Conditions | 11 |
Total Lines | 99 |
Lines | 0 |
Ratio | 0 % |
Tests | 34 |
CRAP Score | 11 |
Changes | 7 | ||
Bugs | 2 | Features | 2 |
Small methods make your code easier to understand, in particular if combined with a good name. Besides, if your method is small, finding a good name is usually much easier.
For example, if you find yourself adding comments to a method's body, this is usually a good sign to extract the commented part to a new method, and use the comment as a starting point when coming up with a good name for this new method.
Commonly applied refactorings include:
If many parameters/temporary variables are present:
Complex classes like read_smiles() often do a lot of different things. To break such a class down, we need to identify a cohesive component within that class. A common approach to find such a component is to look for fields/methods that share the same prefixes, or suffixes.
Once you have determined the fields that belong together, you can apply the Extract Class refactoring. If the component makes sense as a sub-class, Extract Subclass is also a candidate, and is often faster.
1 | #! /usr/bin/env python |
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21 | 1 | def read_smiles(smiles_file, smiles_column=0, name_column=None, delimiter='\t', |
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22 | title_line=False, error_bad_mol=False, warn_bad_mol=True, |
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23 | drop_bad_mol=True, *args, **kwargs): |
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24 | |||
25 | """Read a smiles file into a pandas dataframe. |
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26 | |||
27 | The class wraps the pandas read_csv function. |
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28 | |||
29 | smiles_file (str, file-like): |
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30 | Location of data to load, specified as a string or passed directly as a |
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31 | file-like object. URLs may also be used, see the pandas.read_csv |
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32 | documentation. |
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33 | smiles_column (int): |
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34 | The column index at which SMILES are provided. |
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35 | Defaults to `0`. |
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36 | name_column (int): |
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37 | The column index at which compound names are provided, for use as the |
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38 | index in the DataFrame. If None, use the default index. |
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39 | Defaults to `None`. |
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40 | delimiter (str): |
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41 | The delimiter used. |
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42 | Defaults to `\\t`. |
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43 | title_line (bool): |
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44 | Whether a title line is provided, to use as column titles. |
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45 | Defaults to `False`. |
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46 | error_bad_mol (bool): |
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47 | Whether an error should be raised when a molecule fails to parse. |
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48 | Defaults to `False`. |
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49 | warn_bad_mol (bool): |
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50 | Whether a warning should be raised when a molecule fails to parse. |
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51 | Defaults to `True`. |
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52 | drop_bad_mol (bool): |
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53 | If true, drop any column with smiles that failed to parse. Otherwise, |
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54 | the field is None. Defaults to `True`. |
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55 | args, kwargs: |
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56 | Arguments will be passed to pandas read_csv arguments. |
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57 | |||
58 | Returns: |
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59 | pandas.DataFrame: |
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60 | The loaded data frame, with Mols supplied in the `structure` field. |
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61 | |||
62 | See Also: |
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63 | pandas.read_csv |
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64 | skchem.Mol.from_smiles |
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65 | skchem.io.sdf |
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66 | """ |
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67 | |||
68 | 1 | with Suppressor(): |
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69 | |||
70 | # set the header line to pass to the pandas parser |
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71 | # we accept True as being line zero, as is usual for smiles |
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72 | # if user specifies a header already, then do nothing |
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73 | |||
74 | 1 | header = kwargs.pop('header', None) |
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75 | 1 | if title_line is True: |
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76 | 1 | header = 0 |
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77 | 1 | elif header is not None: |
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78 | 1 | pass #remove from the kwargs to not pass it twice |
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79 | else: |
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80 | 1 | header = None |
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81 | |||
82 | # read the smiles file |
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83 | 1 | data = pd.read_csv(smiles_file, delimiter=delimiter, header=header, |
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84 | *args, **kwargs) |
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85 | |||
86 | # replace the smiles column with the structure column |
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87 | 1 | lst = list(data.columns) |
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88 | 1 | lst[smiles_column] = 'structure' |
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89 | 1 | if name_column: |
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90 | 1 | lst[name_column] = 'batch' |
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91 | 1 | data.columns = lst |
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92 | |||
93 | 1 | def parse(row): |
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94 | """ Parse smiles for row """ |
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95 | 1 | try: |
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96 | 1 | return Mol.from_smiles(row.structure) |
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97 | 1 | except ValueError: |
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98 | 1 | msg = 'Molecule {} could not be decoded.'.format(row.name) |
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99 | 1 | if error_bad_mol: |
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100 | 1 | raise ValueError(msg) |
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101 | 1 | elif warn_bad_mol: |
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102 | 1 | warnings.warn(msg) |
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103 | |||
104 | 1 | return None |
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105 | |||
106 | 1 | data['structure'] = data['structure'].apply(str) |
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107 | 1 | data['structure'] = data.apply(parse, axis=1) |
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108 | |||
109 | 1 | if drop_bad_mol: |
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110 | 1 | data = data[data['structure'].notnull()] |
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111 | |||
112 | # set index if passed |
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113 | 1 | if name_column is not None: |
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114 | 1 | data = data.set_index(data.columns[name_column]) |
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115 | |||
116 | 1 | cols = data.columns.tolist() |
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117 | 1 | cols.remove('structure') |
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118 | 1 | data = data[['structure'] + cols] |
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119 | 1 | return squeeze(data, axis=1) |
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120 | |||
165 |
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