diff --git a/modules/mol/mm/examples/ethanol_example.py b/modules/mol/mm/examples/ethanol_example.py
index f76253adcc377cbfd9102c2e0a44a057da2069ae..3cb71c3426f31b5860b51ef094ec4294bbb2941a 100644
--- a/modules/mol/mm/examples/ethanol_example.py
+++ b/modules/mol/mm/examples/ethanol_example.py
@@ -54,7 +54,7 @@ building_block.AddAtom("OH","OH",0.418)
bonds = list()
for i in range(8):
- bonds.append(MMInteraction(FuncType.HarmonicBond))
+ bonds.append(Interaction(FuncType.HarmonicBond))
bonds[0].SetNames(["H11","C1"])
bonds[1].SetNames(["H12","C1"])
@@ -77,10 +77,10 @@ ff.AddMass("H",1.008)
ff.AddMass("OH",1.008)
#generate bonds and add them to the forcefield
-h_c_bond = MMInteraction(FuncType.HarmonicBond)
-c_c_bond = MMInteraction(FuncType.HarmonicBond)
-c_o_bond = MMInteraction(FuncType.HarmonicBond)
-o_h_bond = MMInteraction(FuncType.HarmonicBond)
+h_c_bond = Interaction(FuncType.HarmonicBond)
+c_c_bond = Interaction(FuncType.HarmonicBond)
+c_o_bond = Interaction(FuncType.HarmonicBond)
+o_h_bond = Interaction(FuncType.HarmonicBond)
h_c_bond.SetTypes(["H","C"])
c_c_bond.SetTypes(["C","C"])
@@ -98,11 +98,11 @@ ff.AddBond(c_o_bond)
ff.AddBond(o_h_bond)
#generate angles and add them to the forcefield
-h_c_h_angle = MMInteraction(FuncType.UreyBradleyAngle)
-h_c_c_angle = MMInteraction(FuncType.UreyBradleyAngle)
-h_c_o_angle = MMInteraction(FuncType.UreyBradleyAngle)
-c_c_o_angle = MMInteraction(FuncType.UreyBradleyAngle)
-c_o_h_angle = MMInteraction(FuncType.UreyBradleyAngle)
+h_c_h_angle = Interaction(FuncType.UreyBradleyAngle)
+h_c_c_angle = Interaction(FuncType.UreyBradleyAngle)
+h_c_o_angle = Interaction(FuncType.UreyBradleyAngle)
+c_c_o_angle = Interaction(FuncType.UreyBradleyAngle)
+c_o_h_angle = Interaction(FuncType.UreyBradleyAngle)
h_c_h_angle.SetTypes(["H","C","H"])
h_c_c_angle.SetTypes(["H","C","C"])
@@ -123,11 +123,11 @@ ff.AddAngle(c_c_o_angle)
ff.AddAngle(c_o_h_angle)
#generate dihedrals and add them to the forcefield
-x_c_c_x_dihedral = MMInteraction(FuncType.PeriodicDihedral)
-c_c_o_h_dihedral_one = MMInteraction(FuncType.PeriodicDihedral)
-c_c_o_h_dihedral_two = MMInteraction(FuncType.PeriodicDihedral)
-c_c_o_h_dihedral_three = MMInteraction(FuncType.PeriodicDihedral)
-x_c_o_x_dihedral = MMInteraction(FuncType.PeriodicDihedral)
+x_c_c_x_dihedral = Interaction(FuncType.PeriodicDihedral)
+c_c_o_h_dihedral_one = Interaction(FuncType.PeriodicDihedral)
+c_c_o_h_dihedral_two = Interaction(FuncType.PeriodicDihedral)
+c_c_o_h_dihedral_three = Interaction(FuncType.PeriodicDihedral)
+x_c_o_x_dihedral = Interaction(FuncType.PeriodicDihedral)
x_c_c_x_dihedral.SetTypes(["X","C","C","X"])
c_c_o_h_dihedral_one.SetTypes(["C","C","O","OH"])
@@ -148,10 +148,10 @@ ff.AddDihedral(c_c_o_h_dihedral_three)
ff.AddDihedral(x_c_o_x_dihedral)
#add lj parameters
-c_lj = MMInteraction(FuncType.LJ)
-o_lj = MMInteraction(FuncType.LJ)
-h_lj = MMInteraction(FuncType.LJ)
-oh_lj = MMInteraction(FuncType.LJ)
+c_lj = Interaction(FuncType.LJ)
+o_lj = Interaction(FuncType.LJ)
+h_lj = Interaction(FuncType.LJ)
+oh_lj = Interaction(FuncType.LJ)
c_lj.SetTypes(["C"])
o_lj.SetTypes(["O"])
@@ -174,7 +174,7 @@ ff.SetFudgeLJ(0.5)
ff.SetFudgeQQ(0.5)
#construct settings
-settings = MMSettings()
+settings = Settings()
settings.init_temperature = 310
settings.forcefield = ff
diff --git a/modules/mol/mm/examples/ethanol_example_using_topology.py b/modules/mol/mm/examples/ethanol_example_using_topology.py
index 41104e2a2ecbc72e177eb4fa6706e626fb3ec287..dc5f8ff62383e573d30109bbb4ffced16fe78089 100644
--- a/modules/mol/mm/examples/ethanol_example_using_topology.py
+++ b/modules/mol/mm/examples/ethanol_example_using_topology.py
@@ -136,7 +136,7 @@ top.AddLJPair(6,8,0.5*(sigmas[6]+sigmas[8]),sqrt(epsilons[6]*epsilons[8]))
top.AddLJPair(7,8,0.5*(sigmas[7]+sigmas[8]),sqrt(epsilons[7]*epsilons[8]))
top.AddLJPair(0,8,0.5*(sigmas[0]+sigmas[8]),sqrt(epsilons[0]*epsilons[8]))
-settings = MMSettings()
+settings = Settings()
settings.init_temperature = 310
settings.integrator = VerletIntegrator(0.0001)
diff --git a/modules/mol/mm/examples/gb_example.py b/modules/mol/mm/examples/gb_example.py
index 24be5a298bc4e189c184ad218a451dc2381e8546..d8a0b766399fbfacfbd92928162d521d9af3465f 100644
--- a/modules/mol/mm/examples/gb_example.py
+++ b/modules/mol/mm/examples/gb_example.py
@@ -22,7 +22,7 @@ class Anim(QtCore.QTimer):
prot=ost.mol.CreateEntityFromView(io.LoadPDB('1CRN.pdb').Select('peptide=true'),True)
-settings = mm.MMSettings()
+settings = mm.Settings()
settings.integrator = mm.LangevinIntegrator(310,1,0.002)
settings.constrain_bonds = True
diff --git a/modules/mol/mm/examples/gb_example_traj.dcd b/modules/mol/mm/examples/gb_example_traj.dcd
index a3b16707652ff63865c1e1068966cc29d9f0dd9f..45087025b3083a8ce747c5c4bbfa0d6716af27de 100644
Binary files a/modules/mol/mm/examples/gb_example_traj.dcd and b/modules/mol/mm/examples/gb_example_traj.dcd differ
diff --git a/modules/mol/mm/examples/gb_example_traj.pdb b/modules/mol/mm/examples/gb_example_traj.pdb
index afb415a36cb19b045dff9136144b7355face8c46..a1da60b3f73ab5a617747f15dc302a2d2ad2e5fb 100644
--- a/modules/mol/mm/examples/gb_example_traj.pdb
