質問編集履歴
2
成功したfor文追記しました。
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File without changes
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@@ -124,4 +124,13 @@
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124
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90 structure = self.structure_builder.get_structure()
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91
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92 return structure
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127
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```
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128
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129
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PDBParserのせいでは無かったようです。
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130
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以下で上手くいきました。
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131
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132
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```ここに言語を入力
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133
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for filenames in glob.glob("complex.*.pdb"):
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134
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id=os.path.splitext(filenames)[0]
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135
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pdb=PDBParser().get_structure(id,filenames)
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127
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```
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1
PDBParserについて追記しました。
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@@ -8,4 +8,120 @@
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8
8
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In [5]: for filenames in glob.glob("complex.*.pdb"):
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9
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...: for lignames in glob.glob("complex.*.pdb"):
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10
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...: pdb=PDBParser().get_structure(lignames,filenames)
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11
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```
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12
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13
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追記です。
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14
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Pythonについての質問です。
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15
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教えていただいたコマンドにて以下の様にいくつかのファイルをカレントディレクトリに置いてそれぞれ、id、filenamesを得ることが出来ました。
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16
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しかし、PDBParser().get_structure(lignames,filenames)に入力すると何故かcomplex.7.pdbしか処理されませんでした。
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17
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PDBParserの仕様によるものだと思うのですが、どなたか原因をご教授ください。
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18
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19
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20
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```ここに言語を入力
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21
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In [8]: for filenames in glob.glob("complex.*.pdb"):
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...: id, ext=os.path.splitext(filenames)
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...: print(id)
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...:
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25
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...:
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...:
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27
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complex.10
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28
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complex.1-2
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complex.4
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complex.5
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31
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complex.8
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complex.3
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complex.6
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34
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complex.2
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35
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complex.9
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36
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complex.7
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```
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```ここに言語を入力
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40
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In [9]: for filenames in glob.glob("complex.*.pdb"):
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41
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...: id, ext=os.path.splitext(filenames)
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...: print(filenames)
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...:
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...:
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...:
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...:
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complex.10.pdb
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48
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complex.1-2.pdb
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complex.4.pdb
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complex.5.pdb
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complex.8.pdb
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complex.3.pdb
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complex.6.pdb
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54
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complex.2.pdb
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complex.9.pdb
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56
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complex.7.pdb
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57
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```
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59
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以下のサイトよりPDBParserのクラス内容です。
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60
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https://biopython.org/DIST/docs/api/Bio.PDB.PDBParser%27-pysrc.html#PDBParser.get_structure
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61
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62
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```ここに言語を入力
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63
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1 # Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
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2 # This code is part of the Biopython distribution and governed by its
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3 # license. Please see the LICENSE file that should have been included
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66
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4 # as part of this package.
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5
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68
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6 """Parser for PDB files."""
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69
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7
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8 from __future__ import print_function
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9
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72
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10 import warnings
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73
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11
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74
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12 try:
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75
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13 import numpy
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76
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14 except ImportError:
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15 from Bio import MissingPythonDependencyError
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16 raise MissingPythonDependencyError(
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17 "Install NumPy if you want to use the PDB parser.")
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80
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18
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81
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19 from Bio.File import as_handle
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82
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20
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83
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21 from Bio.PDB.PDBExceptions import PDBConstructionException
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84
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22 from Bio.PDB.PDBExceptions import PDBConstructionWarning
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85
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23
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86
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24 from Bio.PDB.StructureBuilder import StructureBuilder
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87
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25 from Bio.PDB.parse_pdb_header import _parse_pdb_header_list
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88
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26
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89
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27
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90
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28 # If PDB spec says "COLUMNS 18-20" this means line[17:20]
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91
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29
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92
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30
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93
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31 -class PDBParser(object):
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32 """Parse a PDB file and return a Structure object."""
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33
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96
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34 + def __init__(self, PERMISSIVE=True, get_header=False,
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97
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35 structure_builder=None, QUIET=False):
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98
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...
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65
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100
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66 # Public methods
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101
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67
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102
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68 - def get_structure(self, id, file):
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103
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69 """Return the structure.
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70
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105
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71 Arguments:
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72 - id - string, the id that will be used for the structure
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73 - file - name of the PDB file OR an open filehandle
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108
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74
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109
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75 """
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110
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76 with warnings.catch_warnings():
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111
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77 if self.QUIET:
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112
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78 warnings.filterwarnings("ignore", category=PDBConstructionWarning)
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113
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79
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114
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80 self.header = None
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115
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81 self.trailer = None
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116
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82 # Make a StructureBuilder instance (pass id of structure as parameter)
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117
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83 self.structure_builder.init_structure(id)
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118
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84
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119
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85 with as_handle(file, mode='rU') as handle:
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120
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86 self._parse(handle.readlines())
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121
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87
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122
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88 self.structure_builder.set_header(self.header)
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123
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89 # Return the Structure instance
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124
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90 structure = self.structure_builder.get_structure()
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125
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91
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92 return structure
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127
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```
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