Esempio n. 1
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    def __init__(self, filename, mode="wa", numterms=None, preamble=None, **kwargs):
        """Set up for writing to *filename*.

        :Arguments:
           *filename*
               output file
           *mode*
               overwrite ("w") for every write, append ("a") to existing
               file, or overwrite an existing file and then append ("wa") ["wa"]
           *numterms*
               number of individual index numbers per line for output
               formats that write multiple entries in one line. If set
               to 0 or ``False`` then no special formatting is done  [8]
           *preamble*
               string that is written as a comment at the top of the file []
           *kwargs*
               use as defaults for :meth:`write`
        """
        self.filename = util.filename(filename, ext=self.ext)
        if not mode in ('a', 'w', 'wa'):
            raise ValueError("mode must be one of 'w', 'a', 'wa', not %r" % mode)
        self.mode = mode
        self._current_mode = mode[0]
        if numterms is None or numterms < 0:
            self.numterms = self.default_numterms
        elif numterms is False:
            self.numterms = 0
        else:
            self.numterms = numterms
        self.preamble = preamble
        self.otherargs = kwargs  # hack
        self.number = 0

        self.write_preamble()
Esempio n. 2
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 def testNamedStream(self):
     ns = util.NamedStream(cStringIO.StringIO(), self.filename)
     fn = util.filename(ns, ext=self.ext)
     # assert_equal replace by this if loop to avoid segfault on some systems
     if fn != ns:
         raise AssertionError("fn and ns are different")
     assert_equal(str(fn), self.filename2)
     assert_equal(ns.name, self.filename2)
Esempio n. 3
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    def __init__(self, filename, convert_units=None, **kwargs):
        """Set up a GROWriter with a precision of 3 decimal places.

        :Arguments:
           *filename*
              output filename
        """
        self.filename = util.filename(filename, ext='gro')

        if convert_units is None:
            convert_units = MDAnalysis.core.flags['convert_lengths']
        self.convert_units = convert_units  # convert length and time to base units
Esempio n. 4
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    def __init__(self, filename, convert_units=None, **kwargs):
        """Set up a GROWriter with a precision of 3 decimal places.

        :Arguments:
           *filename*
              output filename
        """
        self.filename = util.filename(filename, ext="gro")

        if convert_units is None:
            convert_units = MDAnalysis.core.flags["convert_lengths"]
        self.convert_units = convert_units  # convert length and time to base units
Esempio n. 5
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    def __init__(self, filename, convert_units=None, **kwargs):
        """Set up a PQRWriter with full whitespace separation.

        :Arguments:
          *filename*
             output filename
          *remarks*
             remark lines (list of strings) or single string to be added to the
             top of the PQR file
        """
        self.filename = util.filename(filename, ext='pqr')

        if convert_units is None:
            convert_units = MDAnalysis.core.flags['convert_lengths']
        self.convert_units = convert_units  # convert length and time to base units

        self.remarks = kwargs.pop('remarks', "PQR file written by MDAnalysis")
Esempio n. 6
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    def __init__(self,
                 filename,
                 mode="wa",
                 numterms=None,
                 preamble=None,
                 **kwargs):
        """Set up for writing to *filename*.

        :Arguments:
           *filename*
               output file
           *mode*
               overwrite ("w") for every write, append ("a") to existing
               file, or overwrite an existing file and then append ("wa") ["wa"]
           *numterms*
               number of individual index numbers per line for output
               formats that write multiple entries in one line. If set
               to 0 or ``False`` then no special formatting is done  [8]
           *preamble*
               string that is written as a comment at the top of the file []
           *kwargs*
               use as defaults for :meth:`write`
        """
        self.filename = util.filename(filename, ext=self.ext)
        if not mode in ('a', 'w', 'wa'):
            raise ValueError("mode must be one of 'w', 'a', 'wa', not %r" %
                             mode)
        self.mode = mode
        self._current_mode = mode[0]
        if numterms is None or numterms < 0:
            self.numterms = self.default_numterms
        elif numterms is False:
            self.numterms = 0
        else:
            self.numterms = numterms
        self.preamble = preamble
        self.otherargs = kwargs  # hack
        self.number = 0

        self.write_preamble()
Esempio n. 7
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 def __init__(self, filename, **kwargs):
     self.filename = util.filename(filename, ext='crd')
     self.crd = None
Esempio n. 8
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 def __init__(self, filename, **kwargs):
     self.filename = util.filename(filename, ext='pdbqt')
     self.pdb = util.anyopen(self.filename, 'w')
Esempio n. 9
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 def __init__(self, filename, **kwargs):
     self.filename = util.filename(filename, ext='crd')
     self.crd = None
Esempio n. 10
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 def __init__(self, filename, **kwargs):
     self.filename = util.filename(filename, ext='pdbqt')
     self.pdb = util.anyopen(self.filename, 'w')
Esempio n. 11
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 def testStringRootExtKeep(self):
     fn = util.filename(self.root, ext=self.ext, keep=True)
     assert_equal(fn, self.filename2)
Esempio n. 12
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 def testStringRootExt(self):
     fn = util.filename(self.root, ext=self.ext)
     assert_equal(fn, self.filename2)
Esempio n. 13
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 def testStringKeep(self):
     fn = util.filename(self.filename, ext=self.ext, keep=True)
     assert_equal(fn, self.filename)
Esempio n. 14
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 def testStringNoExt(self):
     fn = util.filename(self.filename)
     assert_equal(fn, self.filename)