[PyMOL] Problems using chempy.tinker without numeric_type.

[Truls A. Tangstad]

I'm trying to programmatically load a PDB-file, using chempy.io.pdb,
then run an energy minimization with tinker. The problem is that the
tinker-wrapper stores files to the tinker xyz-format, which requires
that the numeric_type or text_type attribute is set
correctly. PDB.fromFile() doesn't seem to set these attributes at
all. 

Is there a simple way of getting around this problem or setting the
numeric_type correctly?

Currently, loading PDB-files with chempy.io.pdb.fromFile() keeps the
default numeric_type -9999, and the text_type '??', which ends up
raising a KeyError trying to find the matching numeric_type when
storing the xyz-format input file to tinker.

I'm using PyMOL 0.90-1 on Debian unstable where running the attached
testscript yields the following stacktrace:

Traceback (most recent call last):
  File "tinkertestsnippet.py", line 13, in ?
    s.minimize()
  File "/usr/lib/python2.3/site-packages/chempy/tinker/state.py", line 105, in 
minimize
    io.xyz.toFile(self.model,self.prefix+"_inp.xyz")
  File "/usr/lib/python2.3/site-packages/chempy/__init__.py", line 186, in 
toFile
    result = fp.writelines(apply(self.toList,(indexed,),params))
  File "/usr/lib/python2.3/site-packages/chempy/xyz.py", line 83, in toList
    n_type = mapping[a.text_type]
KeyError: '??'

-- 
Truls - kerfue+pymol-us...@herocamp.org

import chempy.io
from chempy.tinker.state import *

modelFile = "test.pdb"

model = io.pdb.fromFile(modelFile)

s = State()
s.model = model
s.minimize()

test.pdb
Description: test data for use with tinkertestsnippet.py