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FortranFormat.py

# This module defines a class that handles I/O using
# Fortran-compatible format specifications.
#
#
# Warning: Fortran formatting is a complex business and I don't
# claim that this module works for anything complicated. It knows
# only the most frequent formatting options. Known limitations:
#
# 1) Only A, D, E, F, G, I, and X formats are supported (plus string constants
#    for output).
# 2) No direct support for complex numbers. You have to split them into
#    real and imaginary parts before output, and for input you get
#    two float numbers anyway.
# 3) No overflow check. If an output field gets too large, it will
#    take more space, instead of being replaced by stars.
#
#
# Written by Konrad Hinsen <hinsen@cnrs-orleans.fr>
# Changed by Andreas Prlic <andreas@came.sbg.ac.at> (small change)
# last revision: 2001-05-28
#

"""Fortran-compatible input/output

This module provides two classes that aid in reading and writing
Fortran-formatted text files.

Examples:

  Input:

  >>>s = '   59999'
  >>>format = FortranFormat('2I4')
  >>>line = FortranLine(s, format)
  >>>print line[0]
  >>>print line[1]

  prints

  >>>5
  >>>9999


  Output:

  >>>format = FortranFormat('2D15.5')
  >>>line = FortranLine([3.1415926, 2.71828], format)
  >>>print str(line)

  prints

  '3.14159D+00    2.71828D+00'
"""

import string

#
# The class FortranLine represents a single line of input/output,
# which can be accessed as text or as a list of items.
#
00061 class FortranLine:

    """Fortran-style record in formatted files

    FortranLine objects represent the content of one record of a
    Fortran-style formatted file. Indexing yields the contents as
    Python objects, whereas transformation to a string (using the
    built-in function 'str') yields the text representation.

    Constructor: FortranLine(|data|, |format|, |length|='80')

    Arguments:

    |data| -- either a sequence of Python objects, or a string
              formatted according to Fortran rules

    |format| -- either a Fortran-style format string, or a
                FortranFormat object. A FortranFormat should
                be used when the same format string is used repeatedly,
                because then the rather slow parsing of the string
                is performed only once.

    |length| -- the length of the Fortran record. This is relevant
                only when |data| is a string; this string is then
                extended by spaces to have the indicated length.
                The default value of 80 is almost always correct.

    Restrictions:

    1) Only A, D, E, F, G, I, and X formats are supported (plus string
       constants for output).

    2) No direct support for complex numbers; they must be split into
       real and imaginary parts before output.

    3) No overflow check. If an output field gets too large, it will
       take more space, instead of being replaced by stars according
       to Fortran conventions.
    """
    
    def __init__(self, line, format, length = 80):
      if type(line) == type(''):
          self.text = line
          self.data = None
      else:
          self.text = None
          self.data = line
      if type(format) == type(''):
          self.format = FortranFormat(format)
      else:
          self.format = format
      self.length = length
      if self.text is None:
          self._output()
      if self.data is None:
          self._input()

    def __len__(self):
      return len(self.data)

    def __getitem__(self, i):
      return self.data[i]

    def __getslice__(self, i, j):
      return self.data[i:j]

    def __str__(self):
      return self.text

    def isBlank(self):
      return len(string.strip(self.text)) == 0

    def _input(self):
      text = self.text
      if len(text) < self.length: text = text + (self.length-len(text))*' '
      self.data = []
      for field in self.format:
          l = field[1]
          s = text[:l]
          text = text[l:]
          type = field[0]
          value = None
          if type == 'A':
            value = s
          elif type == 'I':
            s = string.strip(s)
            if len(s) == 0:
                value = 0
            else:
                # by AP
                # sometimes a line does not match to expected format, 
                # e.g.: pdb2myd.ent.Z chain: - model: 0 : CONECT*****
                # catch this and set value to None
                try:
                  value = string.atoi(s)
                except:
                  value = None
          elif type == 'D' or type == 'E' or type == 'F' or type == 'G':
            s = string.lower(string.strip(s))
            n = string.find(s, 'd')
            if n >= 0:
                s = s[:n] + 'e' + s[n+1:]
            if len(s) == 0:
                value = 0.
            else:
                try:
                        value = string.atof(s)
                except:
                  value = None
          if value is not None:
            self.data.append(value)

    def _output(self):
      data = self.data
      self.text = ''
      for field in self.format:
          type = field[0]
          if type == "'":
            self.text = self.text + field[1]
          elif type == 'X':
            self.text = self.text + field[1]*' '
          else: # fields that use input data
            length = field[1]
            if len(field) > 2: fraction = field[2]
            value = data[0]
            data = data[1:]
            if type == 'A':
                self.text = self.text + (value+length*' ')[:length]
            else: # numeric fields
                    if value is None:
                        s = ''
                elif type == 'I':
                  s = `value`
                elif type == 'D':
                  s = ('%'+`length`+'.'+`fraction`+'e') % value
                  n = string.find(s, 'e')
                  s = s[:n] + 'D' + s[n+1:]
                elif type == 'E':
                  s = ('%'+`length`+'.'+`fraction`+'e') % value
                elif type == 'F':
                  s = ('%'+`length`+'.'+`fraction`+'f') % value
                elif type == 'G':
                  s = ('%'+`length`+'.'+`fraction`+'g') % value
                else:
                  raise ValueError, 'Not yet implemented'
                s = string.upper(s)
                self.text = self.text + ((length*' ')+s)[-length:]
        self.text = string.rstrip(self.text)

#
# The class FortranFormat represents a format specification.
# It ought to work for correct specifications, but there is
# little error checking.
#
00215 class FortranFormat:

    """Parsed fortran-style format string

    Constructor: FortranFormat(|format|), where |format| is a
    format specification according to Fortran rules.
    """

    def __init__(self, format, nested = 0):
      fields = []
      format = string.strip(format)
      while format and format[0] != ')':
          n = 0
          while format[0] in string.digits:
            n = 10*n + string.atoi(format[0])
            format = format[1:]
          if n == 0: n = 1
          type = string.upper(format[0])
          if type == "'":
            eof = string.find(format, "'", 1)
            text = format[1:eof]
            format = format[eof+1:]
          else:
            format = string.strip(format[1:])
          if type == '(':
            subformat = FortranFormat(format, 1)
            fields = fields + n*subformat.fields
            format = subformat.rest
            eof = string.find(format, ',')
            if eof >= 0:
                format = format[eof+1:]
          else:
            eof = string.find(format, ',')
            if eof >= 0:
                field = format[:eof]
                format = format[eof+1:]
            else:
                eof = string.find(format, ')')
                if eof >= 0:
                  field = format[:eof]
                  format = format[eof+1:]
                else:
                  field = format
                  format = ''
            if type == "'":
                field = (type, text)
            else:
                dot = string.find(field, '.')
                if dot > 0:
                  length = string.atoi(field[:dot])
                  fraction = string.atoi(field[dot+1:])
                  field = (type, length, fraction)
                else:
                  if field:
                      length = string.atoi(field)
                  else:
                      length = 1
                  field = (type, length)
            fields = fields + n*[field]
      self.fields = fields
      if nested:
          self.rest = format

    def __len__(self):
      return len(self.fields)

    def __getitem__(self, i):
      return self.fields[i]


# Test code

if __name__ == '__main__':
    f = FortranFormat("'!!',D10.3,F10.3,G10.3,'!!'")
    l = FortranLine([1.5707963, 3.14159265358, 2.71828], f)
    print str(l)
    f = FortranFormat("F12.0")
    l = FortranLine('2.1D2', f)
    print l[0]

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