Tidy-up Phenix: remove mmtbx/command_line/validate_waters.py and refa…

…ctor test mmtbx/validation/regression/tst_waters.py

mmtbx/validation/regression/tst_waters.py

@@ -5,12 +5,15 @@
 from libtbx.utils import null_out
 from libtbx import easy_pickle
 from libtbx import group_args
+from iotbx.data_manager import DataManager
+from mmtbx.regression import make_fake_anomalous_data
+import mmtbx.ions.utils
+import iotbx.pdb
+import mmtbx.model
+from mmtbx.validation import waters
 
 def exercise_heavy():
-  from mmtbx.regression import make_fake_anomalous_data
-  from mmtbx.command_line import validate_waters
-  import mmtbx.ions.utils
-  import iotbx.pdb
+
   file_base = "tst_validate_waters_1"
   pdb_file = make_fake_anomalous_data.write_pdb_input_cd_cl(file_base=file_base)
   mtz_file = make_fake_anomalous_data.generate_mtz_file(
@@ -20,14 +23,22 @@ def exercise_heavy():
       group_args(selection="element CD", fp=-0.29, fdp=2.676),
       group_args(selection="element CL", fp=0.256, fdp=0.5),
     ])
+
   pdb_in = iotbx.pdb.input(pdb_file)
-  hierarchy = pdb_in.construct_hierarchy()
-  hierarchy, n = mmtbx.ions.utils.anonymize_ions(hierarchy, log=null_out())
-  hierarchy.write_pdb_file("%s_start.pdb" % file_base,
-    crystal_symmetry=pdb_in.crystal_symmetry())
-  args = ["tst_validate_waters_1_start.pdb", "tst_validate_waters_1.mtz",
-    "skip_twin_detection=True"]
-  results = validate_waters.run(args=args, out=null_out())
+  m1 = mmtbx.model.manager(model_input = pdb_in, log = null_out())
+  hierarchy, n = mmtbx.ions.utils.anonymize_ions(m1.get_hierarchy(),
+                                                 log=null_out())
+  fn_anonymized = file_base + '_start.pdb'
+  hierarchy.write_pdb_file(fn_anonymized,crystal_symmetry=m1.crystal_symmetry())
+  dm = DataManager()
+  m = dm.get_model(fn_anonymized)
+  ma = dm.get_miller_arrays(filename = mtz_file)
+  fmo = dm.get_fmodel(scattering_table="n_gaussian")
+  results = waters.waters(
+    pdb_hierarchy=m.get_hierarchy(),
+    xray_structure=m.get_xray_structure(),
+    fmodel=fmo,
+    collect_all=True)
   out = StringIO()
   results.show(out=out)
   s = easy_pickle.dumps(results)