From 19e4a4f5dec8d373cca014377f1f1ad2b1581386 Mon Sep 17 00:00:00 2001
From: Valerio Mariani <valerio.mariani@unibas.ch>
Date: Tue, 27 Nov 2012 09:42:10 +0100
Subject: [PATCH] Set feasibility check to off by default
---
modules/conop/src/builder.hh | 2 +-
modules/io/doc/profile.rst | 6 +++---
modules/io/pymod/export_pdb_io.cc | 2 +-
modules/io/src/mol/io_profile.hh | 2 +-
modules/io/tests/test_io_pdb.py | 6 +++---
5 files changed, 9 insertions(+), 9 deletions(-)
diff --git a/modules/conop/src/builder.hh b/modules/conop/src/builder.hh
index 4b915681a..5cf1f6302 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 a0a43565e..9349b7c1c 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 c5abad5d4..7d97682df 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 b4802583a..ee880e31b 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 348fde1d9..76537e9f7 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
--
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