Refactoring out usage of hierarchy.input.

mmtbx/disorder/tst.py

@@ -1,7 +1,7 @@
 
 from __future__ import absolute_import, division, print_function
 from mmtbx import disorder
-import iotbx.pdb.hierarchy
+import iotbx.pdb
 from libtbx.test_utils import approx_equal
 from libtbx.utils import null_out
 
@@ -58,8 +58,8 @@ def exercise():
 ATOM      3  CA  LYS A  75      37.173   3.719  10.662  0.01 13.28           C
 ENDMDL
 """
-  pdb_in = iotbx.pdb.hierarchy.input(pdb_string=pdb_str)
-  hierarchy = pdb_in.hierarchy
+  pdb_in = iotbx.pdb.input(source_info=None, lines=pdb_str)
+  hierarchy = pdb_in.construct_hierarchy()
   disorder.set_ensemble_b_factors_to_xyz_displacement(
     pdb_hierarchy=hierarchy,
     method="rmsf",

mmtbx/disorder/tst_analyze_model.py

@@ -2,15 +2,15 @@
 from __future__ import absolute_import, division, print_function
 from mmtbx.disorder import analyze_model
 from mmtbx.validation import molprobity
-import iotbx.pdb.hierarchy
+import iotbx.pdb
 from libtbx.utils import null_out
 import libtbx.load_env
 import mmtbx.model
 from six.moves import cStringIO as StringIO
 
 def analyze_fragment(pdb_str):
-  pdb_in = iotbx.pdb.hierarchy.input(pdb_string=pdb_str)
-  model = mmtbx.model.manager(pdb_in.input)
+  pdb_in = iotbx.pdb.input(source_info=None, lines=pdb_str)
+  model = mmtbx.model.manager(pdb_in)
   validation = molprobity.molprobity(model, outliers_only=False)
   result = analyze_model.process_pdb_hierarchy(
     pdb_hierarchy=model.get_hierarchy(),

mmtbx/disorder/tst_backbone.py

@@ -1,7 +1,7 @@
 
 from __future__ import absolute_import, division, print_function
 from mmtbx.disorder import backbone
-import iotbx.pdb.hierarchy
+import iotbx.pdb
 from six.moves import cStringIO as StringIO
 
 pdb_raw = """
@@ -103,11 +103,11 @@
 """
 
 def exercise():
-  pdb_in = iotbx.pdb.hierarchy.input(pdb_string=pdb_raw)
+  hierarchy = iotbx.pdb.input(source_info=None, lines=pdb_raw).construct_hierarchy()
   with open("tmp.pdb", "w") as f:
-    f.write(pdb_in.hierarchy.as_pdb_string())
+    f.write(hierarchy.as_pdb_string())
   backrubs = backbone.find_backrubs(
-    pdb_hierarchy=pdb_in.hierarchy)
+    pdb_hierarchy=hierarchy)
   assert (len(backrubs) == 1)
   out = StringIO()
   backrubs[0].show(out=out)

mmtbx/regression/tst_command_line_input.py

@@ -128,14 +128,15 @@ def exercise_combine_symmetry():
   """
   from mmtbx.regression import model_1yjp
   import mmtbx.command_line
-  import iotbx.pdb.hierarchy
+  import iotbx.pdb
   from cctbx import sgtbx
   from cctbx import uctbx
   # 1yjp, as usual
-  pdb_in = iotbx.pdb.hierarchy.input(pdb_string=model_1yjp)
-  xrs = pdb_in.input.xray_structure_simple()
+  pdb_in = iotbx.pdb.input(source_info=None, lines=model_1yjp)
+  hierarchy = pdb_in.construct_hierarchy()
+  xrs = pdb_in.xray_structure_simple()
   f = open("tst_combine_symmetry.pdb", "w")
-  f.write(pdb_in.hierarchy.as_pdb_string(crystal_symmetry=xrs))
+  f.write(hierarchy.as_pdb_string(crystal_symmetry=xrs))
   f.close()
   f_calc = abs(xrs.structure_factors(d_min=1.5).f_calc())
   # Make up slightly more exact unit cell, but set SG to P2
@@ -251,7 +252,7 @@ def exercise_load_unmerged():
   flex.set_random_seed(123456)
   random.seed(123456)
   base = "tst_load_unmerged"
-  pdb_in = iotbx.pdb.hierarchy.input(pdb_string=model_1yjp)
+  pdb_in = iotbx.pdb.input(source_info=None, lines=model_1yjp)
   xrs = pdb_in.xray_structure_simple()
   xrs.set_inelastic_form_factors(
     photon=1.54,

mmtbx/regression/tst_pdbtools.py

@@ -6,13 +6,11 @@
 from mmtbx import utils
 from libtbx.test_utils import approx_equal, not_approx_equal, run_command, \
   show_diff
-import iotbx.pdb.hierarchy
+import iotbx.pdb
 from scitbx.array_family import flex
 from cctbx import adptbx
 import mmtbx.model
-import iotbx.pdb
-from six.moves import cStringIO as StringIO
-from six.moves import zip
+from six.moves import cStringIO as StringIO, zip
 from libtbx import easy_run
 
 full_params = mmtbx.model.manager.get_default_pdb_interpretation_params()
@@ -562,13 +560,12 @@ def exercise_truncate_to_polyala():
   print(cmd)
   run_command(command=cmd)
   gly_atom_names = [" N  ", " CA ", " C  ", " O  ", " CB "]
-  pdb_inp = iotbx.pdb.hierarchy.input(
+  pdb_inp = iotbx.pdb.input(
     file_name="exercise_exercise_truncate_to_polyala_modified.pdb")
-  for a in pdb_inp.hierarchy.atoms_with_labels():
+  for a in pdb_inp.construct_hierarchy().atoms_with_labels():
     assert a.name in gly_atom_names
 
