Refactor out hierarchy.input usage.

mmtbx/refinement/ensemble_refinement/ensemble_probability.py

@@ -3,7 +3,6 @@
 from iotbx.option_parser import iotbx_option_parser
 from mmtbx import utils
 from iotbx import file_reader
-from iotbx.pdb import hierarchy
 import iotbx.phil
 import libtbx.phil
 from libtbx.utils import Sorry
@@ -350,10 +349,10 @@ def run(self, args, command_name, out=sys.stdout):
     # process PDB
     pdb_file.assert_file_type("pdb")
     #
-    pdb_in = hierarchy.input(file_name=pdb_file.file_name)
+    pdb_in = pdb.input(file_name=pdb_file.file_name)
     ens_pdb_hierarchy = pdb_in.construct_hierarchy()
     ens_pdb_hierarchy.atoms().reset_i_seq()
-    ens_pdb_xrs_s = pdb_in.input.xray_structures_simple()
+    ens_pdb_xrs_s = pdb_in.xray_structures_simple()
     number_structures = len(ens_pdb_xrs_s)
     print('Number of structure in ensemble : ', number_structures, file=self.log)
 

mmtbx/refinement/real_space/tst_flipbase.py

@@ -148,7 +148,7 @@ def exercise():
     crystal_symmetry=xrs_good.crystal_symmetry())
 
 def exercise2():
-  pdb_in = iotbx.pdb.hierarchy.input(pdb_string="""\
+  pdb_in = iotbx.pdb.input(source_info=None, lines="""\
 ATOM   3988  P    DA G  10       2.095 -23.407  14.671  1.00 24.76           P
 ATOM   3989  OP1  DA G  10       2.702 -22.768  13.479  1.00 24.54           O
 ATOM   3990  OP2  DA G  10       1.098 -22.688  15.497  1.00 26.02           O
@@ -172,7 +172,7 @@ def exercise2():
 ATOM   4008  C4   DA G  10       7.629 -27.865  15.998  1.00 13.67           C
 """)
   #open("tmp1.pdb", "w").write(pdb_in.hierarchy.as_pdb_string())
-  base = pdb_in.hierarchy.only_atom_group()
+  base = pdb_in.construct_hierarchy().only_atom_group()
   xyz = base.atoms().extract_xyz().deep_copy()
   flipbase.flip_base(base, angle=180)
   xyz_new = base.atoms().extract_xyz()

mmtbx/refinement/tst_select_best_starting_model.py

@@ -1,17 +1,17 @@
-
 from __future__ import absolute_import, division, print_function
+
 from libtbx.test_utils import Exception_expected
 from libtbx.utils import null_out, Sorry
 from libtbx import easy_run
+from scitbx.array_family import flex
+from cctbx import uctbx, sgtbx
+import iotbx.pdb
+from iotbx import file_reader
+from mmtbx.refinement import select_best_starting_model
+import random
 from six.moves import range
 
 def exercise_main():
-  from mmtbx.refinement import select_best_starting_model
-  from iotbx import file_reader
-  from cctbx import uctbx
-  from cctbx import sgtbx
-  from scitbx.array_family import flex
-  import random
   unit_cell = (24.937, 8.866, 25.477, 90.00, 107.08, 90.00)
   space_group = "P21"
   pdb_base = """\
@@ -194,9 +194,6 @@ def random_double(size, factor=1):
   assert (result.best_model_name == "tst_start_model_1.pdb"), result.best_model_name
 
 def exercise_misc():
-  from mmtbx.refinement import select_best_starting_model
-  from iotbx import file_reader
-  import iotbx.pdb.hierarchy
   pdb_str = """\
 REMARK this is a remark record!
 CRYST1   21.937    4.866   23.477  90.00 107.08  90.00 P 1 21 1
@@ -335,9 +332,9 @@ def exercise_misc():
   pdb_file = "tst_start_model_misc.pdb"
   with open(pdb_file, "w") as f:
     f.write(pdb_str)
-  pdb_in = iotbx.pdb.hierarchy.input(pdb_file)
-  pdb_hierarchy = pdb_in.hierarchy
-  xray_structure = pdb_in.input.xray_structure_simple()
+  pdb_in = iotbx.pdb.input(file_name=pdb_file)
+  pdb_hierarchy = pdb_in.construct_hierarchy()
+  xray_structure = pdb_in.xray_structure_simple()
   hd_sel = xray_structure.hd_selection()
   assert hd_sel.count(True) == 55
   xray_structure.convert_to_anisotropic(selection=~hd_sel)
@@ -405,8 +402,8 @@ def exercise_misc():
     preserve_remarks=True,
     output_file="tst_start_model_misc_new.pdb",
     log=null_out())
-  pdb_new = iotbx.pdb.hierarchy.input(file_name="tst_start_model_misc_new.pdb")
-  assert len(pdb_new.input.remark_section()) == 1
+  pdb_new = iotbx.pdb.input(file_name="tst_start_model_misc_new.pdb")
+  assert len(pdb_new.remark_section()) == 1
   # reset HETATM
   hierarchy_new, xrs_new = select_best_starting_model.strip_model(
     file_name=pdb_file,

