Set feasibility check to off by default

modules/conop/src/builder.hh

@@ -54,7 +54,7 @@ typedef enum {
 class DLLEXPORT_OST_CONOP Builder {
 public:
   
-  Builder(): dialect_(PDB_DIALECT), strict_(false), bond_feasibility_check_(true) { }
+  Builder(): dialect_(PDB_DIALECT), strict_(false), bond_feasibility_check_(false) { }
   virtual ~Builder();
   
   ///  \brief add any missing atoms to the residue based on its key,

modules/io/doc/profile.rst

@@ -45,7 +45,7 @@ STRICT
 
     IOProfile(dialect='PDB', strict_hydrogens=False, quack_mode=False,
               fault_tolerant=False, join_spread_atom_records=False,
-              no_hetatms=False, bond_feasibility_check=True)
+              no_hetatms=False, bond_feasibility_check=False)
 
 SLOPPY:
 
@@ -55,7 +55,7 @@ SLOPPY:
 
     IOProfile(dialect='PDB', strict_hydrogens=False, quack_mode=True,
               fault_tolerant=True, join_spread_atom_records=False,
-              no_hetatms=False, bond_feasibility_check=True)
+              no_hetatms=False, bond_feasibility_check=False)
 
 CHARMM:
 
@@ -66,7 +66,7 @@ CHARMM:
 
     IOProfile(dialect='CHARMM', strict_hydrogens=False, quack_mode=True,
               fault_tolerant=True, join_spread_atom_records=True,
-              no_hetatms=False, bond_feasibility_check=True)
+              no_hetatms=False, bond_feasibility_check=False)
 
 
 The IOProfile Class

modules/io/pymod/export_pdb_io.cc

@@ -43,7 +43,7 @@ void export_pdb_io()
                                                           arg("join_spread_atom_records")=false,
                                                           arg("no_hetatms")=false,
                                                           arg("calpha_only")=false,
-						          arg("bond_feasibility_check")=true)))
+						          arg("bond_feasibility_check")=false)))
     .def_readwrite("dialect", &IOProfile::dialect)
     .def_readwrite("fault_tolerant", &IOProfile::fault_tolerant)
     .def_readwrite("quack_mode", &IOProfile::quack_mode)

modules/io/src/mol/io_profile.hh

@@ -33,7 +33,7 @@ public:
   { }
   IOProfile(): dialect("PDB"), strict_hydrogens(true), quack_mode(false),
     fault_tolerant(false), join_spread_atom_records(false), no_hetatms(false),
-    calpha_only(false), bond_feasibility_check(true)
+    calpha_only(false), bond_feasibility_check(false)
   { }
   virtual ~IOProfile() { }
 

modules/io/tests/test_io_pdb.py

@@ -17,13 +17,13 @@ class TestPDB(unittest.TestCase):
 
   def test_compnd_parser(self):
     profiles=io.IOProfiles()
-    profiles['NO_FEAS_CHECK']=io.IOProfile(bond_feasibility_check=False)
+    profiles['FEAS_CHECK']=io.IOProfile(bond_feasibility_check=True)
         
-    e=io.LoadPDB('testfiles/pdb/simple_defective.pdb', restrict_chains="A",profile='NO_FEAS_CHECK')
+    e=io.LoadPDB('testfiles/pdb/simple_defective.pdb', restrict_chains="A",profile='FEAS_CHECK')
     
     res=e.FindResidue('A',3)
         
-    self.assertTrue(mol.BondExists(res.FindAtom("CA"),res.FindAtom("CB")))
+    self.assertFalse(mol.BondExists(res.FindAtom("CA"),res.FindAtom("CB")))
     
 if __name__== '__main__':
   from ost import testutils