+++ b/modules/mol/mm/examples/gb_example_traj.pdb
@@ -628,12 +628,12 @@ ATOM 627 HB3 ALA 45 14.788 6.644 17.011 1.00 0.00 A H
ATOM 628 N ASN 46 13.966 6.502 13.739 1.00 5.80 A N
ATOM 629 CA ASN 46 13.512 5.395 12.878 1.00 6.15 A C
ATOM 630 C ASN 46 13.311 5.853 11.455 1.00 6.61 A C
-ATOM 631 OT1 ASN 46 13.733 6.929 11.026 1.00 7.18 A O
+ATOM 631 OT1 ASN 46 13.539 7.141 11.084 1.00 7.18 A O
ATOM 632 CB ASN 46 12.266 4.769 13.501 1.00 7.27 A C
ATOM 633 CG ASN 46 12.538 4.304 14.922 1.00 7.98 A C
ATOM 634 OD1 ASN 46 11.982 4.849 15.886 1.00 11.00 A O
ATOM 635 ND2 ASN 46 13.407 3.298 15.015 1.00 10.32 A N
-ATOM 636 OT2 ASN 46 12.703 4.973 10.746 1.00 7.86 A O
+ATOM 636 OT2 ASN 46 12.893 4.996 10.485 1.00 7.86 A O
ATOM 637 HN ASN 46 13.338 7.259 13.921 1.00 0.00 A H
ATOM 638 HA ASN 46 14.216 4.687 12.825 1.00 0.00 A H
ATOM 639 HB1 ASN 46 11.532 5.448 13.515 1.00 0.00 A H
diff --git a/modules/mol/mm/examples/gb_example_writing_trajectory.py b/modules/mol/mm/examples/gb_example_writing_trajectory.py
index 74e77ce41c5f866472c1e5e2622c49051865139c..051f6ebc8015751002729345af0dfd14c96c0ea6 100644
--- a/modules/mol/mm/examples/gb_example_writing_trajectory.py
+++ b/modules/mol/mm/examples/gb_example_writing_trajectory.py
@@ -3,7 +3,7 @@ from ost.mol.mm import *
prot=io.LoadPDB('1CRN.pdb')
#set up the simulation
-settings = MMSettings()
+settings = Settings()
settings.integrator = LangevinIntegrator(310,1,0.002)
settings.add_gbsa = True
settings.forcefield = LoadCHARMMForcefield()
diff --git a/modules/mol/mm/pymod/export_forcefield.cc b/modules/mol/mm/pymod/export_forcefield.cc
index db80c3b1990bfb188bf8cd940a0b63d8a69473e3..76659583454fb509e7ad40c89f8e98a16fae6b46 100644
--- a/modules/mol/mm/pymod/export_forcefield.cc
+++ b/modules/mol/mm/pymod/export_forcefield.cc
@@ -25,11 +25,11 @@ using namespace boost::python;
namespace{
- ost::mol::mm::MMInteractionPtr GetLJOneType(ost::mol::mm::ForcefieldPtr p, String type){
+ ost::mol::mm::InteractionPtr GetLJOneType(ost::mol::mm::ForcefieldPtr p, String type){
return p->GetLJ(type);
}
- ost::mol::mm::MMInteractionPtr GetLJTwoTypes(ost::mol::mm::ForcefieldPtr p, String type1, String type2, bool pair){
+ ost::mol::mm::InteractionPtr GetLJTwoTypes(ost::mol::mm::ForcefieldPtr p, String type1, String type2, bool pair){
return p->GetLJ(type1,type2,pair);
}
diff --git a/modules/mol/mm/pymod/export_interaction.cc b/modules/mol/mm/pymod/export_interaction.cc
index c9a223dea7ba5f0d668a4a2b317221697d2fecf2..5af850baea30bbad5c4a1e3fd4245b9ac456e0e1 100644
--- a/modules/mol/mm/pymod/export_interaction.cc
+++ b/modules/mol/mm/pymod/export_interaction.cc
@@ -1,7 +1,7 @@
#include <boost/python.hpp>
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
-#include <ost/mol/mm/mm_interaction.hh>
+#include <ost/mol/mm/interaction.hh>
#include <vector>
@@ -27,39 +27,39 @@ std::vector<T> ListToVec(boost::python::list& l){
return vec;
}
-boost::python::list WrapGetNames(ost::mol::mm::MMInteractionPtr p){
+boost::python::list WrapGetNames(ost::mol::mm::InteractionPtr p){
std::vector<String> names = p->GetNames();
return VecToList<String>(names);
}
-boost::python::list WrapGetTypes(ost::mol::mm::MMInteractionPtr p){
+boost::python::list WrapGetTypes(ost::mol::mm::InteractionPtr p){
std::vector<String> types = p->GetTypes();
return VecToList<String>(types);
}
-boost::python::list WrapGetParam(ost::mol::mm::MMInteractionPtr p){
+boost::python::list WrapGetParam(ost::mol::mm::InteractionPtr p){
std::vector<Real> param = p->GetParam();
return VecToList<Real>(param);
}
-void WrapSetNames(ost::mol::mm::MMInteractionPtr p, boost::python::list l){
+void WrapSetNames(ost::mol::mm::InteractionPtr p, boost::python::list l){
std::vector<String> names = ListToVec<String>(l);
p->SetNames(names);
}
-void WrapSetTypes(ost::mol::mm::MMInteractionPtr p, boost::python::list l){
+void WrapSetTypes(ost::mol::mm::InteractionPtr p, boost::python::list l){
std::vector<String> types = ListToVec<String>(l);
p->SetTypes(types);
}
-void WrapSetParam(ost::mol::mm::MMInteractionPtr p, boost::python::list l){
+void WrapSetParam(ost::mol::mm::InteractionPtr p, boost::python::list l){
std::vector<Real> param = ListToVec<Real>(l);
p->SetParam(param);
}
}
-void export_MMInteraction()
+void export_Interaction()
{
enum_<ost::mol::mm::FuncType>("FuncType")
@@ -80,29 +80,29 @@ void export_MMInteraction()
.value("HarmonicDistanceRestraint", ost::mol::mm::HarmonicDistanceRestraint)
;
- class_<ost::mol::mm::MMInteraction>("MMInteraction",init<ost::mol::mm::FuncType>())
+ class_<ost::mol::mm::Interaction>("Interaction",init<ost::mol::mm::FuncType>())
.def("SetTypes",&WrapSetTypes)
.def("SetNames",&WrapSetNames)
.def("SetParam",&WrapSetParam)
.def("GetTypes",&WrapGetTypes)
.def("GetNames",&WrapGetNames)
.def("GetParam",&WrapGetParam)
- .def("GetAtoms",&ost::mol::mm::MMInteraction::GetAtoms)
- .def("GetFuncType",&ost::mol::mm::MMInteraction::GetFuncType)
- .def("ReplaceAtom",&ost::mol::mm::MMInteraction::ReplaceAtom)
- .def("MatchTypes",&ost::mol::mm::MMInteraction::MatchTypes)
- .def("MatchNames",&ost::mol::mm::MMInteraction::MatchNames)
