在Windows上使用python科学模块时出现属性错误

Question

当我们的程序在使用Linux2.6的Windows XP上运行时，我得到了以下错误(尽管它在ActivePerl上运行得很好)。你知道是怎么回事吗？这是模块中的错误还是我们代码的问题？

错误日志：

      File "C:\Python26\lib\site-packages\Scientific\IO\PDB.py", line 1163, in __ini
    t__
        self.parseFile(PDBFile(file_or_filename))
      File "C:\Python26\lib\site-packages\Scientific\IO\PDB.py", line 1371, in parse
    File
        type, data = file.readLine()
     File "C:\Python26\lib\site-packages\Scientific\IO\PDB.py", line 200, in readLi
   ne
        line = self.file.readline()
    AttributeError: 'unicode' object has no attribute 'readline'
    Exception AttributeError: "'unicode' object has no attribute 'close'" in <bound
    method PDBFile.__del__ of <Scientific.IO.PDB.PDBFile instance at 0x00FD0440>> ig
    nored

更新:按照Joe的建议，我得到了以下错误：

Traceback (most recent call last):
  File "NewParseV1_00.py", line 47, in <module>
    PromptUser()
  File "NewParseV1_00.py", line 45, in PromptUser
    parseGroupFile(grpfilepath, outputPPYfilepath, sorcePDBfilepath)
  File "NewParseV1_00.py", line 39, in parseGroupFile
    return GeneratePPY(LL,GRPNAME,SRCPDB,OUTPPY)
  File "NewParseV1_00.py", line 10, in __init__
    self.PDBStruct = Scientific.IO.PDB.Structure(SRCPDB)
  File "C:\Python26\lib\site-packages\Scientific\IO\PDB.py", line 1163, in __ini
t__
    self.parseFile(PDBFile(file_or_filename))
  File "C:\Python26\lib\site-packages\Scientific\IO\PDB.py", line 161, in __init
__
    if isinstance(file_or_filename, basestr):
NameError: global name 'basestr' is not defined
Exception AttributeError: "PDBFile instance has no attribute 'open'" in <bound m
ethod PDBFile.__del__ of <Scientific.IO.PDB.PDBFile instance at 0x00FDB418>> ign
ored

Answer 1

我猜，但它看起来像是Scientific.IO.PDB中的一个bug，他们这样做：

if type(file_or_filename) == str:
    file = open(file_or_filename)
else:
    file = file_or_filename

而不是做：

if isinstance(file_or_filename, basestr):
    ...

无论出于什么原因，您似乎在Windows端传递了一个unicode文件名，在Linux端传递了一个原始字符串。

不过，我再说一次，我只是猜测。我假设这里的Scientific是这个模块？http://dirac.cnrs-orleans.fr/plone/software/scientificpython/ (我不熟悉它...)

编辑:是的！

以下是来自Scientific.IO.PDB的相关代码

class PDBFile:

    """
    X{PDB} file with access at the record level

    The low-level file access is handled by the module
    L{Scientific.IO.TextFile}, therefore compressed files and URLs
    (for reading) can be used as well.
    """

    def __init__(self, file_or_filename, mode = 'r', subformat = None):
        """
        @param file_or_filename: the name of the PDB file, or a file object
        @type file_or_filename: C{str} or C{file}
        @param mode: the file access mode, 'r' (read) or 'w' (write)
        @type mode: C{str}
        @param subformat: indicates a specific dialect of the PDB format.
                          Subformats are defined in
                          L{Scientific.IO.PDBExportFilters}; they are used
                          only when writing.
        @type subformat: C{str} or C{NoneType}
        """
        if isinstance(file_or_filename, str):
            self.file = TextFile(file_or_filename, mode)
        else:
            self.file = file_or_filename
        <snip>

它应该和将isinstance(file_or_filename, str)更改为isinstance(file_or_filename, basestr)一样简单。你可能需要提交一份错误报告...

Answer 2

按照Joe的解释，更改Scientific.IO.PDB中的代码需要进行最后一次修改才能生效：

在第161行，将if isinstance(file_or_filename, str):更改为if isinstance(file_or_filename, basestring):

(请注意，Joe写道，第二个参数应该是basestr，但这在原始问题的更新中给出了错误。)