 def exercise_set_charge():
-  from iotbx import file_reader
   input_pdb = """
 ATOM      1  CL  CL  X   1       0.000   0.000   0.000  1.00 20.00          CL
 END
@@ -578,8 +575,8 @@ def exercise_set_charge():
   cmd='phenix.pdbtools tmp_cl.pdb charge_selection="element Cl" charge=-1'
   print(cmd)
   run_command(command=cmd, verbose=False)
-  pdb_in = file_reader.any_file("tmp_cl_modified.pdb").file_object
-  hierarchy = pdb_in.hierarchy
+  pdb_in = iotbx.pdb.input("tmp_cl_modified.pdb")
+  hierarchy = pdb_in.construct_hierarchy()
   xrs = pdb_in.xray_structure_simple()
   assert (xrs.scatterers()[0].scattering_type == 'Cl1-')
   assert (hierarchy.atoms()[0].charge == '1-')

mmtbx/regression/tst_real_space_correlation.py

@@ -3,7 +3,7 @@
 from mmtbx import real_space_correlation
 import mmtbx.utils
 from iotbx import file_reader
-import iotbx.pdb.hierarchy
+import iotbx.pdb
 from scitbx.array_family import flex
 import libtbx.load_env
 from libtbx.test_utils import approx_equal
@@ -21,10 +21,10 @@ def exercise_1():
   if (None in [pdb_file, mtz_file]):
     print("phenix_regression not found, skipping test")
     return False
-  pdb_in = file_reader.any_file(pdb_file)
-  hierarchy = pdb_in.file_object.hierarchy
+  pdb_in = iotbx.pdb.input(pdb_file)
+  hierarchy = pdb_in.construct_hierarchy()
   hierarchy.atoms().reset_i_seq()
-  xrs = pdb_in.file_object.xray_structure_simple()
+  xrs = pdb_in.xray_structure_simple()
   mtz_in = file_reader.any_file(mtz_file)
   f_obs = mtz_in.file_server.miller_arrays[0]
   r_free = mtz_in.file_server.miller_arrays[1]
@@ -114,8 +114,9 @@ def exercise_2():
 ATOM     21  OXT TYR B   7       7.316   5.408   8.654  1.00 18.49           O
 END
 """
-  pdb_in = iotbx.pdb.hierarchy.input(pdb_string=pdb_str)
-  xrs = pdb_in.input.xray_structure_simple()
+  pdb_in = iotbx.pdb.input(source_info=None, lines=pdb_str)
+  hierarchy = pdb_in.construct_hierarchy()
+  xrs = pdb_in.xray_structure_simple()
   fc = abs(xrs.structure_factors(d_min=1.5).f_calc())
   fc = fc.set_observation_type_xray_amplitude()
   sigf = flex.double(fc.size(), 0.1) + (fc.data() * 0.03)
@@ -131,13 +132,13 @@ def exercise_2():
   assert (fmodel.twin_law is not None)
   map_stats = real_space_correlation.extract_map_stats_for_single_atoms(
     xray_structure=xrs,
-    pdb_atoms=pdb_in.hierarchy.atoms(),
+    pdb_atoms=hierarchy.atoms(),
     fmodel=fmodel)
-  sel_cache = pdb_in.hierarchy.atom_selection_cache()
+  sel_cache = hierarchy.atom_selection_cache()
   sel = sel_cache.selection("chain B")
   map_stats_2 = real_space_correlation.extract_map_stats_for_single_atoms(
     xray_structure=xrs,
-    pdb_atoms=pdb_in.hierarchy.atoms(),
+    pdb_atoms=hierarchy.atoms(),
     fmodel=fmodel,
     selection=sel)
   map_stats_3 = real_space_correlation.map_statistics_for_atom_selection(

mmtbx/regression/tst_table_one.py

@@ -4,7 +4,7 @@
 
 from mmtbx.regression import model_1yjp
 from mmtbx.command_line import table_one
-import iotbx.pdb.hierarchy
+import iotbx.pdb
 from cctbx import sgtbx
 from scitbx.array_family import flex
 from libtbx.utils import null_out
@@ -15,7 +15,7 @@ def exercise():
   flex.set_random_seed(123456)
   random.seed(123456)
   base = "tst_table_one"
-  pdb_in = iotbx.pdb.hierarchy.input(pdb_string=model_1yjp)
+  pdb_in = iotbx.pdb.input(source_info=None, lines=model_1yjp)
   xrs = pdb_in.xray_structure_simple()
   xrs.set_inelastic_form_factors(
     photon=1.54,
@@ -87,7 +87,7 @@ def exercise_counts():
   pdb_file = libtbx.env.under_dist('mmtbx', 'regression/pdbs/two_chains_ligand_water.pdb')
   base = "tst_table_one_counts"
   mtz_file = base + ".mtz"
-  pdb_in = iotbx.pdb.hierarchy.input(pdb_file)
+  pdb_in = iotbx.pdb.input(pdb_file)
   xrs = pdb_in.xray_structure_simple()
   xrs.set_inelastic_form_factors(photon=1.54, table="sasaki")
   fc = abs(xrs.structure_factors(d_min=4.0).f_calc()).average_bijvoet_mates()