- .def("HasName",&ost::mol::mm::MMInteraction::HasName)
- .def("HasType",&ost::mol::mm::MMInteraction::HasType)
- .def("IsParametrized",&ost::mol::mm::MMInteraction::IsParametrized)
- .def("HasTypeWildcard",&ost::mol::mm::MMInteraction::HasTypeWildcard)
- .def("HasNameWildcard",&ost::mol::mm::MMInteraction::HasNameWildcard)
+ .def("GetAtoms",&ost::mol::mm::Interaction::GetAtoms)
+ .def("GetFuncType",&ost::mol::mm::Interaction::GetFuncType)
+ .def("ReplaceAtom",&ost::mol::mm::Interaction::ReplaceAtom)
+ .def("MatchTypes",&ost::mol::mm::Interaction::MatchTypes)
+ .def("MatchNames",&ost::mol::mm::Interaction::MatchNames)
+ .def("HasName",&ost::mol::mm::Interaction::HasName)
+ .def("HasType",&ost::mol::mm::Interaction::HasType)
+ .def("IsParametrized",&ost::mol::mm::Interaction::IsParametrized)
+ .def("HasTypeWildcard",&ost::mol::mm::Interaction::HasTypeWildcard)
+ .def("HasNameWildcard",&ost::mol::mm::Interaction::HasNameWildcard)
;
- boost::python::register_ptr_to_python<ost::mol::mm::MMInteractionPtr>();
+ boost::python::register_ptr_to_python<ost::mol::mm::InteractionPtr>();
- class_<std::vector<ost::mol::mm::MMInteractionPtr> >("MMInteractionList", init<>())
- .def(vector_indexing_suite<std::vector<ost::mol::mm::MMInteractionPtr>, true>())
+ class_<std::vector<ost::mol::mm::InteractionPtr> >("InteractionList", init<>())
+ .def(vector_indexing_suite<std::vector<ost::mol::mm::InteractionPtr>, true>())
;
}
diff --git a/modules/mol/mm/pymod/export_modeller.cc b/modules/mol/mm/pymod/export_modeller.cc
index 59aceeedbf52734e6b0b10fe8ac9dfd972c4c502..c186f8b4aa2da4e72fe0537f64d113e2444bf5da 100644
--- a/modules/mol/mm/pymod/export_modeller.cc
+++ b/modules/mol/mm/pymod/export_modeller.cc
@@ -1,6 +1,6 @@
#include <boost/python.hpp>
#include <ost/mol/mm/block_modifiers.hh>
-#include <ost/mol/mm/mm_modeller.hh>
+#include <ost/mol/mm/modeller.hh>
using namespace boost::python;
@@ -8,14 +8,13 @@ using namespace boost::python;
void export_Modeller()
{
- class_<ost::mol::mm::MMModeller>("MMModeller", no_init)
- .def("GenerateDisulfidBonds",&ost::mol::mm::MMModeller::GenerateDisulfidBonds,(arg("ent"))).staticmethod("GenerateDisulfidBonds")
- .def("GenerateCYSHEMEBonds",&ost::mol::mm::MMModeller::GenerateCYSHEMEBonds,(arg("ent"))).staticmethod("GenerateCYSHEMEBonds")
- .def("GenerateHISHEMEBonds",&ost::mol::mm::MMModeller::GenerateHISHEMEBonds,(arg("ent"))).staticmethod("GenerateHISHEMEBonds")
- .def("GenerateMETHEMEBonds",&ost::mol::mm::MMModeller::GenerateDisulfidBonds,(arg("ent"))).staticmethod("GenerateMETHEMEBonds")
- .def("AssignPDBNaming",&ost::mol::mm::MMModeller::AssignPDBNaming,(arg("ent"))).staticmethod("AssignPDBNaming")
- .def("AssignGromacsNaming",&ost::mol::mm::MMModeller::AssignGromacsNaming,(arg("ent"))).staticmethod("AssignGromacsNaming")
-
+ class_<ost::mol::mm::Modeller>("MMModeller", no_init)
+ .def("GenerateDisulfidBonds",&ost::mol::mm::Modeller::GenerateDisulfidBonds,(arg("ent"))).staticmethod("GenerateDisulfidBonds")
+ .def("GenerateCYSHEMEBonds",&ost::mol::mm::Modeller::GenerateCYSHEMEBonds,(arg("ent"))).staticmethod("GenerateCYSHEMEBonds")
+ .def("GenerateHISHEMEBonds",&ost::mol::mm::Modeller::GenerateHISHEMEBonds,(arg("ent"))).staticmethod("GenerateHISHEMEBonds")
+ .def("GenerateMETHEMEBonds",&ost::mol::mm::Modeller::GenerateDisulfidBonds,(arg("ent"))).staticmethod("GenerateMETHEMEBonds")
+ .def("AssignPDBNaming",&ost::mol::mm::Modeller::AssignPDBNaming,(arg("ent"))).staticmethod("AssignPDBNaming")
+ .def("AssignGromacsNaming",&ost::mol::mm::Modeller::AssignGromacsNaming,(arg("ent"))).staticmethod("AssignGromacsNaming")
;
}
\ No newline at end of file
diff --git a/modules/mol/mm/pymod/export_observers.cc b/modules/mol/mm/pymod/export_observers.cc
index 1fa316c6986279c9a0e907159ec458484b4376e3..896236847da4f60bedd925d04e1712c3bdd740d8 100644
--- a/modules/mol/mm/pymod/export_observers.cc
+++ b/modules/mol/mm/pymod/export_observers.cc
@@ -1,6 +1,6 @@
#include <boost/python.hpp>
#include <boost/shared_ptr.hpp>
-#include <ost/mol/mm/mm_observer.hh>
+#include <ost/mol/mm/observer.hh>
using namespace boost::python;
@@ -8,18 +8,18 @@ using namespace boost::python;
void export_Observers()
{
- class_<ost::mol::mm::MMObserver, boost::noncopyable>("MMObserver", no_init);
+ class_<ost::mol::mm::Observer, boost::noncopyable>("Observer", no_init);
- class_<ost::mol::mm::TrajObserver, bases<ost::mol::mm::MMObserver> >("TrajObserver", init<int>())
+ class_<ost::mol::mm::TrajObserver, bases<ost::mol::mm::Observer> >("TrajObserver", init<int>())
.def("GetTraj", &ost::mol::mm::TrajObserver::GetTraj)
;
//noncopyable, because TrajWriter contains a unique ofstream
- class_<ost::mol::mm::TrajWriter, boost::noncopyable, bases<ost::mol::mm::MMObserver> >("TrajWriter", init<int, String, String>())
+ class_<ost::mol::mm::TrajWriter, boost::noncopyable, bases<ost::mol::mm::Observer> >("TrajWriter", init<int, String, String>())
.def("Finalize", &ost::mol::mm::TrajWriter::Finalize)
;
- boost::python::register_ptr_to_python<ost::mol::mm::MMObserverPtr>();
+ boost::python::register_ptr_to_python<ost::mol::mm::ObserverPtr>();
