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