skchem.io.read_smiles()

Complexity

Conditions

11

Size

Total Lines

78

Duplication

Lines	0
Ratio	0 %

1 Method

Rating	Name	Duplication	Size	Complexity
A	parse()	0	11	1

#! /usr/bin/env python
#
# Copyright (C) 2007-2009 Rich Lewis <rl403@cam.ac.uk>
# License: 3-clause BSD

"""
skchem.io.smiles

Defining input and output operations for smiles files.
"""

import skchem
import pandas as pd

The import pandas could not be resolved.

from skchem.utils import Suppressor

def read_smiles(smiles_file, smiles_column=0, name_column=None, delimiter='\t',

Too many arguments (6/5)

                        title_line=False, force=False, *args, **kwargs):

Wrong continued indentation.
title_line=False, force=False, *args, **kwargs):
| ^

    """
    Read a smiles file into a pandas dataframe.  The class wraps the pandas read_csv function.

    @param smiles_file      A file path provided as a :str:, or a :file-like: object.
    @param smiles_column    The column index as an :int: in which the smiles strings are provided.
                            Defaults to _zero_.
    @param name_column      The column index as an :int: in which compound names are provided,
                            for use as the index in the dataframe.  Defaults to _None_.
    @param delimiter        The delimiter used, specified as a :str:.
                            Defaults to _<tab>_.
    @param title_line       A :bool: specifying whether a title line is provided,
                            to use as column titles.
    @param force            A :bool: specifying whether poorly parsed molecules should be skipped,
                            or an error thrown.
    Additionally, pandas read_csv arguments may be provided.

    @returns df             A dataframe of type :pandas.core.frame.DataFrame:.
    """

    with Suppressor():

        # set the header line to pass to the pandas parser
        # we accept True as being line zero, as is usual for smiles
        # if user specifies a header already, then do nothing

        header = kwargs.get('header', None)
        if title_line is True:
            header = 0
        elif header is not None:
            kwargs.pop('header') #remove from the kwargs to not pass it twice
        else:
            header = None

        # open file if not already open
        if isinstance(smiles_file, str):
            smiles_file = open(smiles_file, 'r')

        # read the smiles file
        df = pd.read_csv(smiles_file, delimiter=delimiter, header=header, *args, **kwargs)

The name df does not conform to the variable naming conventions ([a-z_][a-z0-9_]{2,30}$).

        # replace the smiles column with the structure column
        lst = list(df.columns)
        lst[smiles_column] = 'structure'
        df.columns = lst

        # apply the from smiles constructor
        if force:
            def parse(smiles):

                """
                Parse a molecule from smiles string and return None if it doesn't load
                (restoring rdkit functionality)
                """

                try:
                    return skchem.Mol.from_smiles(smiles)

The Class Mol does not seem to have a member named from_smiles.

                except ValueError:
                    return None
        else:
            def parse(smiles):
                """
                Parse a molecule from smiles string
                """
                return skchem.Mol.from_smiles(smiles)

The Class Mol does not seem to have a member named from_smiles.

        df['structure'] = df['structure'].apply(str).apply(parse) #make sure is a string

        if force:
            df = df[df['structure'].notnull()]

The name df does not conform to the variable naming conventions ([a-z_][a-z0-9_]{2,30}$).

        # set index if passed
        if name_column is not None:
            df = df.set_index(df.columns[name_column])

The name df does not conform to the variable naming conventions ([a-z_][a-z0-9_]{2,30}$).

        return df

@classmethod
def from_smiles(_, *args, **kwargs):
    """ Create a DataFrame from a smiles file """
    return read_smiles(*args, **kwargs)

#set on pandas dataframe
pd.DataFrame.from_smiles = from_smiles