boost::python::register_ptr_to_python<ost::mol::mm::TrajObserverPtr>();
boost::python::register_ptr_to_python<ost::mol::mm::TrajWriterPtr>();
}
\ No newline at end of file
diff --git a/modules/mol/mm/pymod/export_settings.cc b/modules/mol/mm/pymod/export_settings.cc
index 3aba50adde1723a1387bc46cf25a87ef6afbbe8a..518cb4c8e1b1855fe6069f55237ffe511e34476f 100644
--- a/modules/mol/mm/pymod/export_settings.cc
+++ b/modules/mol/mm/pymod/export_settings.cc
@@ -17,13 +17,13 @@
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
#include <boost/python.hpp>
-#include <ost/mol/mm/mm_settings.hh>
+#include <ost/mol/mm/settings.hh>
#include <OpenMM.h> //for definition of Integrator
using namespace boost::python;
-void export_MMSettings()
+void export_Settings()
{
enum_<ost::mol::mm::Platform>("Platform")
@@ -50,50 +50,50 @@ void export_MMSettings()
//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("add_gbsa",&ost::mol::mm::MMSettings::add_gbsa)
- .def_readwrite("constrain_hbonds",&ost::mol::mm::MMSettings::constrain_hbonds)
- .def_readwrite("constrain_bonds",&ost::mol::mm::MMSettings::constrain_bonds)
- .def_readwrite("rigid_water",&ost::mol::mm::MMSettings::rigid_water)
- .def_readwrite("strict_interactions",&ost::mol::mm::MMSettings::strict_interactions)
- .def_readwrite("ideal_bond_length_constraints",&ost::mol::mm::MMSettings::ideal_bond_length_constraints)
- .def_readwrite("fix_heavy_atoms",&ost::mol::mm::MMSettings::fix_heavy_atoms)
- .def_readwrite("kill_electrostatics",&ost::mol::mm::MMSettings::kill_electrostatics)
- .def_readwrite("generate_disulfid_bonds",&ost::mol::mm::MMSettings::generate_disulfid_bonds)
- .def_readwrite("nonbonded_method",&ost::mol::mm::MMSettings::nonbonded_method)
- .def_readwrite("nonbonded_cutoff",&ost::mol::mm::MMSettings::nonbonded_cutoff)
- .def_readwrite("remove_cmm_motion",&ost::mol::mm::MMSettings::remove_cmm_motion)
- .def_readwrite("periodic_box_extents",&ost::mol::mm::MMSettings::periodic_box_extents)
- .def_readwrite("init_temperature",&ost::mol::mm::MMSettings::init_temperature)
- .def_readwrite("forcefield",&ost::mol::mm::MMSettings::forcefield)
- .def_readwrite("termini_exceptions",&ost::mol::mm::MMSettings::termini_exceptions)
- .def_readwrite("platform",&ost::mol::mm::MMSettings::platform)
- .def_readwrite("add_thermostat",&ost::mol::mm::MMSettings::add_thermostat)
- .def_readwrite("thermostat_temperature",&ost::mol::mm::MMSettings::thermostat_temperature)
- .def_readwrite("thermostat_collision_frequency",&ost::mol::mm::MMSettings::thermostat_collision_frequency)
- .def_readwrite("add_barostat",&ost::mol::mm::MMSettings::add_barostat)
- .def_readwrite("barostat_temperature",&ost::mol::mm::MMSettings::barostat_temperature)
- .def_readwrite("barostat_pressure",&ost::mol::mm::MMSettings::barostat_pressure)
- .def_readwrite("barostat_frequency",&ost::mol::mm::MMSettings::barostat_frequency)
- .def_readwrite("integrator",&ost::mol::mm::MMSettings::integrator)
- .def_readwrite("solvent_dielectric",&ost::mol::mm::MMSettings::solvent_dielectric)
- .def_readwrite("solute_dielectric",&ost::mol::mm::MMSettings::solute_dielectric)
- .def_readwrite("reaction_field_dielectric",&ost::mol::mm::MMSettings::reaction_field_dielectric)
- .def_readwrite("use_dispersion_correction",&ost::mol::mm::MMSettings::use_dispersion_correction)
- .def_readwrite("keep_ff_specific_naming",&ost::mol::mm::MMSettings::keep_ff_specific_naming)
- .def_readwrite("openmm_plugin_directory",&ost::mol::mm::MMSettings::openmm_plugin_directory)
- .def_readwrite("custom_plugin_directory",&ost::mol::mm::MMSettings::custom_plugin_directory)
+ class_<ost::mol::mm::Settings>("Settings",init<>())
+ .def_readwrite("add_bonds",&ost::mol::mm::Settings::add_bonds)
+ .def_readwrite("add_angles",&ost::mol::mm::Settings::add_angles)
+ .def_readwrite("add_dihedrals",&ost::mol::mm::Settings::add_dihedrals)
+ .def_readwrite("add_impropers",&ost::mol::mm::Settings::add_impropers)
+ .def_readwrite("add_cmaps",&ost::mol::mm::Settings::add_cmaps)
+ .def_readwrite("add_exclusions",&ost::mol::mm::Settings::add_exclusions)
+ .def_readwrite("add_nonbonded",&ost::mol::mm::Settings::add_nonbonded)
+ .def_readwrite("add_gbsa",&ost::mol::mm::Settings::add_gbsa)
+ .def_readwrite("constrain_hbonds",&ost::mol::mm::Settings::constrain_hbonds)
+ .def_readwrite("constrain_bonds",&ost::mol::mm::Settings::constrain_bonds)
+ .def_readwrite("rigid_water",&ost::mol::mm::Settings::rigid_water)
+ .def_readwrite("strict_interactions",&ost::mol::mm::Settings::strict_interactions)
+ .def_readwrite("ideal_bond_length_constraints",&ost::mol::mm::Settings::ideal_bond_length_constraints)
+ .def_readwrite("fix_heavy_atoms",&ost::mol::mm::Settings::fix_heavy_atoms)
+ .def_readwrite("kill_electrostatics",&ost::mol::mm::Settings::kill_electrostatics)
+ .def_readwrite("generate_disulfid_bonds",&ost::mol::mm::Settings::generate_disulfid_bonds)
+ .def_readwrite("nonbonded_method",&ost::mol::mm::Settings::nonbonded_method)
+ .def_readwrite("nonbonded_cutoff",&ost::mol::mm::Settings::nonbonded_cutoff)
+ .def_readwrite("remove_cmm_motion",&ost::mol::mm::Settings::remove_cmm_motion)
