RoughEmbedding

Complexity

Total Complexity

1

Size/Duplication

Total Lines	3
Duplicated Lines	0 %

Importance

Changes

0

1 Method

Rating	Name	Duplication	Size	Complexity
A	_optimize()	0	2	1

#! /usr/bin/env python
#
# Copyright (C) 2015 Rich Lewis <rl403@cam.ac.uk>
# License: 3-clause BSD

"""
## skchem.forcefields.base

Module specifying base class for forcefields.
"""
import warnings
import pandas as pd

The import pandas could not be resolved.

import progressbar

The import progressbar could not be resolved.

from rdkit.Chem.rdDistGeom import EmbedMolecule

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

from .. import core

class ForceField(object):

This class should have a docstring.

    def __init__(self, embed=True, warn_on_fail=True, error_on_fail=False, drop_failed=True, add_hs=True):

This line is too long as per the coding-style (106/100).

Too many arguments (6/5)

        self.add_hs = add_hs
        self.drop_failed = drop_failed
        self.warn_on_fail = warn_on_fail
        self.error_on_fail = error_on_fail
        self.preembed = embed

    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
            else:
                pass

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

        return mol


    def optimize(self, mol):

This method should have a docstring.

        # TODO: likely need to handle which conformer here

TODO and FIXME comments should generally be avoided.

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

        if mol is None:
            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

    def _optimize(self, mol):
        raise NotImplementedError

    def transform(self, obj):

This method should have a docstring.

        if isinstance(obj, core.Mol):
            self.optimize(obj)
            return obj
        elif isinstance(obj, pd.Series):
            bar = progressbar.ProgressBar()

Black listed name "bar"

            for i, mol in enumerate(bar(obj)):
                res = self.optimize(mol)
                if res is None and self.drop_failed:
                    obj = obj.drop(obj.index[i])
            return obj
        elif isinstance(obj, pd.DataFrame):
            res = self.transform(obj.structure)
            return obj.ix[res.index]
        elif isinstance(obj, (tuple, list)):
            return self.transform(pd.Series(obj, [mol.name for mol in obj]))
        else:
            raise NotImplementedError

class RoughEmbedding(ForceField):

This class should have a docstring.

    def _optimize(self, mol):
        return mol