diff --git a/modules/conop/src/builder.hh b/modules/conop/src/builder.hh index 4b915681a51d2d47c6d36fe449424f5b189de772..5cf1f63026a95df93569be1698455451997bbd92 100644 --- a/modules/conop/src/builder.hh +++ b/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, diff --git a/modules/io/doc/profile.rst b/modules/io/doc/profile.rst index a0a43565e6631ca9c2adc28449930a9ffbe3656c..9349b7c1c12e9e1eb695797273fbc726a3945e07 100644 --- a/modules/io/doc/profile.rst +++ b/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 diff --git a/modules/io/pymod/export_pdb_io.cc b/modules/io/pymod/export_pdb_io.cc index c5abad5d434ddbdf1285c854cf4a427a8d0f34b9..7d97682df3f006fc41959edc3f9c4e623041031e 100644 --- a/modules/io/pymod/export_pdb_io.cc +++ b/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) diff --git a/modules/io/src/mol/io_profile.hh b/modules/io/src/mol/io_profile.hh index b4802583a838156ef5aac62048c158b50bff65d3..ee880e31bb781681fbd244283f709a70a2d74ad9 100644 --- a/modules/io/src/mol/io_profile.hh +++ b/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() { } diff --git a/modules/io/tests/test_io_pdb.py b/modules/io/tests/test_io_pdb.py index 348fde1d929669405e612cb92d3a274ceb5636f1..76537e9f7990629ec3f48b2972b375292c1a52f3 100644 --- a/modules/io/tests/test_io_pdb.py +++ b/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