+ .def_readwrite("periodic_box_extents",&ost::mol::mm::Settings::periodic_box_extents)
+ .def_readwrite("init_temperature",&ost::mol::mm::Settings::init_temperature)
+ .def_readwrite("forcefield",&ost::mol::mm::Settings::forcefield)
+ .def_readwrite("termini_exceptions",&ost::mol::mm::Settings::termini_exceptions)
+ .def_readwrite("platform",&ost::mol::mm::Settings::platform)
+ .def_readwrite("add_thermostat",&ost::mol::mm::Settings::add_thermostat)
+ .def_readwrite("thermostat_temperature",&ost::mol::mm::Settings::thermostat_temperature)
+ .def_readwrite("thermostat_collision_frequency",&ost::mol::mm::Settings::thermostat_collision_frequency)
+ .def_readwrite("add_barostat",&ost::mol::mm::Settings::add_barostat)
+ .def_readwrite("barostat_temperature",&ost::mol::mm::Settings::barostat_temperature)
+ .def_readwrite("barostat_pressure",&ost::mol::mm::Settings::barostat_pressure)
+ .def_readwrite("barostat_frequency",&ost::mol::mm::Settings::barostat_frequency)
+ .def_readwrite("integrator",&ost::mol::mm::Settings::integrator)
+ .def_readwrite("solvent_dielectric",&ost::mol::mm::Settings::solvent_dielectric)
+ .def_readwrite("solute_dielectric",&ost::mol::mm::Settings::solute_dielectric)
+ .def_readwrite("reaction_field_dielectric",&ost::mol::mm::Settings::reaction_field_dielectric)
+ .def_readwrite("use_dispersion_correction",&ost::mol::mm::Settings::use_dispersion_correction)
+ .def_readwrite("keep_ff_specific_naming",&ost::mol::mm::Settings::keep_ff_specific_naming)
+ .def_readwrite("openmm_plugin_directory",&ost::mol::mm::Settings::openmm_plugin_directory)
+ .def_readwrite("custom_plugin_directory",&ost::mol::mm::Settings::custom_plugin_directory)
;
- boost::python::register_ptr_to_python<ost::mol::mm::MMSettingsPtr>();
+ boost::python::register_ptr_to_python<ost::mol::mm::SettingsPtr>();
boost::python::register_ptr_to_python<ost::mol::mm::TerminiExceptionsPtr>();
}
diff --git a/modules/mol/mm/pymod/export_simulation.cc b/modules/mol/mm/pymod/export_simulation.cc
index edeee9faaeda79943ca29036233285bb087f5019..9b7a6f93e9be1a09c7442a822e4fcb310019eb70 100644
--- a/modules/mol/mm/pymod/export_simulation.cc
+++ b/modules/mol/mm/pymod/export_simulation.cc
@@ -48,8 +48,8 @@ void export_Simulation()
{
class_<ost::mol::mm::Simulation>("Simulation",no_init)
- .def(init<const ost::mol::EntityHandle, const ost::mol::mm::MMSettingsPtr>())
- .def(init<const ost::mol::mm::TopologyPtr,const ost::mol::EntityHandle&,const ost::mol::mm::MMSettingsPtr>())
+ .def(init<const ost::mol::EntityHandle, const ost::mol::mm::SettingsPtr>())
+ .def(init<const ost::mol::mm::TopologyPtr,const ost::mol::EntityHandle&,const ost::mol::mm::SettingsPtr>())
.def("Save",&ost::mol::mm::Simulation::Save)
.def("Load",&ost::mol::mm::Simulation::Load).staticmethod("Load")
.def("Steps",&ost::mol::mm::Simulation::Steps)
diff --git a/modules/mol/mm/pymod/wrap_mol_mm.cc b/modules/mol/mm/pymod/wrap_mol_mm.cc
index 739b8ad50124db27ac6c58554856ead84a9fe538..9ddcec57e166bd34b2a88af8c10ede960de50d3e 100644
--- a/modules/mol/mm/pymod/wrap_mol_mm.cc
+++ b/modules/mol/mm/pymod/wrap_mol_mm.cc
@@ -4,12 +4,12 @@
using namespace boost::python;
-void export_MMSettings();
+void export_Settings();
void export_Simulation();
void export_OpenMM();
void export_Observers();
void export_GromacsReader();
-void export_MMInteraction();
+void export_Interaction();
void export_Buildingblock();
void export_Forcefield();
void export_BlockModifiers();
@@ -20,12 +20,12 @@ void export_Modeller();
BOOST_PYTHON_MODULE(_ost_mol_mm)
{
export_Forcefield();
- export_MMSettings();
+ export_Settings();
export_Simulation();
export_OpenMM();
export_Observers();
export_GromacsReader();
- export_MMInteraction();
+ export_Interaction();
export_Buildingblock();
export_BlockModifiers();
export_Topology();
diff --git a/modules/mol/mm/src/CMakeLists.txt b/modules/mol/mm/src/CMakeLists.txt
index 3c95ac8eb1b8ab1f9482bcce0f9cdbcd83d8b00e..6fc560ef2a2f31e148a22e978c0845972b795391 100644
--- a/modules/mol/mm/src/CMakeLists.txt
+++ b/modules/mol/mm/src/CMakeLists.txt
@@ -5,11 +5,11 @@ set(OST_MOL_MM_HEADERS
block_modifiers.hh
gromacs_block_modifiers.hh
heuristic_block_modifiers.hh
- mm_interaction.hh
- mm_settings.hh
+ interaction.hh
+ settings.hh
simulation.hh
- mm_modeller.hh
- mm_observer.hh
+ modeller.hh
+ observer.hh
state_extractor.hh
system_creator.hh
topology_creator.hh
@@ -25,11 +25,11 @@ set(OST_MOL_MM_SOURCES
buildingblock.cc
gromacs_block_modifiers.cc
heuristic_block_modifiers.cc
- mm_interaction.cc
+ interaction.cc
simulation.cc
- mm_modeller.cc
+ modeller.cc
state_extractor.cc
- mm_observer.cc
+ observer.cc
system_creator.cc
topology_creator.cc
topology.cc
diff --git a/modules/mol/mm/src/buildingblock.cc b/modules/mol/mm/src/buildingblock.cc
index 3d6a8b2b1b2cecc5d08784fd48dfd989928a1685..ffb5e662e858d2bb609cde7d5958994302715d84 100644
--- a/modules/mol/mm/src/buildingblock.cc
+++ b/modules/mol/mm/src/buildingblock.cc
@@ -13,41 +13,41 @@ BuildingBlock::BuildingBlock(const BuildingBlock& block){
//There would be to danger to mess around with an interaction,
//that is associated with another building block.
