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schwede
openstructure
Commits
6050f85c
Commit
6050f85c
authored
10 years ago
by
Studer Gabriel
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remove unnecessary file
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e1406943
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modules/mol/mm/pymod/export_mm.cc
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modules/mol/mm/pymod/export_mm.cc
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e1406943
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2011 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
<OpenMM.h>
#include
<boost/python.hpp>
#include
<boost/shared_ptr.hpp>
#include
<ost/mol/mm/force_field.hh>
#include
<ost/mol/mm/simulation.hh>
#include
<ost/mol/mm/mm_algorithms.hh>
#include
<ost/mol/residue_handle.hh>
#include
<ost/mol/mm/mm_settings.hh>
using
namespace
boost
::
python
;
using
namespace
ost
::
mol
::
mm
;
namespace
{
std
::
vector
<
std
::
pair
<
String
,
ost
::
mol
::
ResNum
>
>
list_to_vec
(
boost
::
python
::
list
&
l
){
std
::
vector
<
std
::
pair
<
String
,
ost
::
mol
::
ResNum
>
>
return_vec
;
boost
::
python
::
tuple
t
;
String
s
;
ost
::
mol
::
ResNum
rn
;
for
(
int
i
=
0
;
i
<
boost
::
python
::
len
(
l
);
++
i
){
t
=
boost
::
python
::
extract
<
boost
::
python
::
tuple
>
(
l
[
0
]);
s
=
boost
::
python
::
extract
<
String
>
(
t
[
0
]);
rn
=
boost
::
python
::
extract
<
ost
::
mol
::
ResNum
>
(
t
[
1
]);
return_vec
.
push_back
(
std
::
make_pair
(
s
,
rn
));
}
return
return_vec
;
}
ost
::
mol
::
mm
::
SimulationPtr
WrapSimulationConstructor
(
ost
::
mol
::
EntityHandle
&
e
,
ost
::
mol
::
mm
::
ForcefieldPtr
ff
,
ost
::
mol
::
mm
::
IntegratorPtr
integrator
,
ost
::
mol
::
mm
::
MMSettingsPtr
settings
,
list
&
d_protonated_his
,
list
&
e_protonated_his
,
list
&
positive_his
,
list
&
neutral_glutamates
,
list
&
neutral_aspartates
){
std
::
vector
<
std
::
pair
<
String
,
ost
::
mol
::
ResNum
>
>
v_d_protonated_his
=
list_to_vec
(
d_protonated_his
);
std
::
vector
<
std
::
pair
<
String
,
ost
::
mol
::
ResNum
>
>
v_e_protonated_his
=
list_to_vec
(
e_protonated_his
);
std
::
vector
<
std
::
pair
<
String
,
ost
::
mol
::
ResNum
>
>
v_positive_his
=
list_to_vec
(
positive_his
);
std
::
vector
<
std
::
pair
<
String
,
ost
::
mol
::
ResNum
>
>
v_neutral_glutamates
=
list_to_vec
(
neutral_glutamates
);
std
::
vector
<
std
::
pair
<
String
,
ost
::
mol
::
ResNum
>
>
v_neutral_aspartates
=
list_to_vec
(
neutral_aspartates
);
ost
::
mol
::
mm
::
SimulationPtr
p
(
new
ost
::
mol
::
mm
::
Simulation
(
e
,
ff
,
integrator
,
settings
,
v_d_protonated_his
,
v_e_protonated_his
,
v_positive_his
,
v_neutral_glutamates
,
v_neutral_aspartates
));
return
p
;
}
ost
::
mol
::
mm
::
SimulationPtr
WrapSimulationConstructorNoSettings
(
ost
::
mol
::
EntityHandle
&
e
,
ost
::
mol
::
mm
::
ForcefieldPtr
ff
,
ost
::
mol
::
mm
::
IntegratorPtr
integrator
,
list
&
d_protonated_his
,
list
&
e_protonated_his
,
list
&
