def do_calc(n): logger = get_logger("MADByTE") try: result = core.construct_spin_system( name=n, input_dir=input_dir, project_dir=project_dir, nmr_data_type=nmr_data_type, entity=entity, hppm_error=hppm_error, tocsy_error=tocsy_error, merge_multiplets=merge_multiplets, restart=restart, solvent=solvent, ) except Exception as e: import traceback logger.error(traceback.format_exc(e)) logger.error(f"{n} failed...") else: logger.info(f"{n} finished processing") return result
from pathlib import Path from random import choice import networkx as nx import numpy as np import pandas as pd import rtree from joblib import Parallel, delayed from tqdm import tqdm from madbyte import dereplicator import madbyte.plotting as plot from madbyte.logging import get_logger logger = get_logger("MADByTE") def establish_file_structure(project_dir): """Create output data directory and empty spin system master if required for MADByTE Args: output_dir (str or Path): desired output directory project_dir (str or Path): project directory """ project_dir = Path(project_dir) master = project_dir.joinpath("Spin_Systems_Master.json") if not master.exists(): master_df = pd.DataFrame(
import logging import os import pandas as pd from madbyte.logging import get_logger # from lxml import etree # Define module logger as child to App logger logger = get_logger("MADByTE.parsers") def topspin_parser(name, input_dir, output_dir, tocsy_precision=3, hsqc_precision=3): """Load Topspin data from specified input directory to preprocessed state. Dumps temp files to output_dir Args: name (str): Extract name input_dir (str): Directory name of input data output_dir (str): Directory name for output data """ data_dir = os.path.join(input_dir, name) hsqc_dir = None tocsy_dir = None # Iterate over all dirs in topspin data dir for sample