sm.engine package

Subpackages

• sm.engine.msm_basic package
  • Submodules
  • sm.engine.msm_basic.formula_imager module
  • sm.engine.msm_basic.formula_imager_segm module
  • sm.engine.msm_basic.formula_img_validator module
  • sm.engine.msm_basic.msm_basic_search module
  • Module contents
• sm.engine.tests package
  • Subpackages
    • sm.engine.tests.msm_basic package
      • Submodules
      • sm.engine.tests.msm_basic.test_formula_imager module
      • sm.engine.tests.msm_basic.test_formula_imager_segm module
      • sm.engine.tests.msm_basic.test_formula_img_validator module
      • sm.engine.tests.msm_basic.test_msm_basic_search module
      • Module contents
  • Submodules
  • sm.engine.tests.test_dataset module
  • sm.engine.tests.test_fdr module
  • sm.engine.tests.test_formulas module
  • sm.engine.tests.test_imzml_txt_converter module
  • sm.engine.tests.test_isocalc_wrapper module
  • sm.engine.tests.test_theor_peaks_gen module
  • sm.engine.tests.util module
  • Module contents

Submodules

sm.engine.dataset module

sm.engine.db module

sm.engine.es_export module

sm.engine.fdr module

class sm.engine.fdr.FDR(job_id, db_id, decoy_sample_size, target_adducts, db)

Bases: object

clean_target_decoy_table()

decoy_adduct_selection()

estimate_fdr(msm_df)

sm.engine.formulas_segm module

class sm.engine.formulas_segm.FormulasSegm(job_id, db_id, ds_config, db)

Bases: object

A class representing a molecule database to search through. Provides several data structured used in the engine to speedup computation

job_id: int db_id: int ds_config : dict

Dataset configuration

db : engine.db.DB

static check_formula_uniqueness(sf_df)

get_sf_adduct_peaksn()

: list

An array of triples (formula id, adduct, number of theoretical peaks)

get_sf_adduct_sorted_df()

get_sf_peak_df()

get_sf_peak_ints()

static sf_peak_gen(sf_df)

sm.engine.imzml_txt_converter module

sm.engine.isocalc_wrapper module

sm.engine.metabolights module

sm.engine.queue module

sm.engine.search_algorithm module

class sm.engine.search_algorithm.SearchAlgorithm(sc, ds, formulas, fdr, ds_config)

Bases: object

calc_metrics(sf_images)

estimate_fdr(all_sf_metrics_df)

filter_sf_images(sf_images, sf_metrics_df)

filter_sf_metrics(sf_metrics_df)

search()

sm.engine.search_job module

sm.engine.search_results module

sm.engine.theor_peaks_gen module

sm.engine.util module

class sm.engine.util.SMConfig

Bases: object

Engine configuration manager

classmethod get_conf()

: dict

SM engine configuration

classmethod set_path(path)

Set path for a SM configuration file

path : String

sm.engine.util.cmd(template, *args)

sm.engine.util.cmd_check(template, *args)

sm.engine.util.init_logger(log_config=None)

sm.engine.util.local_path(path)

sm.engine.util.proj_root()

sm.engine.util.read_json(path)

sm.engine.util.s3_path(path)

sm.engine.work_dir module

Module contents