Switch random_bool to random_selection in hierarchy remove_atoms() to…

… have consistent number of atoms removed every time. Fix tests.

iotbx/pdb/hierarchy.py

@@ -2056,7 +2056,8 @@ def rename_chain_id(self, old_id, new_id):
 
   def remove_atoms(self, fraction):
     assert fraction>0 and fraction<1.
-    sel_keep = flex.random_bool(self.atoms_size(), 1-fraction)
+    n_atoms_to_keep = int(self.atoms_size() * (1-fraction))
+    sel_keep = flex.random_selection(self.atoms_size(), n_atoms_to_keep)
     return self.select(sel_keep)
 
   def set_atomic_charge(self, iselection, charge):

iotbx/pdb/tst_hierarchy.py

@@ -6996,8 +6996,6 @@ def exercise_set_atomic_charge():
   assert (ph.atoms()[0].charge == '1-')
 
 def exercise_remove_atoms():
-  random.seed(1)
-  flex.set_random_seed(1)
   pdb_str = """
 ATOM      1  N  AMET B  37       7.525   5.296   6.399  1.00 10.00           N
 ATOM      2  CA AMET B  37       6.533   6.338   6.634  1.00 10.00           C
@@ -7052,11 +7050,9 @@ def exercise_remove_atoms():
   """
   pi = pdb.input(source_info=None, lines=pdb_str)
   ph_in = pi.construct_hierarchy()
-  s1 = ph_in.atoms_size()
+  assert ph_in.atoms_size() == 48
   ph = ph_in.remove_atoms(fraction=0.1)
-  s2 = ph.atoms_size()
-  f = s2*100./s1
-  assert f>90 and f<100
+  assert ph.atoms_size() == 43
 
 def exercise_set_atomic_charge():
   pdb_str = """

mmtbx/regression/tst_pdbtools.py

@@ -718,9 +718,6 @@ def exercise_neutralize_scatterers():
     assert line1 == line2
 
 def exercise_remove_atoms():
-  import random
-  random.seed(1)
-  flex.set_random_seed(1)
   pdb_str = """
 ATOM      1  N  AMET B  37       7.525   5.296   6.399  1.00 10.00           N
 ATOM      2  CA AMET B  37       6.533   6.338   6.634  1.00 10.00           C
@@ -773,24 +770,18 @@ def exercise_remove_atoms():
 TER
 END
   """
-  pi = iotbx.pdb.input(source_info=None, lines=pdb_str)
-  ph_in = pi.construct_hierarchy()
-  s1 = ph_in.atoms_size()
-  pi.write_pdb_file(file_name="exercise_remove_atoms.pdb")
+  # Initial size - 48 atoms
+  with open("exercise_remove_atoms.pdb", 'w') as f:
+    f.write(pdb_str)
   cmd = " ".join([
     "phenix.pdbtools",
     "exercise_remove_atoms.pdb",
     "remove_fraction=0.1"])
   print(cmd)
   run_command(command=cmd, verbose=False)
-  pi = iotbx.pdb.input(file_name="exercise_remove_atoms_modified.pdb")
-  ph_in = pi.construct_hierarchy()
-  s2 = ph_in.atoms_size()
-  f = s2*100./s1
-  #
-  # UNSTABLE 3x
-  #
-  assert f>77 and f<100, f # was getting 79.16, 70.8333 on anaconda t96,
+  inp = iotbx.pdb.input(file_name="exercise_remove_atoms_modified.pdb")
+  # removed 5 atoms (~10%).
+  assert inp.atoms().size() == 43, inp.atoms().size()
 
 def exercise_change_of_basis():
   with open("tmp_pdbtools_cb_op.pdb", "w") as f: