diff --git a/modules/conop/pymod/export_builder.cc b/modules/conop/pymod/export_builder.cc
index 28608ab6ee36e49f6ad539d56b210be6c5cd9cb2..1897983f90b7c4065316633db738732c0ba4b93f 100644
--- a/modules/conop/pymod/export_builder.cc
+++ b/modules/conop/pymod/export_builder.cc
@@ -36,7 +36,7 @@ void export_Builder() {
.add_property("dialect", &Builder::GetDialect, &Builder::SetDialect)
.add_property("strict_hydrogens", &Builder::GetStrictHydrogenMode,
&Builder::SetStrictHydrogenMode)
- .add_property("feasibility_check", &Builder::GetBondFeasibilityCheck,
+ .add_property("bond_feasibility_check", &Builder::GetBondFeasibilityCheck,
&Builder::SetBondFeasibilityCheck)
.def("GetDialect", &Builder::GetDialect)
.def("SetDialect", &Builder::SetDialect)
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index ab19f54eedafd79ff57b017e4bc94b79011dea86..6e2f319b0ccd824c7f6e6763264802cf4676e790 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -86,7 +86,7 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=None,
fault_tolerant=None, load_multi=False, quack_mode=None,
join_spread_atom_records=None, calpha_only=None,
profile='DEFAULT', remote=False, dialect=None,
- strict_hydrogens=None, seqres=False, bond_feasibility=None):
+ strict_hydrogens=None, seqres=False, bond_feasibility_check=None):
"""
Load PDB file from disk and return one or more entities. Several options
allow to customize the exact behaviour of the PDB import. For more information
@@ -147,7 +147,7 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=None,
prof.quack_mode=_override(prof.quack_mode, quack_mode)
prof.strict_hydrogens=_override(prof.strict_hydrogens, strict_hydrogens)
prof.fault_tolerant=_override(prof.fault_tolerant, fault_tolerant)
- prof.bond_feasibility=_override(prof.bond_feasibility, bond_feasibility)
+ prof.bond_feasibility_check=_override(prof.bond_feasibility_check, bond_feasibility_check)
prof.join_spread_atom_records=_override(prof.join_spread_atom_records,
join_spread_atom_records)
@@ -165,7 +165,7 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=None,
elif prof.dialect=='CHARMM':
builder.dialect=conop.CHARMM_DIALECT
builder.strict_hydrogens=prof.strict_hydrogens
- builder.bond_feasibility=prof.bond_feasibility
+ builder.bond_feasibility_check=prof.bond_feasibility_check
reader=PDBReader(filename, prof)
reader.read_seqres=seqres
try:
diff --git a/modules/io/pymod/export_pdb_io.cc b/modules/io/pymod/export_pdb_io.cc
index 6f7566906d43c81d8b1921168fadbf551c9f7a11..c5abad5d434ddbdf1285c854cf4a427a8d0f34b9 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")=true)))
+ arg("bond_feasibility_check")=true)))
.def_readwrite("dialect", &IOProfile::dialect)
.def_readwrite("fault_tolerant", &IOProfile::fault_tolerant)
.def_readwrite("quack_mode", &IOProfile::quack_mode)
@@ -51,7 +51,7 @@ void export_pdb_io()
.def_readwrite("no_hetatms", &IOProfile::no_hetatms)
.def_readwrite("calpha_only", &IOProfile::calpha_only)
.def_readwrite("join_spread_atom_records", &IOProfile::join_spread_atom_records)
- .def_readwrite("bond_feasibility", &IOProfile::bond_feasibilty)
+ .def_readwrite("bond_feasibility_check", &IOProfile::bond_feasibility_check)
.def("Copy", &IOProfile::Copy)
.def(self_ns::str(self))
;
diff --git a/modules/io/src/mol/io_profile.hh b/modules/io/src/mol/io_profile.hh
index a51572636e43cc1da175929b00d94e5c290b855e..b4802583a838156ef5aac62048c158b50bff65d3 100644
--- a/modules/io/src/mol/io_profile.hh
+++ b/modules/io/src/mol/io_profile.hh
@@ -29,11 +29,11 @@ struct DLLEXPORT IOProfile {
public:
IOProfile(String d, bool sh, bool qm, bool ft, bool js, bool nh, bool co, bool bf):
dialect(d), strict_hydrogens(sh), quack_mode(qm), fault_tolerant(ft),
- join_spread_atom_records(js), no_hetatms(nh), calpha_only(co), bond_feasibilty(bf)
+ join_spread_atom_records(js), no_hetatms(nh), calpha_only(co), bond_feasibility_check(bf)
{ }
IOProfile(): dialect("PDB"), strict_hydrogens(true), quack_mode(false),
fault_tolerant(false), join_spread_atom_records(false), no_hetatms(false),
- calpha_only(false), bond_feasibilty(true)
+ calpha_only(false), bond_feasibility_check(true)
{ }
virtual ~IOProfile() { }
@@ -44,12 +44,12 @@ public:
bool join_spread_atom_records;
bool no_hetatms;
bool calpha_only;
- bool bond_feasibilty;
+ bool bond_feasibility_check;
IOProfile Copy()
{
return IOProfile(dialect, strict_hydrogens, quack_mode, fault_tolerant,
- join_spread_atom_records, no_hetatms, calpha_only, bond_feasibilty);
+ join_spread_atom_records, no_hetatms, calpha_only, bond_feasibility_check);
}
virtual void PostImport(mol::EntityHandle ent) { }
};
@@ -62,8 +62,8 @@ inline std::ostream& operator<<(std::ostream& stream, const IOProfile& p)
<< (p.join_spread_atom_records ? "True" : "False") << ", no_hetatms="
<< (p.no_hetatms ? "True" : "False") << ", calpha_only="
<< (p.calpha_only ? "True" : "False") << ", fault_tolerant="
- << (p.fault_tolerant ? "True" : "False") << ", bond_feasibilty="
- << (p.bond_feasibilty ? "True" : "False") << ")";
+ << (p.fault_tolerant ? "True" : "False") << ", bond_feasibility_check="
+ << (p.bond_feasibility_check ? "True" : "False") << ")";
return stream;
}
diff --git a/modules/io/tests/test_io_pdb.py b/modules/io/tests/test_io_pdb.py
index c8bb3902dbd45b1fb08aea68b81982662d3178a1..6c43dd4214f6ea4c594f9833caa3edcde4137588 100644
--- a/modules/io/tests/test_io_pdb.py
+++ b/modules/io/tests/test_io_pdb.py
@@ -11,7 +11,22 @@ class TestPDB(unittest.TestCase):
ch = e.FindChain("A");
self.assertEquals(ch.GetIntProp("mol_id"), 1)
+class TestPDB(unittest.TestCase):
+ def setUp(self):
+ pass
+
+ def test_compnd_parser(self):
+ profiles=io.IOProfiles()
+ profiles['NO_FEAS_CHECK']=io.IOProfile(bond_feasibility_check=False)
+
+ e=io.LoadPDB('testfiles/pdb/simple_defective.pdb', restrict_chains="A",profile='NO_FEAS_CHECK')
+
+ res=e.FindResidue('A',3)
+
+ self.assertTrue(mol.BondExists(res.FindAtom("CA"),res.FindAtom("CB")))
+
if __name__== '__main__':
unittest.main()
+
\ No newline at end of file