Xtrapol8: create command line tool phenix.development.xtrapol8

mmtbx/command_line/xtrapol8.py

@@ -0,0 +1,8 @@
+# LIBTBX_SET_DISPATCHER_NAME phenix.development.xtrapol8
+from __future__ import absolute_import, division, print_function
+
+from iotbx.cli_parser import run_program
+from mmtbx.programs import xtrapol8
+
+if __name__ == '__main__':
+  run_program(program_class=xtrapol8.Program)

mmtbx/programs/xtrapol8.py

@@ -0,0 +1,53 @@
+from __future__ import absolute_import, division, print_function
+from phenix.program_template import ProgramTemplate
+from libtbx.utils import Sorry
+
+master_phil_str = '''
+include scope libtbx.phil.interface.tracking_params
+n_alpha = 10
+  .type = int
+  .help = number of alpha values to test
+'''
+
+#  =============================================================================
+
+class Program(ProgramTemplate):
+
+  description = """
+Run xtrapol8.
+
+  phenix.xtrapol8 reference_model.pdb reference.mtz triggered.mtz
+"""
+
+  datatypes = ['model', 'phil', 'miller_array', 'restraint']
+
+  master_phil_str = master_phil_str
+
+  # ---------------------------------------------------------------------------
+
+  def validate(self):
+    print('Validate inputs:', file = self.logger)
+    self.data_manager.has_models(
+      raise_sorry = True,
+      expected_n  = 1,
+      exact_count = True)
+    fs  = self.data_manager.has_miller_arrays(
+      raise_sorry = False,
+      expected_n  = 2,
+      exact_count = True)
+    if (len(self.data_manager.get_miller_array_names()) != 2):
+      raise Sorry('Exactly 2 reflection files are expected.')
+
+    print('  ...all good.', file = self.logger)
+
+  # ---------------------------------------------------------------------------
+
+  def run(self):
+
+    print('Using model file:', self.data_manager.get_default_model_name(),
+      file=self.logger)
+    print('Using reflection file(s):', self.data_manager.get_miller_array_names(),
+      file=self.logger)
+
+    hkls = self.data_manager.get_miller_array_names()
+    model = self.data_manager.get_model()