- std::vector<MMInteractionPtr> bonds = block.GetBonds();
- std::vector<MMInteractionPtr> angles = block.GetAngles();
- std::vector<MMInteractionPtr> dihedrals = block.GetDihedrals();
- std::vector<MMInteractionPtr> impropers = block.GetImpropers();
- std::vector<MMInteractionPtr> exclusions = block.GetExclusions();
- std::vector<MMInteractionPtr> cmaps = block.GetCMaps();
- std::vector<MMInteractionPtr> constraints = block.GetConstraints();
-
- for(std::vector<MMInteractionPtr>::iterator i = bonds.begin();
+ std::vector<InteractionPtr> bonds = block.GetBonds();
+ std::vector<InteractionPtr> angles = block.GetAngles();
+ std::vector<InteractionPtr> dihedrals = block.GetDihedrals();
+ std::vector<InteractionPtr> impropers = block.GetImpropers();
+ std::vector<InteractionPtr> exclusions = block.GetExclusions();
+ std::vector<InteractionPtr> cmaps = block.GetCMaps();
+ std::vector<InteractionPtr> constraints = block.GetConstraints();
+
+ for(std::vector<InteractionPtr>::iterator i = bonds.begin();
i != bonds.end(); ++i){
- bonds_.push_back(MMInteractionPtr(new MMInteraction(**i)));
+ bonds_.push_back(InteractionPtr(new Interaction(**i)));
}
- for(std::vector<MMInteractionPtr>::iterator i = angles.begin();
+ for(std::vector<InteractionPtr>::iterator i = angles.begin();
i != angles.end(); ++i){
- angles_.push_back(MMInteractionPtr(new MMInteraction(**i)));
+ angles_.push_back(InteractionPtr(new Interaction(**i)));
}
- for(std::vector<MMInteractionPtr>::iterator i = dihedrals.begin();
+ for(std::vector<InteractionPtr>::iterator i = dihedrals.begin();
i != dihedrals.end(); ++i){
- dihedrals_.push_back(MMInteractionPtr(new MMInteraction(**i)));
+ dihedrals_.push_back(InteractionPtr(new Interaction(**i)));
}
- for(std::vector<MMInteractionPtr>::iterator i = impropers.begin();
+ for(std::vector<InteractionPtr>::iterator i = impropers.begin();
i != impropers.end(); ++i){
- impropers_.push_back(MMInteractionPtr(new MMInteraction(**i)));
+ impropers_.push_back(InteractionPtr(new Interaction(**i)));
}
- for(std::vector<MMInteractionPtr>::iterator i = exclusions.begin();
+ for(std::vector<InteractionPtr>::iterator i = exclusions.begin();
i != exclusions.end(); ++i){
- exclusions_.push_back(MMInteractionPtr(new MMInteraction(**i)));
+ exclusions_.push_back(InteractionPtr(new Interaction(**i)));
}
- for(std::vector<MMInteractionPtr>::iterator i = cmaps.begin();
+ for(std::vector<InteractionPtr>::iterator i = cmaps.begin();
i != cmaps.end(); ++i){
- cmaps_.push_back(MMInteractionPtr(new MMInteraction(**i)));
+ cmaps_.push_back(InteractionPtr(new Interaction(**i)));
}
- for(std::vector<MMInteractionPtr>::iterator i = constraints.begin();
+ for(std::vector<InteractionPtr>::iterator i = constraints.begin();
i != constraints.end(); ++i){
- constraints_.push_back(MMInteractionPtr(new MMInteraction(**i)));
+ constraints_.push_back(InteractionPtr(new Interaction(**i)));
}
}
@@ -87,7 +87,7 @@ bool BuildingBlock::Match(const ost::mol::ResidueHandle& handle, bool match_conn
//check connectivity by extracting all unique bonds from handle,
//also bonds to other residues.
std::set<std::pair<String,String> > raw_bonds_handle;
- std::vector<MMInteractionPtr> bonds_handle;
+ std::vector<InteractionPtr> bonds_handle;
ost::mol::AtomHandleList atom_list = handle.GetAtomList();
ost::mol::ResidueHandle prev = handle.GetPrev();
ost::mol::ResidueHandle next = handle.GetNext();
@@ -130,7 +130,7 @@ bool BuildingBlock::Match(const ost::mol::ResidueHandle& handle, bool match_conn
for(std::set<std::pair<String,String> >::iterator i = raw_bonds_handle.begin();
i != raw_bonds_handle.end(); ++i){
- MMInteractionPtr p(new MMInteraction(HarmonicBond));
+ InteractionPtr p(new Interaction(HarmonicBond));
names[0] = i->first;
names[1] = i->second;
p->SetNames(names);
@@ -139,10 +139,10 @@ bool BuildingBlock::Match(const ost::mol::ResidueHandle& handle, bool match_conn
bool found;
//let's first check for bonds
- for(std::vector<MMInteractionPtr>::const_iterator i = bonds_.begin();
+ for(std::vector<InteractionPtr>::const_iterator i = bonds_.begin();
i!=bonds_.end(); ++i){
found = false;
- for(std::vector<MMInteractionPtr>::iterator j = bonds_handle.begin();
+ for(std::vector<InteractionPtr>::iterator j = bonds_handle.begin();
j != bonds_handle.end(); ++j){
if((*j)->MatchNames((*i)->GetNames())){
found = true;
@@ -162,9 +162,9 @@ bool BuildingBlock::Match(const ost::mol::ResidueHandle& handle, bool match_conn
}
//If there is a distance constraint matching a remaining raw bond, we also
//remove it from raw bonds
- for(std::vector<MMInteractionPtr>::const_iterator i = constraints_.begin();
+ for(std::vector<InteractionPtr>::const_iterator i = constraints_.begin();
i != constraints_.end(); ++i){
- for(std::vector<MMInteractionPtr>::iterator j = bonds_handle.begin();
+ for(std::vector<InteractionPtr>::iterator j = bonds_handle.begin();
j != bonds_handle.end(); ++j){
if((*j)->MatchNames((*i)->GetNames())){
std::vector<String> names = (*j)->GetNames();
@@ -202,7 +202,7 @@ void BuildingBlock::Connect(ost::mol::ResidueHandle& handle, ost::mol::XCSEditor
String name1, name2;
- for(std::vector<MMInteractionPtr>::iterator i = bonds_.begin();
+ for(std::vector<InteractionPtr>::iterator i = bonds_.begin();
i != bonds_.end(); ++i){
names = (*i)->GetNames();
@@ -267,7 +267,7 @@ Real BuildingBlock::GetMass(const String& name) const{
}
-void BuildingBlock::AddBond(MMInteractionPtr p, bool replace_existing){
+void BuildingBlock::AddBond(InteractionPtr p, bool replace_existing){
this->CheckInteractionToAdd(p);
if(replace_existing){
std::vector<String> names = p->GetNames();
@@ -281,7 +281,7 @@ void BuildingBlock::AddBond(MMInteractionPtr p, bool replace_existing){
bonds_.push_back(p);
