Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
O
openstructure
Manage
Activity
Members
Code
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Deploy
Releases
Container registry
Model registry
Analyze
Contributor analytics
Repository analytics
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
Community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
schwede
openstructure
Commits
79903792
Commit
79903792
authored
2 years ago
by
Studer Gabriel
Browse files
Options
Downloads
Patches
Plain Diff
delete dead code
parent
35a1f93b
No related branches found
No related tags found
No related merge requests found
Changes
1
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
modules/conop/tests/test_heuristic_builder.cc
+0
-224
0 additions, 224 deletions
modules/conop/tests/test_heuristic_builder.cc
with
0 additions
and
224 deletions
modules/conop/tests/test_heuristic_builder.cc
deleted
100644 → 0
+
0
−
224
View file @
35a1f93b
// ------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
// Copyright (C) 2008-2020 by the OpenStructure authors
// This library is free software; you can redistribute it and/or modify it under
// the terms of the GNU Lesser General Public License as published by the Free
// Software Foundation; either version 3.0 of the License, or (at your option)
// any later version.
// This library is distributed in the hope that it will be useful, but WITHOUT
// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
// details.
// You should have received a copy of the GNU Lesser General Public License
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
// ------------------------------------------------------------------------------
#include
<ost/mol/mol.hh>
#include
<ost/conop/heuristic_builder.hh>
#define BOOST_TEST_DYN_LINK
#include
<boost/test/unit_test.hpp>
#include
<ost/log.hh>
using
boost
::
unit_test_framework
::
test_suite
;
using
namespace
ost
;
using
namespace
ost
::
conop
;
using
namespace
ost
::
mol
;
namespace
{
}
// anon ns
ResidueHandle
make_arg
(
ChainHandle
chain
)
{
XCSEditor
e
=
chain
.
GetEntity
().
EditXCS
();
ResidueHandle
res
=
e
.
AppendResidue
(
chain
,
"ARG"
);
e
.
InsertAtom
(
res
,
"N"
,
geom
::
Vec3
(
20.202
,
33.112
,
58.011
));
e
.
InsertAtom
(
res
,
"CA"
,
geom
::
Vec3
(
19.396
,
31.903
,
58.033
));
e
.
InsertAtom
(
res
,
"C"
,
geom
::
Vec3
(
18.608
,
31.739
,
59.328
));
e
.
InsertAtom
(
res
,
"O"
,
geom
::
Vec3
(
17.651
,
30.965
,
59.381
));
e
.
InsertAtom
(
res
,
"CB"
,
geom
::
Vec3
(
20.284
,
30.681
,
57.801
));
e
.
InsertAtom
(
res
,
"CG"
,
geom
::
Vec3
(
20.665
,
30.488
,
56.342
));
e
.
InsertAtom
(
res
,
"CD"
,
geom
::
Vec3
(
21.557
,
29.281
,
56.154
));
e
.
InsertAtom
(
res
,
"NE"
,
geom
::
Vec3
(
22.931
,
29.557
,
56.551
));
e
.
InsertAtom
(
res
,
"CZ"
,
geom
::
Vec3
(
23.901
,
28.653
,
56.528
));
e
.
InsertAtom
(
res
,
"NH1"
,
geom
::
Vec3
(
23.640
,
27.417
,
56.130
));
e
.
InsertAtom
(
res
,
"NH2"
,
geom
::
Vec3
(
25.132
,
28.980
,
56.893
));
return
res
;
}
ResidueHandle
make_leu
(
ChainHandle
chain
)
{
XCSEditor
e
=
chain
.
GetEntity
().
EditXCS
();
ResidueHandle
res
=
e
.
AppendResidue
(
chain
,
"LEU"
);
e
.
InsertAtom
(
res
,
"N"
,
geom
::
Vec3
(
19.003
,
32.473
,
60.366
));
e
.
InsertAtom
(
res
,
"CA"
,
geom
::
Vec3
(
18.330
,
32.402
,
61.664
));
e
.
InsertAtom
(
res
,
"C"
,
geom
::
Vec3
(
17.884
,
33.787
,
62.117
));
e
.
InsertAtom
(
res
,
"O"
,
geom
::
Vec3
(
17.853
,
34.091
,
63.308
));
e
.
InsertAtom
(
res
,
"CB"
,
geom
::
Vec3
(
19.269
,
31.793
,
62.710
));
e
.
InsertAtom
(
res
,
"CG"
,
geom
::
Vec3
(
19.695
,
30.340
,
62.501
));
e
.
InsertAtom
(
res
,
"CD1"
,
geom
::
Vec3
(
20.585
,
29.897
,
63.648
));
e
.
InsertAtom
(
res
,
"CD2"
,
geom
::
Vec3
(
18.461
,
29.459
,
62.420
));
return
res
;
}
ResidueHandle
make_defective_leu
(
ChainHandle
chain
)
{
XCSEditor
e
=
chain
.
GetEntity
().
EditXCS
();
ResidueHandle
res
=
e
.
