sm.engine package¶
Subpackages¶
- sm.engine.msm_basic package
- sm.engine.tests package
- Subpackages
- 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¶
-
class
sm.engine.dataset.
Dataset
(sc, name, owner_email, ds_config, wd_manager, db)[source]¶ Bases:
object
A class representing a mass spectrometry dataset. Backed by a couple of plain text files containing coordinates and spectra.
- sc : pyspark.SparkContext
- Spark context object
- name : String
- Dataset name
- ds_config : dict
- Dataset config file
wd_manager : engine.local_dir.WorkDir db : engine.db.DB
-
get_norm_img_pixel_inds
()[source]¶ - : ndarray
- One-dimensional array of indexes for dataset pixels taken in row-wise manner
sm.engine.db module¶
sm.engine.es_export module¶
sm.engine.fdr module¶
sm.engine.formulas module¶
-
class
sm.engine.formulas.
Formulas
(job_id, db_id, ds_config, db)[source]¶ Bases:
object
A class representing a molecule database to search through. Provides several data structured used in the engine to speedup computation
- ds_config : dict
- Dataset configuration
db : engine.db.DB
-
get_sf_adduct_peaksn
()[source]¶ - : list
- An array of triples (formula id, adduct, number of theoretical peaks)
-
get_sf_peak_bounds
()[source]¶ - : tuple
- A pair of ndarrays with bound mz values for each molecule from the molecule database