| import os | |
| from datetime import datetime | |
| now = datetime.now() | |
| date = now.strftime("%d%b%Y") | |
| ##in notebook use: | |
| # import pyhxexpress | |
| # import test_config as config | |
| # pyhxexpress.config = config | |
| ########################################## | |
| '''Settings for Test Data Sets''' | |
| ########################################## | |
| WRITE_PARAMS = True #save the params to hdxms_params_$.py file in Data_DIR, can then be read in as PARAMS_FILE | |
| Allow_Overwrite = True #don't create a new filename if file already exists | |
| Test_Data = True | |
| Data_Type = 1 | |
| Save_Spectra = False | |
| process_ALL = True | |
| Data_DIR = 'C:\\Users\\tuttl\\OneDrive\\Documents\\My Documents\\KlevitHahn\\hdx-ms\\pyHXExpress\\Bimodal_HDX_Data' | |
| #Data_DIR = '/home/tuttle/data/HDX-MS/pyHXExpress/Bimodal_HDX_Data' | |
| Read_Spectra_List = True #get metadf from Metadf_File | |
| Metadf_File = "hdxms_testsets_metadf.csv" | |
| Output_DIR = os.path.join(Data_DIR,'output_'+str(date),'') | |
| #if not os.path.exists(Output_DIR): os.makedirs(Output_DIR) | |
| Preset_Pops = False #Use predetermined number of populations to fit curves, overrides Min/Max_Pops if given | |
| Preset_Pops_File = os.path.join(Data_DIR,"test_configdf_26feb2024.csv") | |
| User_mutants = [''] | |
| User_peptides = [''] | |
| Generate_Plots = True | |
| Hide_Figure_Output = False #True Recommended when processing lots of data. | |
| SVG = False # also save figures as an svg file, slow, but better for making figures | |
| BestFit_of_X = 3 | |
| Residual_Cutoff = 1e-5 | |
| Nboot = 20 # number of individual fits to perform, using n_best_curves from initial round of fits | |
| setNoise = 100 #if noise value is known, specify instead of estimating as Y_ERR % of avg Un+TD peaks | |
| Y_ERR = 1.0 #Percent random error applied during boot as y*+np.random.normal(0,yerr), 0.0 for NoNoise, use ~0.5% for noise added | |
| # the absolute Noise value is then Y_ERR * avg(maxInt of Un and TD) | |
| # this is a very rough way to give a consistent Noise value throughout a dataset. | |
| Dfrac = 0.90 | |
| FullDeut_Time = 1e6 # dummy timept for fully deuterated (TD) sample | |
| Nterm_subtract = 1 # number of N-term residues to remove from possible exchanging NH's (usually 1 or 2) | |
| # This will mostly affect the corrected Dabs value as it is scaled to make TD = theoretical Nex | |
| Zero_Filling = 3 # large value to try to fit 3 binomials on short peptides, not generally recommended. | |
| Peak_Resolution = 70.0 #ppm, sensitivity of peak picker to expected m/z centers #LeuEnk wants higher, pep122 wants lower ... | |
| Binomial_dCorr = True # fit n=1 binomial for UN/TD to calculate d_corr and back exchange values | |
| Env_threshold = 0.1 #find envelope width at Env_threshold * Intensity_max | |
| Limit_by_envelope = False # only fit up to n = int(z*env/3*Env_limit - 2/3) | |
| Env_limit = 0.95 #used if Limit_by_envelope = True, rough measure to constrain n_curves fit according to data width & num fit params | |
| Min_Pops = 1 # Min_Pops to Max_Pops sets the range of populations to fit, set to same value to force single population | |
| Max_Pops = 3 # maximum number of underlying populations to fit | |
| Nex_Max_Scale = 1.2 #multipler of how much to let Nex exceed the number predicted exchangable backbone NHs | |
| Pop_Thresh = 0.03 #fall back to n-1 curves if population is below this, does not apply to bootstrap fits, but does exclude from boot average values | |
| Ncurve_p_accept = 0.05 #stringency for accepting more fit populations, higher permits more populations, reasonable values are 0.01 to 0.05 | |
| Random_Seed = 16 #used for parameter initialization | |
| Scale_Y_Values = True # if Scale_Y_Values = True, plots will be in original Intensity units | |
| # fit will always be on normalized Intensity as it is much faster | |
| Keep_Raw = True # peak_picking will retain the Raw spectrum if True, if False will only keep peaks, auto True for Test_Data | |
| Overlay_replicates = True #add column to figures that is overlay of all available replicates | |
| Use_DiffEvo = False | |
| DiffEvo_threshold = 0 #1e-15 | |
| DiffEvo_kwargs = {'polish':True,'maxiter':1000} | |
| ######################################## | |
| '''end user input'''; | |
| ######################################## | |