}
-void BuildingBlock::AddAngle(MMInteractionPtr p, bool replace_existing){
+void BuildingBlock::AddAngle(InteractionPtr p, bool replace_existing){
this->CheckInteractionToAdd(p);
if(replace_existing){
std::vector<String> names = p->GetNames();
@@ -295,7 +295,7 @@ void BuildingBlock::AddAngle(MMInteractionPtr p, bool replace_existing){
angles_.push_back(p);
}
-void BuildingBlock::AddDihedral(MMInteractionPtr p, bool replace_existing){
+void BuildingBlock::AddDihedral(InteractionPtr p, bool replace_existing){
this->CheckInteractionToAdd(p);
if(replace_existing){
std::vector<String> names = p->GetNames();
@@ -309,7 +309,7 @@ void BuildingBlock::AddDihedral(MMInteractionPtr p, bool replace_existing){
dihedrals_.push_back(p);
}
-void BuildingBlock::AddImproper(MMInteractionPtr p, bool replace_existing){
+void BuildingBlock::AddImproper(InteractionPtr p, bool replace_existing){
this->CheckInteractionToAdd(p);
if(replace_existing){
std::vector<String> names = p->GetNames();
@@ -323,7 +323,7 @@ void BuildingBlock::AddImproper(MMInteractionPtr p, bool replace_existing){
impropers_.push_back(p);
}
-void BuildingBlock::AddExclusion(MMInteractionPtr p, bool replace_existing){
+void BuildingBlock::AddExclusion(InteractionPtr p, bool replace_existing){
this->CheckInteractionToAdd(p);
if(replace_existing){
std::vector<String> names = p->GetNames();
@@ -337,7 +337,7 @@ void BuildingBlock::AddExclusion(MMInteractionPtr p, bool replace_existing){
exclusions_.push_back(p);
}
-void BuildingBlock::AddCMap(MMInteractionPtr p, bool replace_existing){
+void BuildingBlock::AddCMap(InteractionPtr p, bool replace_existing){
this->CheckInteractionToAdd(p);
if(replace_existing){
std::vector<String> names = p->GetNames();
@@ -351,7 +351,7 @@ void BuildingBlock::AddCMap(MMInteractionPtr p, bool replace_existing){
cmaps_.push_back(p);
}
-void BuildingBlock::AddConstraint(MMInteractionPtr p, bool replace_existing){
+void BuildingBlock::AddConstraint(InteractionPtr p, bool replace_existing){
this->CheckInteractionToAdd(p);
if(replace_existing){
std::vector<String> names = p->GetNames();
@@ -436,32 +436,32 @@ void BuildingBlock::ReplaceAtom(const String& name,const String& new_name,
//nothing will happen, if the atom of interest is not part of
//that interaction.
- for(std::vector<MMInteractionPtr>::iterator i = bonds_.begin();
+ for(std::vector<InteractionPtr>::iterator i = bonds_.begin();
i!=bonds_.end(); ++i){
(*i)->ReplaceAtom(name, new_name, new_type);
}
- for(std::vector<MMInteractionPtr>::iterator i = angles_.begin();
+ for(std::vector<InteractionPtr>::iterator i = angles_.begin();
i!=angles_.end(); ++i){
(*i)->ReplaceAtom(name, new_name, new_type);
}
- for(std::vector<MMInteractionPtr>::iterator i = dihedrals_.begin();
+ for(std::vector<InteractionPtr>::iterator i = dihedrals_.begin();
i!=dihedrals_.end(); ++i){
(*i)->ReplaceAtom(name, new_name, new_type);
}
- for(std::vector<MMInteractionPtr>::iterator i = impropers_.begin();
+ for(std::vector<InteractionPtr>::iterator i = impropers_.begin();
i!=impropers_.end(); ++i){
(*i)->ReplaceAtom(name, new_name, new_type);
}
- for(std::vector<MMInteractionPtr>::iterator i = exclusions_.begin();
+ for(std::vector<InteractionPtr>::iterator i = exclusions_.begin();
i!=exclusions_.end(); ++i){
(*i)->ReplaceAtom(name, new_name, new_type);
}
- for(std::vector<MMInteractionPtr>::iterator i = cmaps_.begin();
+ for(std::vector<InteractionPtr>::iterator i = cmaps_.begin();
i!=cmaps_.end(); ++i){
(*i)->ReplaceAtom(name, new_name, new_type);
}
@@ -678,7 +678,7 @@ void BuildingBlock::RemoveInteractionsToNext(){
}
}
-void BuildingBlock::CheckInteractionToAdd(MMInteractionPtr p) const{
+void BuildingBlock::CheckInteractionToAdd(InteractionPtr p) const{
if(p->GetNames().empty()){
throw ost::Error("Expect interaction to have names properly set!");
}
diff --git a/modules/mol/mm/src/buildingblock.hh b/modules/mol/mm/src/buildingblock.hh
index b313255c6476c668a376a3f93cae9cd6bbca8785..9f41ee0158c4fc7e024ae4e5b18b55de0cda93e2 100644
--- a/modules/mol/mm/src/buildingblock.hh
+++ b/modules/mol/mm/src/buildingblock.hh
@@ -7,7 +7,7 @@
#include <boost/shared_ptr.hpp>
-#include <ost/mol/mm/mm_interaction.hh>
+#include <ost/mol/mm/interaction.hh>
#include <ost/message.hh>
#include <ost/mol/bond_handle.hh>
#include <ost/mol/residue_handle.hh>
@@ -49,37 +49,37 @@ public:
Real GetMass(const String& name) const;
- std::vector<MMInteractionPtr> GetBonds() const { return bonds_; }
+ std::vector<InteractionPtr> GetBonds() const { return bonds_; }
- std::vector<MMInteractionPtr> GetAngles() const { return angles_; }
+ std::vector<InteractionPtr> GetAngles() const { return angles_; }
- std::vector<MMInteractionPtr> GetDihedrals() const { return dihedrals_; }
+ std::vector<InteractionPtr> GetDihedrals() const { return dihedrals_; }
- std::vector<MMInteractionPtr> GetImpropers() const { return impropers_; }
+ std::vector<InteractionPtr> GetImpropers() const { return impropers_; }
- std::vector<MMInteractionPtr> GetCMaps() const { return cmaps_; }
+ std::vector<InteractionPtr> GetCMaps() const { return cmaps_; }
- std::vector<MMInteractionPtr> GetExclusions() const { return exclusions_; }
+ std::vector<InteractionPtr> GetExclusions() const { return exclusions_; }
- std::vector<MMInteractionPtr> GetConstraints() const { return constraints_;}
+ std::vector<InteractionPtr> GetConstraints() const { return constraints_;}
//Add data to building block
void AddAtom(const String& name, const String& type, Real charge, Real mass = std::numeric_limits<Real>::quiet_NaN());
- void AddBond(MMInteractionPtr p, bool replace_existing = false);
+ void AddBond(InteractionPtr p, bool replace_existing = false);
- void AddAngle(MMInteractionPtr p, bool replace_existing = false);
