ForceField

Complexity

Total Complexity

15

Size/Duplication

Total Lines	67
Duplicated Lines	0 %

Test Coverage

Coverage

17.5%

Importance

Changes	2
Bugs	0	Features	2

5 Methods

Rating	Name	Duplication	Size	Complexity
B	embed()	0	15	5
A	columns()	0	3	1
A	__init__()	0	8	1
A	_optimize()	0	3	1
C	_transform_mol()	0	23	7

#! /usr/bin/env python
#
# Copyright (C) 2016 Rich Lewis <rl403@cam.ac.uk>
# License: 3-clause BSD

"""
## skchem.forcefields.base

Module specifying base class for forcefields.
"""
import warnings
from abc import ABCMeta, abstractmethod

import pandas as pd

The import pandas could not be resolved.

from rdkit.Chem.rdDistGeom import EmbedMolecule

The import rdkit.Chem.rdDistGeom could not be resolved.

from ..utils import Suppressor
from ..base import Transformer
from ..filters.base import TransformFilter


class ForceField(Transformer, TransformFilter):
    # TODO: Multiple conformer generation handling.

TODO and FIXME comments should generally be avoided.

    """ Base forcefield class.

    Filter drops those that fail to be optimized.

     """

    __metaclass__ = ABCMeta

    def __init__(self, preembed=True, warn_on_fail=True, error_on_fail=False,

Too many arguments (7/5)

                 add_hs=True, n_jobs=1, verbose=True):

        self.add_hs = add_hs
        self.warn_on_fail = warn_on_fail
        self.error_on_fail = error_on_fail
        self.preembed = preembed
        super(ForceField, self).__init__(verbose=verbose, n_jobs=n_jobs)

    @property
    def columns(self):
        return pd.Index(['structure'])

    def embed(self, mol):

This method should have a docstring.

        success = EmbedMolecule(mol)
        if success == -1:
            msg = 'Failed to Embed Molecule {}'.format(mol.name)
            if self.error_on_fail:
                raise RuntimeError(msg)
            elif self.warn_on_fail:
                warnings.warn(msg)
            return None

        if self.add_hs:
            return mol.add_hs(add_coords=True)
        else:
            return mol

    def _transform_mol(self, mol):

        mol = mol.copy()

        with Suppressor():
            if self.preembed:
                mol = self.embed(mol)

            if mol is None:  # embedding failed
                return None

            res = self._optimize(mol)

        if res == -1:
            msg = 'Failed to optimize molecule \'{}\' using {}'.format(
                mol.name, self.__class__)
            if self.error_on_fail:
                raise RuntimeError(msg)
            elif self.warn_on_fail:
                warnings.warn(msg)
            return None

        return mol

    @abstractmethod
    def _optimize(self, mol):
        pass


class RoughEmbedding(ForceField):

This class should have a docstring.

    def _optimize(self, mol):
        return mol