[MMTK] Re: bulding water ice; problems with Peter's code

Peter C. McCluskey pcm@rahul.net
Wed, 14 Jul 1999 16:02:46 -0700

 pcm@rahul.net ("Peter C. McCluskey") writes:
> eugene.leitl@lrz.uni-muenchen.de (Eugene Leitl) writes:
>>Peter, in case you've got some spare time (ha-ha), could you perhaps 
>>adjust the scripts to the new syntax? (It is somewhat difficult to
>>adapt other people's nonrunning code when one is learning both the 
>>language and the particular modeling package).

 Ok, I've adapted it to use the MMTK-2.0a2 code and tested it with Python
1.5.1 and 1.5.2. It's at http://www.rahul.net/pcm/mmtk/mmtk2.0s.tar.gz.
 The hello.py produces seg faults with both versions of Python under RedHat
Linux 5.0, and I haven't made a serious attempt to track that down. Also with
Python 1.5.2 the qhull code seems to seg fault in lego6.py and lego7.py.
Other than that, it's working at least as well as before, but there's
virtually no new stuff. I'm dissatisfied with it's robustness and ease of
use, and I'm wondering how much to try to redesign it before making a
serious attempt to get it into the main MMTK distribution.

 Konrad, I see a class PDBOutputFile in both ConfigIO.py and PDB.py. I
assume the former is obsolete?
 Also, the following code produces a rather useless error message. Is it
a bug, or do you expect users to know that bALA1.pdb isn't the kind of
thing that should be passed to this code?

from MMTK.PDB import PDBConfiguration
configuration = PDBConfiguration('bALA1.pdb')
chains = configuration.createPeptideChains()

Traceback (innermost last):
  File "./bug1.py", line 4, in ?
    chains = configuration.createPeptideChains()
  File "/home/pcm/nanocad/mmtk/MMTK/PDB.py", line 96, in createPeptideChains
    chain = apply(Proteins.PeptideChain, (chain,), properties)
  File "/home/pcm/nanocad/mmtk/MMTK/Proteins.py", line 141, in __init__
    r = Residue(residue, model)
  File "/home/pcm/nanocad/mmtk/MMTK/Proteins.py", line 21, in __init__
    blueprint = _residueBlueprint(name, model)
  File "/home/pcm/nanocad/mmtk/MMTK/Proteins.py", line 91, in _residueBlueprint
    blueprint = Database.BlueprintGroup(name)
  File "/home/pcm/nanocad/mmtk/MMTK/Database.py", line 335, in __init__
    BlueprintObject.__init__(self, type, group_types, memo)
  File "/home/pcm/nanocad/mmtk/MMTK/Database.py", line 305, in __init__
    original = database.findType(original)
  File "/home/pcm/nanocad/mmtk/MMTK/Database.py", line 67, in findType
    filename = databasePath(name, self.directory, 0)
  File "/home/pcm/nanocad/mmtk/MMTK/Database.py", line 48, in databasePath
    raise IOError, "Database entry %s/%s not found" % (directory, filename)
IOError: Database entry Groups/nmethyl not found

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