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| """Global variables used across the package.""" | |
| import pathlib | |
| # Dirs | |
| ROOT_DIR = pathlib.Path(__file__).parent.absolute() | |
| REPO_DIR = ROOT_DIR.parent | |
| DATA_DIR = REPO_DIR / 'data' | |
| TEST_RESULTS_DIR = REPO_DIR / 'experiments' | |
| ASSETS_DIR = REPO_DIR / 'assets' | |
| # C | |
| # CHEM_ELEMS_SMALL = ['H', 'C', 'O', 'N', 'P', 'S', 'Cl', 'F', 'Br', 'I'] | |
| CHEM_ELEMS_SMALL = ['H', 'C', 'O', 'N', 'P', 'S', 'Cl', 'F', 'Br', 'I', 'B', 'As', 'Si', 'Se'] | |
| MSGYM_FORMULA_VECTOR_NORM = [102.0, 59.0, 25.0, 13.0, 3.0, 6.0, 6.0, 17.0, 4.0, 4.0, 1.0, 1.0, 5.0, 2.0] | |
| # MSGYM_FORMULA_VECTOR_NORM = [102.0, 59.0, 25.0, 13.0, 3.0, 6.0, 6.0, 17.0, 4.0, 4.0] | |
| MSGYM_FORMULA_STANDARD = { | |
| 'formula_norm':[6.53758314e+00, 6.26973237e+00, | |
| 8.90610447e-01, 4.73889402e-01, 2.31793513e-02, 3.56956333e-02, | |
| 2.78056172e-02, 3.28356898e-02, 2.19480328e-03, 1.58458297e-03, | |
| 2.34802165e-05, 1.71127001e-05, 1.71127001e-04, 1.69800435e-05], | |
| 'formula_norm': [9.68749281e+00, 7.46795232e+00, | |
| 1.75427539e+00, 9.81685190e-01, 1.52363430e-01, 2.01197446e-01, | |
| 1.93046421e-01, 2.65309185e-01, 4.82433244e-02, 5.23009413e-02, | |
| 4.84558202e-03, 4.13671455e-03, 1.51218609e-02, 5.02040474e-03], | |
| 'formula_max':[102. , 59. , | |
| 25. , 13. , 3. , 6. , | |
| 6. , 17. , 4. , 4. , | |
| 1. , 1. , 5. , 2. ], | |
| 'formula_min' :[0. , 0. , 0. , 0. , | |
| 0. , 0. , 0. , 0. , 0. , | |
| 0. , 0. , 0. , 0. , 0. , | |
| 0. ] | |
| } | |
| #MSGYM standardization | |
| MSGYM_STANDARD_MH = { | |
| 'mz_mean': 195.155185, | |
| 'mz_std':127.591549 | |
| } | |
| MSGYM_STANDARD_all = { # got these from Yinkai | |
| "mz_mean": 80.88304948022557, | |
| "mz_std" : 197.4588028571758} | |
| PRECURSOR_INTENSITY = 1.1 |