mmtbx/scaling/tst_xtriage_twin_analyses.py

@@ -4,7 +4,7 @@
 
 from __future__ import absolute_import, division, print_function
 from mmtbx.scaling import twin_analyses
-import iotbx.pdb.hierarchy
+import iotbx.pdb
 from scitbx.array_family import flex
 from libtbx.test_utils import approx_equal, show_diff
 from libtbx.utils import null_out
@@ -61,8 +61,8 @@ def exercise_twin_detection(verbose=False):
 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)
+  xrs = pdb_in.xray_structure_simple()
   fc = abs(xrs.structure_factors(d_min=2.5).f_calc())
   fc = fc.set_observation_type_xray_amplitude()
   sigf = flex.double(fc.size(), 0.1) + (fc.data() * 0.03)

mmtbx/secondary_structure/tst_insertion_codes.py

@@ -1,13 +1,13 @@
 
 from __future__ import absolute_import, division, print_function
 from mmtbx.secondary_structure import sec_str_master_phil_str, manager
-import iotbx.pdb.hierarchy
+import iotbx.pdb
 import iotbx.pdb.secondary_structure as ioss
 from libtbx.utils import null_out
 
 
 def exercise_helix_bonding_pattern_with_insertions():
-  alpha_h1_ends = iotbx.pdb.hierarchy.input(pdb_string="""\
+  alpha_h1_ends = iotbx.pdb.input(source_info=None, lines="""\
 ATOM      1  N   ALA     1       1.643  -2.366  -1.408  1.00  0.00           N
 ATOM      2  CA  ALA     1       1.280  -3.608  -2.069  1.00  0.00           C
 ATOM      3  C   ALA     1      -0.114  -3.466  -2.684  1.00  0.00           C
@@ -59,9 +59,9 @@ def exercise_helix_bonding_pattern_with_insertions():
 ATOM     49  O   ALA     9A     -5.880  -1.605 -16.177  1.00  0.00           O
 ATOM     50  CB  ALA     9A     -5.358   0.040 -13.274  1.00  0.00           C
 TER
-""")
+""").construct_hierarchy()
 
-  alpha_h1_ac = iotbx.pdb.hierarchy.input(pdb_string="""\
+  alpha_h1_ac = iotbx.pdb.input(source_info=None, lines="""\
 ATOM      1  N  AALA     1       1.643  -2.366  -1.408  0.50  0.00           N
 ATOM      2  CA AALA     1       1.280  -3.608  -2.069  0.50  0.00           C
 ATOM      3  C  AALA     1      -0.114  -3.466  -2.684  0.50  0.00           C
@@ -128,7 +128,7 @@ def exercise_helix_bonding_pattern_with_insertions():
 ATOM     65  O  BALA     9A     -5.780  -1.605 -16.177  0.50  0.00           O
 ATOM     66  CB BALA     9A     -5.258   0.040 -13.274  0.50  0.00           C
 END
-""")
+""").construct_hierarchy()
 
   alpha_annot_1_1 = """\
 HELIX    1   1 ALA      1  ALA      9A 1                                  10
@@ -150,7 +150,7 @@ def exercise_helix_bonding_pattern_with_insertions():
   log = null_out()
   n_hbonds = []
   n_hangles = []
-  for pdb_inp, recs in [
+  for pdb_h, recs in [
                         (alpha_h1_ends, alpha_annot_1_1), #6
                         (alpha_h1_ends, alpha_annot_1_2), #4
                         (alpha_h1_ends, alpha_annot_1_3), #5
@@ -166,7 +166,7 @@ def exercise_helix_bonding_pattern_with_insertions():
     custom_pars = defpars.fetch(iotbx.phil.parse(ann))
     custom_pars_ex = custom_pars.extract()
     ss_manager = manager(
-                pdb_inp.hierarchy,
+                pdb_h,
                 sec_str_from_pdb_file=None,
                 params=custom_pars_ex.secondary_structure,
                 verbose=-1)
@@ -180,7 +180,7 @@ def exercise_helix_bonding_pattern_with_insertions():
   assert n_hangles == [18, 12, 15, 15, 28, 16, 22, 22]
 
