Source Code for Module diffpy.Structure.Parsers.P_rawxyz

  1  ############################################################################## 
  2  # 
  3  # Structure         by DANSE Diffraction group 
  4  #                   Simon J. L. Billinge 
  5  #                   (c) 2007 trustees of the Michigan State University. 
  6  #                   All rights reserved. 
  7  # 
  8  # File coded by:    Pavol Juhas 
  9  # 
 10  # See AUTHORS.txt for a list of people who contributed. 
 11  # See LICENSE.txt for license information. 
 12  # 
 13  ############################################################################## 
 14   
 15  """Parser for raw XYZ file format.  Raw XYZ is a 3 or 4 column text 
 16  file with cartesian coordinates of atoms and an optional first column 
 17  for atom types. 
 18  """ 
 19   
 20  __id__ = "$Id: P_rawxyz.py 2825 2009-03-09 04:33:12Z juhas $" 
 21   
 22  import sys 
 23   
 24  from diffpy.Structure import Structure, Lattice, Atom 
 25  from diffpy.Structure import StructureFormatError 
 26  from diffpy.Structure.utils import isfloat 
 27  from diffpy.Structure.Parsers import StructureParser 
 28   
 29 -class P_rawxyz(StructureParser): 
 30      """Parser --> StructureParser subclass for RAWXYZ format""" 
 31   
 32 -    def __init__(self): 
 33          StructureParser.__init__(self) 
 34          self.format = "rawxyz" 
 35          return 
 36   
 37 -    def parseLines(self, lines): 
 38          """Parse list of lines in RAWXYZ format. 
 39   
 40          Return Structure object or raise StructureFormatError. 
 41          """ 
 42          linefields = [l.split() for l in lines] 
 43          # prepare output structure 
 44          stru = Structure() 
 45          # find first valid record 
 46          start = 0 
 47          for field in linefields: 
 48              if len(field) == 0 or field[0] == "#": 
 49                  start += 1 
 50              else: 
 51                  break 
 52          # find the last valid record 
 53          stop = len(lines) 
 54          while stop > start and len(linefields[stop-1]) == 0: 
 55              stop -= 1 
 56          # get out for empty structure 
 57          if start >= stop: 
 58              return stru 
 59          # here we have at least one valid record line 
 60          # figure out xyz layout from the first line for plain and raw formats 
 61          floatfields = [ isfloat(f) for f in linefields[start] ] 
 62          nfields = len(linefields[start]) 
 63          if nfields not in (3, 4): 
 64              emsg = ("%d: invalid RAWXYZ format, expected 3 or 4 columns" % 
 65                      (start + 1)) 
 66              raise StructureFormatError(emsg) 
 67          if floatfields[:3] == [True, True, True]: 
 68              el_idx, x_idx = (None, 0) 
 69          elif floatfields[:4] == [False, True, True, True]: 
 70              el_idx, x_idx = (0, 1) 
 71          else: 
 72              emsg = "%d: invalid RAWXYZ format" % (start + 1) 
 73              raise StructureFormatError(emsg) 
 74          # now try to read all record lines 
 75          try: 
 76              p_nl = start 
 77              for fields in linefields[start:] : 
 78                  p_nl += 1 
 79                  if fields == []: 
 80                      continue 
 81                  elif len(fields) != nfields: 
 82                      emsg = ('%d: all lines must have ' + 
 83                              'the same number of columns') % p_nl 
 84                      raise StructureFormatError, emsg 
 85                  element = el_idx is not None and fields[el_idx] or "" 
 86                  xyz = [ float(f) for f in fields[x_idx:x_idx+3] ] 
 87                  if len(xyz) == 2: 
 88                      xyz.append(0.0) 
 89                  stru.addNewAtom(element, xyz=xyz) 
 90          except ValueError: 
 91              emsg = "%d: invalid number" % p_nl 
 92              exc_type, exc_value, exc_traceback = sys.exc_info() 
 93              raise StructureFormatError, emsg, exc_traceback 
 94          return stru 
 95      # End of parseLines 
 96   
 97 -    def toLines(self, stru): 
 98          """Convert Structure stru to a list of lines in XYZ format. 
 99   
100          Return list of strings. 
101          """ 
102          lines = [] 
103          for a in stru: 
104              rc = a.xyz_cartn 
105              s = "%s %g %g %g" % (a.element, rc[0], rc[1], rc[2]) 
106              lines.append(s.lstrip()) 
107          return lines 
108      # End of toLines 
109   
110  # End of class P_rawxyz 
111   
112  # Routines 
113   
114 -def getParser(): 
115      return P_rawxyz() 
116   
117  # End of file 
118