def select_right_pdb(hklin, pdb_list):
'''Find a coordinate file which appears to have the right symmetry.'''
candidates = []
im = module_factory().interrogate_mtz()
im.set_hklin(hklin)
im.interrogate_mtz()
reference = ersatz_pointgroup(im.get_symmetry())
reference_cell = im.get_cell()
cells = {}
for xyzin in pdb_list:
ip = module_factory().interrogate_pdb()
ip.set_xyzin(xyzin)
try:
ip.interrogate_pdb()
if reference == ersatz_pointgroup(ip.get_symmetry_full()):
candidates.append(xyzin)
if reference == 'P222':
cells[xyzin] = nearest_orthorhombic(
reference_cell, ip.get_cell())
else:
cells[xyzin] = ip.get_cell()
except RuntimeError, e:
sys.stderr.write('%s\n' % e)
continue
def select_right_pdb(hklin, pdb_list):
'''Find a coordinate file which appears to have the right symmetry.'''
candidates = []
im = module_factory().interrogate_mtz()
im.set_hklin(hklin)
im.interrogate_mtz()
reference = ersatz_pointgroup(im.get_symmetry())
reference_cell = im.get_cell()
cells = { }
for xyzin in pdb_list:
ip = module_factory().interrogate_pdb()
ip.set_xyzin(xyzin)
ip.interrogate_pdb()
if reference == ersatz_pointgroup(ip.get_symmetry_full()):
candidates.append(xyzin)
cells[xyzin] = ip.get_cell()
if len(candidates) == 0:
raise RuntimeError, 'no matching coordinate files found'
# then if there are more than one, see if one matches closer than
# the others... do this by sorting on the absolute differences in
# cell constants then picking the closest match
# erm. doesn't this need to consider permutations for P222?
if len(candidates) == 1:
return candidates[0]
diffs = []
for xyzin in candidates:
diff = sum([math.fabs(reference_cell[j] - cells[xyzin][j]) \
for j in range(6)])
diffs.append((diff, xyzin))
diffs.sort()
return diffs[0][1]
def __init__(self):
self._working_directory = os.getcwd()
self._factory = module_factory()
self._hklin = None
self._nha = None
self._symmetry = None
self._reindex_op = None
self._cc = None
self._cc_weak = None
return
def __init__(self):
self._working_directory = os.getcwd()
self._factory = module_factory()
self._hklin = None
self._hklout = None
self._xyzin = None
self._xyzout = None
self._nres = None
self._symmetry = None
self._reindex_op = None
self._mode = LP_MODE_MS
return
def __init__(self):
self._working_directory = os.getcwd()
self._factory = module_factory()
self._image = None
self._matrix = None
self._spacegroup = None
self._cell = None
self._mosaic = None
self._phi_start = None
self._phi_end = None
self._phi_width = None
self._completeness = None
self._resolution = None
return
if len(candidates) == 0:
raise RuntimeError, 'no candidate pdb files matched %s' % os.getcwd()
hklin = 'fast_dp.mtz'
hklout = 'map.mtz'
xyzout = 'refined.pdb'
xyzin = select_right_pdb(hklin, candidates)
if not xyzin:
raise RuntimeError, 'no candidate pdb files matched %s' % os.getcwd()
print 'Selected %s' % xyzin
im = module_factory().interrogate_mtz()
im.set_hklin(hklin)
im.interrogate_mtz()
reindex_op = None
if ersatz_pointgroup(im.get_symmetry()) == 'P222':
# compare unit cells...
ip = module_factory().interrogate_pdb()
ip.set_xyzin(xyzin)
ip.interrogate_pdb()
reindex_op = test_orthorhombic(ip.get_cell(), im.get_cell())
lp = ligand_pipeline()