AppendResidue
(
chain
,
"LEU"
);
e
.
InsertAtom
(
res
,
"N"
,
geom
::
Vec3
(
19.003
,
32.473
,
60.366
));
e
.
InsertAtom
(
res
,
"CA"
,
geom
::
Vec3
(
18.330
,
32.402
,
61.664
));
e
.
InsertAtom
(
res
,
"C"
,
geom
::
Vec3
(
17.884
,
33.787
,
62.117
));
e
.
InsertAtom
(
res
,
"O"
,
geom
::
Vec3
(
17.853
,
34.091
,
63.308
));
e
.
InsertAtom
(
res
,
"CB"
,
geom
::
Vec3
(
19.269
,
31.793
,
102.710
));
e
.
InsertAtom
(
res
,
"CG"
,
geom
::
Vec3
(
19.695
,
30.340
,
62.501
));
e
.
InsertAtom
(
res
,
"CD1"
,
geom
::
Vec3
(
20.585
,
29.897
,
63.648
));
e
.
InsertAtom
(
res
,
"CD2"
,
geom
::
Vec3
(
18.461
,
29.459
,
62.420
));
return
res
;
}
void
verify_connectivity_x
(
const
ResidueHandle
&
res
)
{
BOOST_CHECK
(
BondExists
(
res
.
FindAtom
(
"XN"
),
res
.
FindAtom
(
"XCA"
)));
BOOST_CHECK
(
BondExists
(
res
.
FindAtom
(
"XCA"
),
res
.
FindAtom
(
"XC"
)));
BOOST_CHECK
(
BondExists
(
res
.
FindAtom
(
"XC"
),
res
.
FindAtom
(
"XO"
)));
BOOST_CHECK
(
BondExists
(
res
.
FindAtom
(
"XCA"
),
res
.
FindAtom
(
"XCB"
)));
BOOST_CHECK
(
BondExists
(
res
.
FindAtom
(
"XCB"
),
res
.
FindAtom
(
"XCG"
)));
if
(
res
.
GetKey
()
==
"ARG"
)
{
BOOST_CHECK
(
BondExists
(
res
.
FindAtom
(
"XCB"
),
res
.
FindAtom
(
"XCG"
)));
BOOST_CHECK
(
BondExists
(
res
.
FindAtom
(
"XCG"
),
res
.
FindAtom
(
"XCD"
)));
BOOST_CHECK
(
BondExists
(
res
.
FindAtom
(
"XCD"
),
res
.
FindAtom
(
"XNE"
)));
BOOST_CHECK
(
BondExists
(
res
.
FindAtom
(
"XNE"
),
res
.
FindAtom
(
"XCZ"
)));
BOOST_CHECK
(
BondExists
(
res
.
FindAtom
(
"XCZ"
),
res
.
FindAtom
(
"XNH1"
)));
BOOST_CHECK
(
BondExists
(
res
.
FindAtom
(
"XCZ"
),
res
.
FindAtom
(
"XNH2"
)));
// TODO: Check that no other atoms are connected!
}
if
(
res
.
GetKey
()
==
"ILE"
)
{
BOOST_CHECK
(
BondExists
(
res
.
FindAtom
(
"XCG"
),
res
.
FindAtom
(
"XCD1"
)));
BOOST_CHECK
(
BondExists
(
res
.
FindAtom
(
"XCG"
),
res
.
FindAtom
(
"XCD2"
)));
// TODO: Check that no other atoms are connected!
}
}
void
verify_connectivity
(
const
ResidueHandle
&
res
)
{
BOOST_CHECK
(
BondExists
(
res
.
FindAtom
(
"N"
),
res
.
FindAtom
(
"CA"
)));
BOOST_CHECK
(
BondExists
(
res
.
FindAtom
(
"CA"
),
res
.
FindAtom
(
"C"
)));
BOOST_CHECK
(
BondExists
(
res
.
FindAtom
(
"C"
),
res
.
FindAtom
(
"O"
)));
BOOST_CHECK
(
BondExists
(
res
.
FindAtom
(
"CA"
),
res
.
FindAtom
(
"CB"
)));
BOOST_CHECK
(
BondExists
(
res
.
FindAtom
(
"CB"
),
res
.
FindAtom
(
"CG"
)));
if
(
res
.
GetKey
()
==
"ARG"
)
{
BOOST_CHECK
(
BondExists
(
res
.
FindAtom
(
"CB"
),
res
.
FindAtom
(
"CG"
)));
BOOST_CHECK
(
BondExists
(
res
.
FindAtom
(
"CG"
),
res
.
FindAtom
(
"CD"
)));
BOOST_CHECK
(
BondExists
(
res
.
FindAtom
(
"CD"
),
res
.
FindAtom
(
"NE"
)));
BOOST_CHECK
(
BondExists
(
res
.
FindAtom
(
"NE"
),
res
.
FindAtom
(
"CZ"
)));
BOOST_CHECK
(
BondExists
(
res
.