positive_his
,
list
&
neutral_glutamates
,
list
&
neutral_aspartates
){
ost
::
mol
::
mm
::
MMSettingsPtr
p
(
new
ost
::
mol
::
mm
::
MMSettings
);
return
WrapSimulationConstructor
(
e
,
ff
,
integrator
,
p
,
d_protonated_his
,
e_protonated_his
,
positive_his
,
neutral_glutamates
,
neutral_aspartates
);
}
void
WrapAssignFFSpecificNames
(
ost
::
mol
::
mm
::
ForcefieldPtr
p
,
ost
::
mol
::
EntityHandle
&
e
,
boost
::
python
::
list
&
d_protonated_his
,
boost
::
python
::
list
&
e_protonated_his
,
boost
::
python
::
list
&
positive_his
,
boost
::
python
::
list
&
neutral_glutamates
,
boost
::
python
::
list
&
neutral_aspartates
){
std
::
vector
<
std
::
pair
<
String
,
ost
::
mol
::
ResNum
>
>
v_d_protonated_his
=
list_to_vec
(
d_protonated_his
);
std
::
vector
<
std
::
pair
<
String
,
ost
::
mol
::
ResNum
>
>
v_e_protonated_his
=
list_to_vec
(
e_protonated_his
);
std
::
vector
<
std
::
pair
<
String
,
ost
::
mol
::
ResNum
>
>
v_positive_his
=
list_to_vec
(
positive_his
);
std
::
vector
<
std
::
pair
<
String
,
ost
::
mol
::
ResNum
>
>
v_neutral_glutamates
=
list_to_vec
(
neutral_glutamates
);
std
::
vector
<
std
::
pair
<
String
,
ost
::
mol
::
ResNum
>
>
v_neutral_aspartates
=
list_to_vec
(
neutral_aspartates
);
p
->
AssignFFSpecificNames
(
e
,
v_d_protonated_his
,
v_e_protonated_his
,
v_positive_his
,
v_neutral_glutamates
,
v_neutral_aspartates
);
}
}
void
export_MM
()
{
//export the settings
class_
<
ost
::
mol
::
mm
::
MMSettings
>
(
"MMSettings"
,
init
<>
())
.
def_readwrite
(
"add_bonds"
,
&
ost
::
mol
::
mm
::
MMSettings
::
add_bonds
)
.
def_readwrite
(
"add_angles"
,
&
ost
::
mol
::
mm
::
MMSettings
::
add_angles
)
.
def_readwrite
(
"add_dihedrals"
,
&
ost
::
mol
::
mm
::
MMSettings
::
add_dihedrals
)
.
def_readwrite
(
"add_impropers"
,
&
ost
::
mol
::
mm
::
MMSettings
::
add_impropers
)
.
def_readwrite
(
"add_cmaps"
,
&
ost
::
mol
::
mm
::
MMSettings
::
add_cmaps
)
.
def_readwrite
(
"add_exclusions"
,
&
ost
::
mol
::
mm
::
MMSettings
::
add_exclusions
)
.
def_readwrite
(
"add_nonbonded"
,
&
ost
::
mol
::
mm
::
MMSettings
::
add_nonbonded
)
.
def_readwrite
(
"kill_electrostatics"
,
&
ost
::
mol
::
mm
::
MMSettings
::
kill_electrostatics
)
.
def_readwrite
(
"nonbonded_method"
,
&
ost
::
mol
::
mm
::
MMSettings
::
nonbonded_method
)
.
def_readwrite
(
"nonbonded_cutoff"
,
&
ost
::
mol
::
mm
::
MMSettings
::
nonbonded_cutoff
)
.
def_readwrite
(
"rigid_water"
,
&
ost
::
mol
::
mm
::
MMSettings
::
rigid_water
)
.
def_readwrite
(
"removeCMMMotion"
,
&
ost
::
mol
::
mm
::
MMSettings
::
removeCMMMotion
)
.
def_readwrite
(
"constraints"
,
&
ost
::
mol
::
mm
::
MMSettings
::
constraints
)
;
boost
::
python
::
register_ptr_to_python
<
ost
::
mol
::
mm
::
MMSettingsPtr
>
();
//we have to tell boost, that the Integrator class is around...
class_
<
OpenMM
::
Integrator
,
boost
::
noncopyable
>
(
"Integrator"
,
no_init
);
//We do not export any further function for the Verlet integrator, since we want
//to perform the steps via the simulation...
