Do not produce flawed PDB files (cases where model does not fit into …

…PDB format). Adjust tests.
cctbx · Nov 6, 2023 · 6b0652b · 6b0652b
1 parent 49645c2
commit 6b0652b
Show file tree

Hide file tree

Showing 8 changed files with 21 additions and 30 deletions.
diff --git a/iotbx/pdb/hierarchy.py b/iotbx/pdb/hierarchy.py
@@ -658,6 +658,8 @@ def as_pdb_string(self,
     :param siguij: write SIGUIJ records if applicable
     :returns: Python str
     """
+    if not self.fits_in_pdb_format():
+      return ""
     if (cstringio is None):
       cstringio = StringIO()
       if (return_cstringio is Auto):

diff --git a/iotbx/regression/tst_hierarchy_long_chain_ids_1.py b/iotbx/regression/tst_hierarchy_long_chain_ids_1.py
@@ -261,10 +261,11 @@ def test1():
   # Note here incorrect/trimmed chain id
   # There's no way to correctly output chain ids longer than 2 char in PDB format
   print(o_pdb_str)
-  assert_lines_in_text(o_pdb_str, """\
-ATOM     61  C   SERA-2   2      72.898  71.361  62.393  1.00 67.20           C
-ATOM     62  O   SERA-2   2      73.055  70.333  61.737  1.00 65.10           O
-    """)
+  assert o_pdb_str==""
+#   assert_lines_in_text(o_pdb_str, """\
+# ATOM     61  C   SERA-2   2      72.898  71.361  62.393  1.00 67.20           C
+# ATOM     62  O   SERA-2   2      73.055  70.333  61.737  1.00 65.10           O
+#     """)
 
   o_cif_str = "%s" % h.as_cif_block()
   assert_lines_in_text(o_cif_str, """\

diff --git a/iotbx/regression/tst_hierarchy_long_resname_1.py b/iotbx/regression/tst_hierarchy_long_resname_1.py
@@ -98,14 +98,15 @@ def test1():
   # Note here incorrect/trimmed residue names
   # There's no way to correctly output resnames longer than 3 char in PDB format
   # print(o_pdb_str)
-  assert_lines_in_text(o_pdb_str, """\
-ATOM      8  CE  LYS A 279      -2.923 -13.799  42.993  1.00 52.86           C
-ATOM      9  NZ  LYS A 279      -3.209 -12.856  44.100  1.00 54.19           N
-TER
-HETATM   10 CA    CA A 301     -17.362 -22.385  28.047  1.00 15.20          CA
-HETATM   11  C10 7ZTVU A 302      -7.646  -6.965   5.796  1.00 22.62           C
-HETATM   12  C2  7ZTVU A 302      -8.462  -5.534   9.265  1.00 16.68           C
-    """)
+  assert o_pdb_str == ""
+#   assert_lines_in_text(o_pdb_str, """\
+# ATOM      8  CE  LYS A 279      -2.923 -13.799  42.993  1.00 52.86           C
+# ATOM      9  NZ  LYS A 279      -3.209 -12.856  44.100  1.00 54.19           N
+# TER
+# HETATM   10 CA    CA A 301     -17.362 -22.385  28.047  1.00 15.20          CA
+# HETATM   11  C10 7ZTVU A 302      -7.646  -6.965   5.796  1.00 22.62           C
+# HETATM   12  C2  7ZTVU A 302      -8.462  -5.534   9.265  1.00 16.68           C
+#     """)
 
   o_cif_str = "%s" % h.as_cif_block()
   # print(o_cif_str)

diff --git a/iotbx/regression/tst_hierarchy_long_resname_2.py b/iotbx/regression/tst_hierarchy_long_resname_2.py
@@ -129,11 +129,7 @@ def test1():
       '   HETATM 10 O . longHOH A 401 ? -3.20900 -12.85600 46.10000 1.000 30.11000 O ? B ? . 1']:
     assert_lines_in_text(model_cif, l)
   model_pdb = model.model_as_pdb()
-  # print(model_pdb)
-  for l in [
-      'LINK         NZ  LYS A 279                 O   longHOH A 401 ',
-      'HETATM   10  O   longHOH A 401      -3.209 -12.856  46.100  1.00 30.11           O']:
-    assert_lines_in_text(model_pdb, l)
+  assert not model.can_be_outputted_as_pdb()
 
 if (__name__ == "__main__"):
   t0 = time.time()

diff --git a/iotbx/regression/tst_hierarchy_long_resname_3.py b/iotbx/regression/tst_hierarchy_long_resname_3.py
@@ -212,12 +212,7 @@ def test1():
     'data_comp_7ZTVU',
     ]:
     assert_lines_in_text(model_cif, l)
-  model_pdb = model.model_as_pdb()
-  print(model_pdb)
-  for l in [
-    'HETATM   10  C10 7ZTVU A 302      -7.646  -6.965   5.796  1.00 22.62           C',
-    ]:
-    assert_lines_in_text(model_pdb, l)
+  assert not model.can_be_outputted_as_pdb()
 
 def test2():
   """

diff --git a/iotbx/regression/tst_hierarchy_long_resname_4.py b/iotbx/regression/tst_hierarchy_long_resname_4.py
@@ -209,11 +209,7 @@ def test1():
     assert_lines_in_text(model_cif, l)
   model_pdb = model.model_as_pdb()
   # print(model_pdb)
-  for l in [
-      'ATOM     20  ND2 ASN A   3      -1.271   0.715   7.306  1.00 13.48           N',
-      'ATOM     21  N   longGLY A   4      -1.005   2.228   3.598  1.00 10.29           N',
-    ]:
-    assert_lines_in_text(model_pdb, l)
+  assert not model.can_be_outputted_as_pdb()
 
 def test2():
   """

diff --git a/iotbx/regression/tst_hierarchy_pdb_v3.py b/iotbx/regression/tst_hierarchy_pdb_v3.py
@@ -277,7 +277,7 @@ def test6():
           for atom_group in residue_group.atom_groups():
             for atom in atom_group.atoms():
               atom.set_segid('UNK')
-  assert ph.as_pdb_string().find("UNK")>-1
+  # assert ph.as_pdb_string().find("UNK")>-1
   assert ph.as_mmcif_string().find("UNK") == -1
   assert ph.as_mmcif_string(segid_as_auth_segid=True).find("UNK") > -1
 

diff --git a/mmtbx/model/model.py b/mmtbx/model/model.py
@@ -1555,7 +1555,7 @@ def _figure_out_hierarchy_to_output(self, do_not_shift_back):
     return hierarchy_to_output
 
   def can_be_outputted_as_pdb(self):
-    return True
+    return self.get_hierarchy().fits_in_pdb_format()
 
   def model_as_pdb(self,
       output_cs = True,