 def exercise_sheets_bonding_pattern_with_insertions():
-  pdb_apar_input = iotbx.pdb.hierarchy.input(pdb_string = """\
+  pdb_apar_h = iotbx.pdb.input(source_info=None, lines = """\
 SCRYST1   46.460   46.460  193.210  90.00  90.00 120.00 P 31 2 1
 SCALE1      0.021524  0.012427  0.000000        0.00000
 SCALE2      0.000000  0.024854  0.000000        0.00000
@@ -268,9 +268,9 @@ def exercise_sheets_bonding_pattern_with_insertions():
 ATOM    237  O   SER A  35A     24.929 -22.095  -0.497  1.00  6.22           O
 ATOM    238  CB  SER A  35A     23.881 -21.071  -3.639  1.00  5.69           C
 ATOM    239  OG  SER A  35A     25.213 -20.561  -3.633  1.00  7.12           O
-""")
+""").construct_hierarchy()
 
-  pdb_par_input = iotbx.pdb.hierarchy.input(pdb_string = """\
+  pdb_par_h = iotbx.pdb.input(source_info=None, lines = """\
 CRYST1   46.460   46.460  193.210  90.00  90.00 120.00 P 31 2 1
 SCALE1      0.021524  0.012427  0.000000        0.00000
 SCALE2      0.000000  0.024854  0.000000        0.00000
@@ -346,9 +346,9 @@ def exercise_sheets_bonding_pattern_with_insertions():
 ATOM    223  CB  ALA A  45A      6.607 -27.026  -9.678  1.00  4.52           C
 TER
 END
-""")
+""").construct_hierarchy()
 
-  pdb_par_ac_input = iotbx.pdb.hierarchy.input(pdb_string = """\
+  pdb_par_ac_h = iotbx.pdb.input(source_info=None, lines = """\
 CRYST1   46.460   46.460  193.210  90.00  90.00 120.00 P 31 2 1
 SCALE1      0.021524  0.012427  0.000000        0.00000
 SCALE2      0.000000  0.024854  0.000000        0.00000
@@ -434,7 +434,7 @@ def exercise_sheets_bonding_pattern_with_insertions():
 ATOM     79  CB  ALA A  46       6.607 -27.026  -9.678  1.00  4.52           C
 TER      80      ALA A  46
 END
-""")
+""").construct_hierarchy()
 
   s_apar_records1 = """\
 SHEET    1   A 2 TYR A   2  VAL A   7  0
@@ -466,22 +466,22 @@ def exercise_sheets_bonding_pattern_with_insertions():
   # defpars = sec_str_master_phil
   n_hbonds = []
   n_hangles = []
-  for pdb_inp, recs in [
-                        (pdb_apar_input, s_apar_records1), # 6
-                        (pdb_apar_input, s_apar_records2), # 6
-                        (pdb_apar_input, s_apar_records3), # 4
-                        (pdb_par_input,  s_par_records1), # 6
-                        (pdb_par_input,  s_par_records2), # 6
-                        (pdb_par_input,  s_par_records3), # 5
-                        (pdb_par_ac_input,  s_par_records1), # 8 hbonds
+  for pdb_h, recs in [
+                        (pdb_apar_h, s_apar_records1), # 6
+                        (pdb_apar_h, s_apar_records2), # 6
+                        (pdb_apar_h, s_apar_records3), # 4
+                        (pdb_par_h,  s_par_records1), # 6
+                        (pdb_par_h,  s_par_records2), # 6
+                        (pdb_par_h,  s_par_records3), # 5
+                        (pdb_par_ac_h,  s_par_records1), # 8 hbonds
                         ]:
     ioss_annotation = ioss.annotation.from_records(records = recs.split('\n'))
     ann = ioss_annotation.as_restraint_groups(prefix_scope="secondary_structure")
     defpars = iotbx.phil.parse(sec_str_master_phil_str)
     custom_pars = defpars.fetch(iotbx.phil.parse(ann))
     custom_pars_ex = custom_pars.extract()
     ss_manager = manager(
-                pdb_inp.hierarchy,
+                pdb_h,
                 sec_str_from_pdb_file=None,
                 params=custom_pars_ex.secondary_structure,
                 verbose=-1)

sphinx/iotbx/iotbx.pdb.rst

@@ -9,11 +9,6 @@ API documentation
 Input methods and objects
 -------------------------
 
-.. autoclass:: iotbx.pdb.hierarchy.input
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 .. autofunction:: iotbx.pdb.input
 
 .. autoclass:: iotbx.pdb.ext.input