ForceField

Complexity

Total Complexity

22

Size/Duplication

Total Lines	69
Duplicated Lines	0 %

Importance

Changes	2
Bugs	0	Features	2

5 Methods

Rating	Name	Duplication	Size	Complexity
A	__init__()	0	7	1
B	embed()	0	15	5
C	transform()	0	17	8
A	_optimize()	0	2	1
C	optimize()	0	22	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
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 .. import core
from ..utils import NamedProgressBar, Suppressor

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

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

        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

    def _optimize(self, mol):
        raise NotImplementedError

    def transform(self, obj):

This method should have a docstring.

        if isinstance(obj, core.Mol):
            return self.optimize(obj)
        elif isinstance(obj, pd.Series):
            bar = NamedProgressBar(name=self.__class__.__name__)

Black listed name "bar"

            res = pd.Series([self.optimize(mol) for mol in bar(obj)], index=obj.index, name=obj.name)

This line is too long as per the coding-style (101/100).

bar does not seem to be callable.

            if self.drop_failed:
                res = res[res.notnull()]
            return res
        elif isinstance(obj, pd.DataFrame):
            res = self.transform(obj.structure)
            res = res.to_frame().join(obj.drop('structure', axis=1))
            return res
        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