FindAtom
(
"CZ"
),
res
.
FindAtom
(
"NH1"
)));
BOOST_CHECK
(
BondExists
(
res
.
FindAtom
(
"CZ"
),
res
.
FindAtom
(
"NH2"
)));
// TODO: Check that no other atoms are connected!
}
if
(
res
.
GetKey
()
==
"ILE"
)
{
BOOST_CHECK
(
BondExists
(
res
.
FindAtom
(
"CG"
),
res
.
FindAtom
(
"CD1"
)));
BOOST_CHECK
(
BondExists
(
res
.
FindAtom
(
"CG"
),
res
.
FindAtom
(
"CD2"
)));
// TODO: Check that no other atoms are connected!
}
}
BOOST_AUTO_TEST_SUITE
(
conop
);
BOOST_AUTO_TEST_CASE
(
name_based_connect
)
{
EntityHandle
e
=
CreateEntity
();
ChainHandle
c
=
e
.
EditXCS
().
InsertChain
(
"A"
);
ResidueHandle
ile
=
make_leu
(
c
);
ResidueHandle
arg
=
make_arg
(
c
);
HeuristicBuilder
heuristic_builder
;
AtomHandleList
atoms
=
e
.
GetAtomList
();
for
(
AtomHandleList
::
const_iterator
i
=
atoms
.
begin
(),
e
=
atoms
.
end
();
i
!=
e
;
++
i
){
heuristic_builder
.
FillAtomProps
(
*
i
);
}
EntityHandle
de
=
CreateEntity
();
ChainHandle
dc
=
de
.
EditXCS
().
InsertChain
(
"A"
);
ResidueHandle
dile
=
make_defective_leu
(
dc
);
HeuristicBuilder
dheuristic_builder
;
dheuristic_builder
.
SetBondFeasibilityCheck
(
false
);
atoms
=
de
.
GetAtomList
();
for
(
AtomHandleList
::
const_iterator
i
=
atoms
.
begin
(),
e
=
atoms
.
end
();
i
!=
e
;
++
i
){
dheuristic_builder
.
FillAtomProps
(
*
i
);
}
BOOST_TEST_MESSAGE
(
"running distance based checks on arginine"
);
heuristic_builder
.
ConnectAtomsOfResidue
(
arg
);
verify_connectivity
(
arg
);
BOOST_TEST_MESSAGE
(
"running distance based checks on leu"
);
heuristic_builder
.
ConnectAtomsOfResidue
(
ile
);
verify_connectivity
(
ile
);
BOOST_TEST_MESSAGE
(
"running distance based checks on defective leu"
);
dheuristic_builder
.
ConnectAtomsOfResidue
(
dile
);
verify_connectivity
(
dile
);
}
BOOST_AUTO_TEST_CASE
(
test_assign_torsions
){
EntityHandle
e
=
CreateEntity
();
ChainHandle
c
=
e
.
EditXCS
().
InsertChain
(
"A"
);
ResidueHandle
l1
=
make_leu
(
c
);
ResidueHandle
a2
=
make_arg
(
c
);
ResidueHandle
l3
=
make_leu
(
c
);
l1
.
SetChemClass
(
ChemClass
(
ChemClass
::
L_PEPTIDE_LINKING
));
a2
.
SetChemClass
(
ChemClass
(
ChemClass
::
L_PEPTIDE_LINKING
));
l3
.
SetChemClass
(
ChemClass
(
ChemClass
::
L_PEPTIDE_LINKING
));
HeuristicBuilder
heuristic_builder
;
AtomHandleList
atoms
=
e
.
GetAtomList
();
for
(
AtomHandleList
::
const_iterator
i
=
atoms
.
begin
(),
e
=
atoms
.
end
();
i
!=
e
;
++
i
){
heuristic_builder
.
FillAtomProps
(
*
i
);
}
heuristic_builder
.
ConnectAtomsOfResidue
(
l1
);
heuristic_builder
.
ConnectAtomsOfResidue
(
a2
);
heuristic_builder
.
ConnectAtomsOfResidue
(
l3
);
XCSEditor
edi
=
e
.
EditXCS
();
edi
.
Connect
(
l1
.
FindAtom
(
"C"
),
a2
.
FindAtom
(
"N"
));
edi
.
Connect
(
a2
.
FindAtom
(
"C"
),
l3
.
FindAtom
(
"N"
));
heuristic_builder
.
AssignTorsions
(
c
);
BOOST_CHECK
(
a2
.
GetPhiTorsion
().
IsValid
());
BOOST_CHECK
(
l3
.
GetPhiTorsion
().
IsValid
());
BOOST_CHECK
(
l1
.
GetPsiTorsion
().
IsValid
());
BOOST_CHECK
(
a2
.
GetPsiTorsion
().
IsValid
());
}
BOOST_AUTO_TEST_SUITE_END
(
);
This diff is collapsed.
Click to expand it.
Preview
0%
Loading
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment