File ExtendedTopochemicalAtom.py has 577 lines of code (exceeds 250 allowed). Consider refactoring.

Open

r"""Extended Topochemical Atom(ETA) descriptor.

References
    * :doi:`10.1021/ci0342066`
    * :doi:`10.1016/j.jhazmat.2013.03.023`

File calculator.py has 355 lines of code (exceeds 250 allowed). Consider refactoring.

Open

from __future__ import print_function

import sys
import warnings
from types import ModuleType

Function calculate has a Cognitive Complexity of 23 (exceeds 5 allowed). Consider refactoring.

Open

    def calculate(self):
        new = Chem.RWMol(Chem.Mol())
        ids = {}
        for a in self.mol.GetAtoms():
            if a.GetAtomicNum() == 1:

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File descriptor.py has 290 lines of code (exceeds 250 allowed). Consider refactoring.

Open

import inspect
import operator
from abc import ABCMeta, abstractmethod
from contextlib import contextmanager
from distutils.version import StrictVersion

File CPSA.py has 290 lines of code (exceeds 250 allowed). Consider refactoring.

Open

r"""charged partial surface area descriptor.

References
    * :doi:`10.1021/ac00220a013`

Function main_process has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.

Open

def main_process(
    input, parser, output, nproc, quiet, stream, descriptor, with3D, verbosity
):
    mols = (m for i in input for m in parser(i))

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Function get_descriptors_in_module has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.

Open

def get_descriptors_in_module(mdl, submodule=True):
    r"""Get descriptors in module.

    Parameters:
        mdl(module): module to search

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Calculator has 25 functions (exceeds 20 allowed). Consider refactoring.

Open

class Calculator(object):
    r"""descriptor calculator.

    Parameters:
        descs: see Calculator.register() method

Descriptor has 23 functions (exceeds 20 allowed). Consider refactoring.

Open

class Descriptor(six.with_metaclass(DescriptorMeta, object)):
    r"""Abstract base class of descriptors.

    Attributes:
        mol(rdkit.Mol): target molecule

Function _get_sulfur_contrib has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

    def _get_sulfur_contrib(cls, atom):
        nH = cls._hydrogen_count(atom)
        cnt = cls._bond_type_count(atom)

        if atom.GetFormalCharge() != 0:

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File _atomic_property.py has 255 lines of code (exceeds 250 allowed). Consider refactoring.

Open

from __future__ import division

import os

import six

Function _calculate_one has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

    def _calculate_one(self, cxt, desc, reset):
        if desc in self._cache:
            return self._cache[desc]

        if reset:

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Function from_query has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

    def from_query(cls, mol, require_3D, explicit_hydrogens, kekulizes, id, config):
        if not isinstance(mol, Chem.Mol):
            raise TypeError("{!r} is not rdkit.Chem.Mol instance".format(mol))

        n_frags = len(Chem.GetMolFrags(mol))

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Function preset has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

    def preset(cls, version):
        for fused in [False, True]:
            for arom in [None, True, False]:
                for hetero in [None, True]:
                    yield cls(None, False, fused, arom, hetero)

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Function merge has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

    def merge(self):
        for i in range(1, len(self.Q) + 1):
            ns, lsp = self.Q[-i]
            common = ns & self.nodes
            if len(common) == 0:

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Function _register has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

    def _register(self, desc, version, ignore_3D):
        if not hasattr(desc, "__iter__"):
            if is_descriptor_class(desc):
                if desc.since > version:
                    return

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Function _bond_ids_to_atom_ids has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

    def _bond_ids_to_atom_ids(self, p):
        it = iter(p)

        try:
            a0f, a0t = self._bonds[next(it)]

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Function main_process has 9 arguments (exceeds 4 allowed). Consider refactoring.

Open

def main_process(

Function _register_one has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

    def _register_one(self, desc, check_only=False, ignore_3D=False):
        if not isinstance(desc, Descriptor):
            raise ValueError("{!r} is not descriptor".format(desc))

        if ignore_3D and desc.require_3D:

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Function _code has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

    def _code(self, tree, before, trail):
        if len(tree) == 0:
            yield trail

        else:

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