[cclib-devel] Bug in cclib's orcaparser

[Xaver W. <xav...@we...>]

Hi,
in case of dummy atoms, orcaparser can't read the atoms. Consider:

>>> cclibdata = cfile.parse()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "cclib/parser/logfileparser.py", line 221, in parse
    self.extract(inputfile, line)
  File "cclib/parser/orcaparser.py", line 196, in extract
    atomnos.append(self.table.number[broken[0]])
KeyError: '-'

I think the lines which orcaparser is trying to read are (sth like):

  138 ---------------------------------
  139 CARTESIAN COORDINATES (ANGSTROEM)
  140 ---------------------------------
  141   Fe     0.000000    0.000000    0.000660
  142   O     -0.592830    1.741600   -0.806850
  143   O      0.592830   -1.741600   -0.806850
  144   C      0.000000    2.934410   -0.176690
  145   C      0.000000   -2.934410   -0.176690
  146   H     -0.018170    3.765540   -0.884740
  147   H      0.018170   -3.765540   -0.884740
  148   C      1.428890    2.563280    0.175900
  149   C     -1.428890   -2.563280    0.175900
  150   H      2.069080    2.492180   -0.707270
  151   H     -2.069080   -2.492180   -0.707270
  152   O      1.366300    1.233000    0.806640
  153   O     -1.366300   -1.233000    0.806640
  154   H     -0.593730    3.184280    0.706460
  155   H      0.593730   -3.184280    0.706460
  156   H      1.849370    3.280780    0.883620
  157   H     -1.849370   -3.280780    0.883620
  158   H     -1.264360    1.976320   -1.465620
  159   H      1.264360   -1.976320   -1.465620
  160   H      2.067340    1.111470    1.465270
  161   H     -2.067340   -1.111470    1.465270
  162   -      0.408688    1.481601    0.017975
  163   -     -0.442210   -1.472899    0.045583

(line numbers by "vi", ignore)

The two last lines are the coordinates of two dummy atoms. They turn up as 
"DA" in the input, but apparently as " - " in the coordinate blocks of the 
output.

Drop me a line if you need more info.

Regards,
Xaver W.
(for ccwatcher.sourceforge.net)