make defaults the same as old

cctbx · Sep 23, 2024 · d82c251 · d82c251
1 parent 12911b3
commit d82c251
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Showing 2 changed files with 8 additions and 1 deletion.
diff --git a/cctbx/geometry_restraints/tst_nonbonded_overlaps.py b/cctbx/geometry_restraints/tst_nonbonded_overlaps.py
@@ -639,6 +639,7 @@ def test_atom_selection(self):
     outstring = '{0} , expected {1:.2f}, actual {2:.2f}'
     params = mmtbx.model.manager.get_default_pdb_interpretation_params()
     params.pdb_interpretation.allow_polymer_cross_special_position=True
+    params.pdb_interpretation.automatic_linking.link_residues=False
     pdb_inp = iotbx.pdb.input(lines=raw_records3.split("\n"), source_info=None)
     model = mmtbx.model.manager(
       model_input = pdb_inp,
@@ -677,11 +678,14 @@ def test_labels_and_addition_scatterers(self):
     Test overlaps when adding and moving scatterers
     Test water scatterers with and without labels
     '''
+    params = mmtbx.model.manager.get_default_pdb_interpretation_params()
+    params.pdb_interpretation.allow_polymer_cross_special_position=True
+    params.pdb_interpretation.automatic_linking.link_residues=False
     pdb_inp = iotbx.pdb.input(lines=raw_records3.split('\n'), source_info=None)
     model = mmtbx.model.manager(
       model_input = pdb_inp,
       log         = null_out())
-    model.process(make_restraints=True)
+    model.process(pdb_interpretation_params=params, make_restraints=True)
     outstring = '{0} , expected {1:.2f}, actual {2:.2f}'
     geometry = model.get_restraints_manager().geometry
     xrs = model.get_xray_structure()
@@ -711,6 +715,7 @@ def test_labels_and_addition_scatterers(self):
     pdb_str = model.model_as_pdb()
     params = mmtbx.model.manager.get_default_pdb_interpretation_params()
     params.pdb_interpretation.allow_polymer_cross_special_position=True
+    params.pdb_interpretation.automatic_linking.link_residues=False
     pdb_inp = iotbx.pdb.input(lines=pdb_str.split('\n'), source_info=None)
     model = mmtbx.model.manager(
       model_input = pdb_inp,
@@ -1078,6 +1083,7 @@ def process_raw_records(
   params = mmtbx.model.manager.get_default_pdb_interpretation_params()
   params.pdb_interpretation.allow_polymer_cross_special_position=True
   params.pdb_interpretation.clash_guard.nonbonded_distance_threshold = None
+  params.pdb_interpretation.automatic_linking.link_residues=False
   pdb_inp = iotbx.pdb.input(lines=records, source_info=None)
   model = mmtbx.model.manager(
     model_input = pdb_inp,

diff --git a/cctbx/geometry_restraints/tst_process_nonbonded_proxies.py b/cctbx/geometry_restraints/tst_process_nonbonded_proxies.py
@@ -44,6 +44,7 @@ def get_clashes_result(raw_records, sel=None):
   params = mmtbx.model.manager.get_default_pdb_interpretation_params()
   params.pdb_interpretation.allow_polymer_cross_special_position=True
   params.pdb_interpretation.clash_guard.nonbonded_distance_threshold = None
+  params.pdb_interpretation.automatic_linking.link_residues=False
   pdb_inp = iotbx.pdb.input(lines=raw_records.split("\n"), source_info=None)
   model = mmtbx.model.manager(
     model_input = pdb_inp,