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locsmith / xcamshift

xcamshift - a port of the camshift chemical shift force-field for xplor-nih
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order of loading RDC and xcamshift force-field #68

Closed theokara closed 9 years ago

theokara commented 9 years ago

The order of load the xcamshift and rdc potentials matters, specifically varTensorTools create_VarTensor has to be called after the xcamshift force-field has been created.

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "CalcMb2m.py", line 67, in <module>
    xcamshift.setup()
  File "/home/bstk/programs/xcamshift/xcamshift/xcamshift/src/xcamshift.py", line 4040, in setup
    self._prepare(TARGET_ATOM_IDS_CHANGED, self._get_active_target_atom_ids())
  File "/home/bstk/programs/xcamshift/xcamshift/xcamshift/src/xcamshift.py", line 3882, in _prepare
    self._prepare_potentials(change, data)
  File "/home/bstk/programs/xcamshift/xcamshift/xcamshift/src/xcamshift.py", line 3857, in _prepare_potentials
    potential._prepare(change, data)
  File "/home/bstk/programs/xcamshift/xcamshift/xcamshift/src/xcamshift.py", line 2167, in _prepare
    self._selected_components = self._build_selected_components(target_atom_ids)
  File "/home/bstk/programs/xcamshift/xcamshift/xcamshift/src/xcamshift.py", line 2509, in _build_selected_components
    self._get_components()['OFFS'] = 0
  File "/home/bstk/programs/xcamshift/xcamshift/xcamshift/src/xcamshift.py", line 2488, in _get_components
    remote_component_list = self._get_component_list('NBRM')
  File "/home/bstk/programs/xcamshift/xcamshift/xcamshift/src/xcamshift.py", line 755, in _get_component_list
    self._build_component_list(name,"(all)")
  File "/home/bstk/programs/xcamshift/xcamshift/xcamshift/src/xcamshift.py", line 719, in _build_component_list
    self._create_components_for_residue(name,segment, residue_number, target_atom_selection)
  File "/home/bstk/programs/xcamshift/xcamshift/xcamshift/src/xcamshift.py", line 706, in _create_components_for_residue
    component_factory.create_components(component_list, table_source, segment, target_residue_number,selected_atoms)
  File "/home/bstk/programs/xcamshift/xcamshift/xcamshift/src/xcamshift.py", line 105, in create_components
    self.create_atom_components(component_list, table, selected_atoms)
  File "/home/bstk/programs/xcamshift/xcamshift/xcamshift/src/xcamshift.py", line 121, in create_atom_components
    contexts = self._build_contexts(atom, table)
  File "/home/bstk/programs/xcamshift/xcamshift/xcamshift/src/xcamshift.py", line 1825, in _build_contexts
    results.append(self.Remote_non_bonded_context(atom, self._all_spheres, table))
  File "/home/bstk/programs/xcamshift/xcamshift/xcamshift/src/xcamshift.py", line 1798, in __init__
    chem_type = table.get_chem_type_translation(raw_chem_type)
  File "/home/bstk/programs/xcamshift/xcamshift/xcamshift/src/non_bonded_table.py", line 99, in get_chem_type_translation
    self._check_chem_type(chem_type)
  File "/home/bstk/programs/xcamshift/xcamshift/xcamshift/src/non_bonded_table.py", line 96, in _check_chem_type
    raise KeyError(message)
KeyError: 'chemical type XXX is not in non bonded table chemical type translations (NC2, HC, HA, NA, NB, CB, C, CN, CC, H, CA, O, N, S, CX, NH1, NH3, NH2, CR
, CP, CW, CV, CT, OH, OC)'
PyInterp::command: error executing: >execfile('CalcMb2m.py')<