flatkinson / standardiser Goto Github PK

import make_logger
logger = make_logger.run(__name__)

ImportError: No module named make_logger

import logging
logger = logging.getLogger(__name__)

Traceback (most recent call last):
  File "/home/berenger/.local/bin/standardiser", line 11, in <module>
    sys.exit(main())
  File "/home/berenger/.local/lib/python3.6/site-packages/standardiser/bin/standardise_mols.py", line 75, in main
    input_type = os.path.splitext(config.infile)[1] # sdf or smi
  File "/usr/lib/python3.6/posixpath.py", line 122, in splitext
    p = os.fspath(p)
TypeError: expected str, bytes or os.PathLike object, not NoneType

$ pip install standardiser
$ standardiser 
Traceback (most recent call last):
  File "~/.local/bin/standardiser", line 7, in <module>
    from standardiser.bin.standardiser import main
ImportError: No module named standardiser

$ cat ~/.local/bin/standardiser 
#!/usr/bin/python

# -*- coding: utf-8 -*-
import re
import sys

from standardiser.bin.standardiser import main

if __name__ == '__main__':
    sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0])
    sys.exit(main())

from rdkit import Chem
from standardiser import standardise
smiles = 'NC(CCC(=O)O)C(=O)O' # glutamate
mol = Chem.MolFromSmiles(smiles, sanitize=False)
clean_mol = standardise.apply(mol) # throws no_non_salt exception

    organic_salt_frags = []

    non_salt_frags = []

    mol = break_bonds.apply(mol)

    for n, frag in enumerate(Chem.GetMolFrags(mol, asMols=True), 1):

        logger.debug("Starting fragment {n} '{smi}'...".format(n=n, smi=Chem.MolToSmiles(frag)))

        logger.debug("1) Check for non-organic elements...")

        if unsalt.is_nonorganic(frag): continue

        logger.debug("2) Attempting to neutralise (first pass)...")

        frag = neutralise.apply(frag)

        logger.debug("3) Applying rules...")

        frag = rules.apply(frag, output_rules_applied=output_rules_applied, verbose=verbose)

        logger.debug("4) Attempting to neutralise (second pass)...")

        frag = neutralise.apply(frag)

        logger.debug("5) Checking if frag is a salt/solvate...")

        if unsalt.is_salt(frag):

            organic_salt_frags.append(frag)

            continue

        logger.debug("...fragment kept.")

        non_salt_frags.append(frag)

    if len(non_salt_frags) == 0:

        logger.debug("No non-salt frags. If there is a single organic salt frag take it.")

        if len(organic_salt_frags) == 1:

            parent = organic_salt_frags[0]

        else:

            raise StandardiseException("no_non_salt")

    elif len(non_salt_frags) > 1:

        raise StandardiseException("multi_component")

    else:

        parent = non_salt_frags[0]