reaction.utilities module pygecko.visualization module pygecko.visualization.utilities module pygecko.visualization.visuals module

Q

Quantification (class in pygecko.gc_tools.analysis.quantification) quantify() (pygecko.gc_tools.injection.fid_injection.FID_Injection method) quantify_analyte() (pygecko.analysis.analysis.Analysis static method)

quantify_calibration() (pygecko.gc_tools.analysis.quantification.Quantification static method) quantify_plate() (pygecko.analysis.analysis.Analysis static method) quantify_polyarc() (pygecko.gc_tools.analysis.quantification.Quantification static method) quantify_ratio() (pygecko.gc_tools.analysis.quantification.Quantification static method)

R

Reaction_Parser (class in pygecko.reaction.reaction_parser) read_json() (in module pygecko.reaction.utilities) read_xy_array() (pygecko.parsers.fid_base_parser.FID_Base_Parser static method) Report (class in pygecko.data_handling.reports) report() (pygecko.gc_tools.injection.fid_injection.FID_Injection method) return_flags_value() (pygecko.visualization.utilities.Flags static method) ri (pygecko.gc_tools.peak.fid_peak.FID_Peak attribute), [1] (pygecko.gc_tools.peak.ms_peak.MS_Peak attribute) (pygecko.gc_tools.peak.peak.Peak attribute), [1]

RI_Calibration (class in pygecko.gc_tools.analysis.retention_indices) rt (pygecko.gc_tools.analyte.Analyte attribute), [1] (pygecko.gc_tools.peak.fid_peak.FID_Peak attribute), [1] (pygecko.gc_tools.peak.ms_peak.MS_Peak attribute) (pygecko.gc_tools.peak.peak.Peak attribute), [1] rt_score (pygecko.gc_tools.analysis.spectral_matching.Spectral_Match attribute), [1] rxn_smarts (pygecko.reaction.transformation.Transformation attribute), [1]

S

sample_description (pygecko.gc_tools.injection.injection.Injection attribute), [1] sample_name (pygecko.gc_tools.injection.injection.Injection attribute), [1] sample_number (pygecko.gc_tools.injection.fid_injection.FID_Injection attribute), [1] sample_type (pygecko.gc_tools.injection.injection.Injection attribute), [1] save() (pygecko.gc_tools.injection.injection.Injection method) (pygecko.gc_tools.sequence.gc_sequence.GC_Sequence method) save_mass_spectrum() (pygecko.gc_tools.peak.ms_peak.MS_Peak method) save_peaks_mass_spectrum() (pygecko.gc_tools.injection.ms_injection.MS_Injection method) save_sequence() (in module pygecko.gc_tools.sequence.gc_sequence) savgol_window (pygecko.gc_tools.analysis.analysis_settings.Analysis_Settings attribute), [1] scan_rate (pygecko.gc_tools.analysis.analysis_settings.Analysis_Settings attribute), [1] scans (pygecko.gc_tools.injection.ms_injection.MS_Injection attribute), [1] sequence_name (pygecko.gc_tools.sequence.fid_sequence.FID_Sequence attribute) (pygecko.gc_tools.sequence.gc_sequence.GC_Sequence attribute), [1] (pygecko.gc_tools.sequence.ms_sequence.MS_Sequence attribute)

set_internal_standard() (pygecko.gc_tools.injection.injection.Injection method) (pygecko.gc_tools.sequence.gc_sequence.GC_Sequence method) set_plate_position() (pygecko.gc_tools.injection.injection.Injection method) shape (pygecko.reaction.layout.Combinatorial_Layout attribute), [1] (pygecko.reaction.layout.Product_Layout attribute), [1] smiles (pygecko.gc_tools.analyte.Analyte attribute), [1] sn (pygecko.gc_tools.analysis.analysis_settings.Analysis_Settings attribute), [1] solvent_delay (pygecko.gc_tools.injection.fid_injection.FID_Injection attribute), [1] (pygecko.gc_tools.injection.ms_injection.MS_Injection attribute), [1] Spectral_Match (class in pygecko.gc_tools.analysis.spectral_matching) stack_chromatograms() (pygecko.visualization.visuals.Visualization static method)

T

time_range (pygecko.gc_tools.analysis.analysis_settings.Analysis_Settings attribute), [1] trace_prominence (pygecko.gc_tools.analysis.analysis_settings.Analysis_Settings attribute), [1]

transform (pygecko.reaction.transformation.Transformation attribute), [1] Transformation (class in pygecko.reaction.transformation) transformation (pygecko.reaction.layout.Combinatorial_Layout attribute), [1]

U

update() (pygecko.gc_tools.analysis.analysis_settings.Analysis_Settings method)

Utilities (class in pygecko.gc_tools.utilities)

V

vial_pos (pygecko.gc_tools.injection.injection.Injection attribute), [1] view_chromatogram() (pygecko.gc_tools.injection.injection.Injection method) (pygecko.visualization.visuals.Visualization static method)

view_mass_spectrum() (pygecko.gc_tools.peak.ms_peak.MS_Peak method) (pygecko.visualization.visuals.Visualization static method) Visualization (class in pygecko.visualization.visuals) visualize_plate() (pygecko.visualization.visuals.Visualization static method)

W

width (pygecko.gc_tools.analysis.analysis_settings.Analysis_Settings attribute), [1] (pygecko.gc_tools.peak.fid_peak.FID_Peak attribute), [1] (pygecko.gc_tools.peak.ms_peak.MS_Peak attribute) (pygecko.gc_tools.peak.peak.Peak attribute), [1]