コード例 #1
0
ファイル: DialsRefiner.py プロジェクト: Anthchirp/xia2
    def Refine(self):
        refine = _Refine()
        params = PhilIndex.params.dials.refine
        refine.set_phil_file(params.phil_file)
        refine.set_working_directory(self.get_working_directory())
        if PhilIndex.params.dials.fast_mode:
            # scan-static refinement in fast mode
            refine.set_scan_varying(False)
        else:
            refine.set_scan_varying(params.scan_varying)
        refine.set_reflections_per_degree(params.reflections_per_degree)
        refine.set_interval_width_degrees(params.interval_width_degrees)
        refine.set_outlier_algorithm(PhilIndex.params.dials.outlier.algorithm)
        if PhilIndex.params.dials.fix_geometry:
            refine.set_detector_fix("all")
            refine.set_beam_fix("all")
        elif PhilIndex.params.dials.fix_distance:
            refine.set_detector_fix("distance")
        refine.set_close_to_spindle_cutoff(
            PhilIndex.params.dials.close_to_spindle_cutoff)
        # For multiple-sweep joint refinement, use the user's preferred restraints or
        # default to restraining using `tie_to_group` with some reasonably tight sigmas.
        if (PhilIndex.params.xia2.settings.multi_sweep_refinement
                and not params.restraints.tie_to_group):
            params.restraints.tie_to_group = (
                restraints_scope.extract().restraints.tie_to_group)
            # If the user hasn't specified otherwise, use default sigmas of 0.01.
            params.restraints.tie_to_group[0].sigmas = 6 * (0.01, )
        # Set any specified restraints for joint refinement of multiple sweeps.
        refine.tie_to_target = params.restraints.tie_to_target
        refine.tie_to_group = params.restraints.tie_to_group

        auto_logfiler(refine, "REFINE")

        return refine
コード例 #2
0
ファイル: DialsIndexer.py プロジェクト: BlenderCN-Org/xia2
 def Refine(self):
     refine = _Refine()
     params = PhilIndex.params.dials
     refine.set_working_directory(self.get_working_directory())
     refine.set_scan_varying(False)
     refine.set_outlier_algorithm(params.outlier.algorithm)
     refine.set_close_to_spindle_cutoff(params.close_to_spindle_cutoff)
     if params.fix_geometry:
         refine.set_detector_fix("all")
         refine.set_beam_fix("all")
     auto_logfiler(refine)
     return refine
コード例 #3
0
ファイル: DialsIndexer.py プロジェクト: xia2/xia2
 def Refine(self):
   refine = _Refine()
   params = PhilIndex.params.dials.refine
   refine.set_working_directory(self.get_working_directory())
   refine.set_scan_varying(False)
   refine.set_outlier_algorithm(PhilIndex.params.dials.outlier.algorithm)
   refine.set_close_to_spindle_cutoff(
     PhilIndex.params.dials.close_to_spindle_cutoff)
   if PhilIndex.params.dials.fix_geometry:
     refine.set_detector_fix('all')
     refine.set_beam_fix('all')
   auto_logfiler(refine)
   return refine
コード例 #4
0
ファイル: DialsRefiner.py プロジェクト: ndevenish/xia2
    def Refine(self):
        refine = _Refine()
        params = PhilIndex.params.dials.refine
        refine.set_phil_file(params.phil_file)
        refine.set_working_directory(self.get_working_directory())
        if PhilIndex.params.dials.fast_mode:
            # scan-static refinement in fast mode
            refine.set_scan_varying(False)
        else:
            refine.set_scan_varying(params.scan_varying)
        refine.set_reflections_per_degree(params.reflections_per_degree)
        refine.set_interval_width_degrees(params.interval_width_degrees)
        refine.set_outlier_algorithm(PhilIndex.params.dials.outlier.algorithm)
        if PhilIndex.params.dials.fix_geometry:
            refine.set_detector_fix('all')
            refine.set_beam_fix('all')
        refine.set_close_to_spindle_cutoff(
            PhilIndex.params.dials.close_to_spindle_cutoff)
        auto_logfiler(refine, 'REFINE')

        return refine
コード例 #5
0
ファイル: DialsRefiner.py プロジェクト: hainm/xia2
  def Refine(self):
    refine = _Refine()
    params = PhilIndex.params.dials.refine
    refine.set_phil_file(params.phil_file)
    refine.set_working_directory(self.get_working_directory())
    if  PhilIndex.params.dials.fast_mode:
      # scan-static refinement in fast mode
      refine.set_scan_varying(False)
    else:
      refine.set_scan_varying(params.scan_varying)
    refine.set_reflections_per_degree(params.reflections_per_degree)
    refine.set_interval_width_degrees(params.interval_width_degrees)
    refine.set_outlier_algorithm(PhilIndex.params.dials.outlier.algorithm)
    if PhilIndex.params.dials.fix_geometry:
      refine.set_detector_fix('all')
      refine.set_beam_fix('all')
    refine.set_close_to_spindle_cutoff(
      PhilIndex.params.dials.close_to_spindle_cutoff)
    auto_logfiler(refine, 'REFINE')

    return refine