class_
<
OpenMM
::
VerletIntegrator
,
bases
<
OpenMM
::
Integrator
>
>
(
"VerletIntegrator"
,
init
<
Real
>
());
boost
::
python
::
register_ptr_to_python
<
ost
::
mol
::
mm
::
IntegratorPtr
>
();
boost
::
python
::
register_ptr_to_python
<
ost
::
mol
::
mm
::
VerletIntegratorPtr
>
();
class_
<
ost
::
mol
::
mm
::
Forcefield
>
(
"Forcefield"
,
init
<
const
String
&>
())
.
def
(
"AssignFFSpecificNames"
,
&
WrapAssignFFSpecificNames
,
(
arg
(
"entity"
),
arg
(
"d_protonated_his"
)
=
boost
::
python
::
list
(),
arg
(
"e_protonated_his"
)
=
boost
::
python
::
list
(),
arg
(
"positive_his"
)
=
boost
::
python
::
list
(),
arg
(
"neutral_glutamates"
)
=
boost
::
python
::
list
(),
arg
(
"neutral_aspartates"
)
=
boost
::
python
::
list
()))
.
def
(
"AddHydrogens"
,
&
ost
::
mol
::
mm
::
Forcefield
::
AddHydrogens
)
.
def
(
"ReadResidueDatabase"
,
&
ost
::
mol
::
mm
::
Forcefield
::
ReadResidueDatabase
)
;
class_
<
ost
::
mol
::
mm
::
Simulation
>
(
"Simulation"
,
no_init
)
.
def
(
"__init__"
,
boost
::
python
::
make_constructor
(
&
WrapSimulationConstructor
,
default_call_policies
(),
(
arg
(
"entity"
),
arg
(
"forcefield"
),
arg
(
"integrator"
),
arg
(
"settings"
),
arg
(
"d_protonated_his"
)
=
boost
::
python
::
list
(),
arg
(
"e_protonated_his"
)
=
boost
::
python
::
list
(),
arg
(
"positive_his"
)
=
boost
::
python
::
list
(),
arg
(
"neutral_glutamates"
)
=
boost
::
python
::
list
(),
arg
(
"neutral_aspartates"
)
=
boost
::
python
::
list
())))
.
def
(
"__init__"
,
boost
::
python
::
make_constructor
(
&
WrapSimulationConstructorNoSettings
,
default_call_policies
(),
(
arg
(
"entity"
),
arg
(
"forcefield"
),
arg
(
"integrator"
),
arg
(
"d_protonated_his"
)
=
boost
::
python
::
list
(),
arg
(
"e_protonated_his"
)
=
boost
::
python
::
list
(),
arg
(
"positive_his"
)
=
boost
::
python
::
list
(),
arg
(
"neutral_glutamates"
)
=
boost
::
python
::
list
(),
arg
(
"neutral_aspartates"
)
=
boost
::
python
::
list
())))
.
def
(
"GetEntity"
,
&
ost
::
mol
::
mm
::
Simulation
::
GetEntity
)
.
def
(
"GetMMEntity"
,
&
ost
::
mol
::
mm
::
Simulation
::
GetMMEntity
)
.
def
(
"UpdatePositions"
,
&
ost
::
mol
::
mm
::
Simulation
::
UpdatePositions
)
.
def
(
"MinimizeEnergy"
,
&
ost
::
mol
::
mm
::
Simulation
::
MinimizeEnergy
,
(
arg
(
"tolerance"
)
=
1.0
,
arg
(
"max_iterations"
)
=
1000
))
.
def
(
"GetTimeSteps"
,
&
ost
::
mol
::
mm
::
Simulation
::
GetTimeSteps
)
.
def
(
"Steps"
,
&
ost
::
mol
::
mm
::
Simulation
::
Steps
,
(
arg
(
"steps"
)
=
1
))
;
boost
::
python
::
register_ptr_to_python
<
ost
::
mol
::
mm
::
SimulationPtr
>
();
//functions from mm_algorithms
def
(
"Minimize"
,
&
ost
::
mol
::
mm
::
Minimize
,
(
arg
(
"ent"
),
arg
(
"ff"
)));
}
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