+ void AddAngle(InteractionPtr p, bool replace_existing = false);
- void AddDihedral(MMInteractionPtr p, bool replace_existing = false);
+ void AddDihedral(InteractionPtr p, bool replace_existing = false);
- void AddImproper(MMInteractionPtr p, bool replace_existing = false);
+ void AddImproper(InteractionPtr p, bool replace_existing = false);
- void AddExclusion(MMInteractionPtr p, bool replace_existing = false);
+ void AddExclusion(InteractionPtr p, bool replace_existing = false);
- void AddCMap(MMInteractionPtr p, bool replace_existing = false);
+ void AddCMap(InteractionPtr p, bool replace_existing = false);
- void AddConstraint(MMInteractionPtr p, bool replace_existing = false);
+ void AddConstraint(InteractionPtr p, bool replace_existing = false);
//modifiers
@@ -136,7 +136,7 @@ public:
int func_type;
if(ds.IsSource()){
ds & func_type;
- bonds_.push_back(MMInteractionPtr(new MMInteraction(FuncType(func_type))));
+ bonds_.push_back(InteractionPtr(new Interaction(FuncType(func_type))));
}
else{
func_type = bonds_[i]->GetFuncType();
@@ -149,7 +149,7 @@ public:
int func_type;
if(ds.IsSource()){
ds & func_type;
- angles_.push_back(MMInteractionPtr(new MMInteraction(FuncType(func_type))));
+ angles_.push_back(InteractionPtr(new Interaction(FuncType(func_type))));
}
else{
func_type = angles_[i]->GetFuncType();
@@ -162,7 +162,7 @@ public:
int func_type;
if(ds.IsSource()){
ds & func_type;
- dihedrals_.push_back(MMInteractionPtr(new MMInteraction(FuncType(func_type))));
+ dihedrals_.push_back(InteractionPtr(new Interaction(FuncType(func_type))));
}
else{
func_type = dihedrals_[i]->GetFuncType();
@@ -175,7 +175,7 @@ public:
int func_type;
if(ds.IsSource()){
ds & func_type;
- impropers_.push_back(MMInteractionPtr(new MMInteraction(FuncType(func_type))));
+ impropers_.push_back(InteractionPtr(new Interaction(FuncType(func_type))));
}
else{
func_type = impropers_[i]->GetFuncType();
@@ -188,7 +188,7 @@ public:
int func_type;
if(ds.IsSource()){
ds & func_type;
- exclusions_.push_back(MMInteractionPtr(new MMInteraction(FuncType(func_type))));
+ exclusions_.push_back(InteractionPtr(new Interaction(FuncType(func_type))));
}
else{
func_type = exclusions_[i]->GetFuncType();
@@ -201,7 +201,7 @@ public:
int func_type;
if(ds.IsSource()){
ds & func_type;
- cmaps_.push_back(MMInteractionPtr(new MMInteraction(FuncType(func_type))));
+ cmaps_.push_back(InteractionPtr(new Interaction(FuncType(func_type))));
}
else{
func_type = cmaps_[i]->GetFuncType();
@@ -214,7 +214,7 @@ public:
int func_type;
if(ds.IsSource()){
ds & func_type;
- constraints_.push_back(MMInteractionPtr(new MMInteraction(FuncType(func_type))));
+ constraints_.push_back(InteractionPtr(new Interaction(FuncType(func_type))));
}
else{
func_type = constraints_[i]->GetFuncType();
@@ -228,19 +228,19 @@ public:
private:
int GetAtomIndex(const String& atom_name) const;
- void CheckInteractionToAdd(MMInteractionPtr p) const;
+ void CheckInteractionToAdd(InteractionPtr p) const;
std::vector<String> atoms_;
std::vector<String> types_;
std::vector<Real> charges_;
std::vector<Real> masses_;
- std::vector<MMInteractionPtr> bonds_;
- std::vector<MMInteractionPtr> angles_;
- std::vector<MMInteractionPtr> dihedrals_;
- std::vector<MMInteractionPtr> impropers_;
- std::vector<MMInteractionPtr> exclusions_;
- std::vector<MMInteractionPtr> cmaps_;
- std::vector<MMInteractionPtr> constraints_;
+ std::vector<InteractionPtr> bonds_;
+ std::vector<InteractionPtr> angles_;
+ std::vector<InteractionPtr> dihedrals_;
+ std::vector<InteractionPtr> impropers_;
+ std::vector<InteractionPtr> exclusions_;
+ std::vector<InteractionPtr> cmaps_;
+ std::vector<InteractionPtr> constraints_;
};
}}}
diff --git a/modules/mol/mm/src/forcefield.cc b/modules/mol/mm/src/forcefield.cc
index 666de94176062ee9737befc05d2e0db0eee9d0af..3a4b15aa4fb07ddcba4a12b5d5eb389559fb585e 100644
--- a/modules/mol/mm/src/forcefield.cc
+++ b/modules/mol/mm/src/forcefield.cc
@@ -53,7 +53,7 @@ ForcefieldPtr Forcefield::Load(const String& filename){
ds & num_bonds;
for(int i = 0; i < num_bonds; ++i){
ds & func_type;
- MMInteractionPtr p(new MMInteraction(FuncType(func_type)));
+ InteractionPtr p(new Interaction(FuncType(func_type)));
ds & *p;
ff_p->AddBond(p);
}
@@ -62,7 +62,7 @@ ForcefieldPtr Forcefield::Load(const String& filename){
ds & num_angles;
for(int i = 0; i < num_angles; ++i){
ds & func_type;
- MMInteractionPtr p(new MMInteraction(FuncType(func_type)));
+ InteractionPtr p(new Interaction(FuncType(func_type)));
ds & *p;
ff_p->AddAngle(p);
}
@@ -71,7 +71,7 @@ ForcefieldPtr Forcefield::Load(const String& filename){
ds & num_lj_pairs;
for(int i = 0; i < num_lj_pairs; ++i){
ds & func_type;
- MMInteractionPtr p(new MMInteraction(FuncType(func_type)));
+ InteractionPtr p(new Interaction(FuncType(func_type)));
ds & *p;
ff_p->AddLJPair(p);
}
@@ -80,7 +80,7 @@ ForcefieldPtr Forcefield::Load(const String& filename){
ds & num_constraints;
for(int i = 0; i < num_constraints; ++i){
ds & func_type;
- MMInteractionPtr p(new MMInteraction(FuncType(func_type)));
+ InteractionPtr p(new Interaction(FuncType(func_type)));
ds & *p;
ff_p->AddConstraint(p);
}
@@ -89,7 +89,7 @@ ForcefieldPtr Forcefield::Load(const String& filename){
ds & num_cmaps;
for(int i = 0; i < num_cmaps; ++i){
ds & func_type;
- MMInteractionPtr p(new MMInteraction(FuncType(func_type)));
+ InteractionPtr p(new Interaction(FuncType(func_type)));
ds & *p;
ff_p->AddCMap(p);
}
@@ -98,7 +98,7 @@ ForcefieldPtr Forcefield::Load(const String& filename){
ds & num_genborn;
for(int i = 0; i < num_genborn; ++i){
ds & func_type;
- MMInteractionPtr p(new MMInteraction(FuncType(func_type)));
+ InteractionPtr p(new Interaction(FuncType(func_type)));
ds & *p;
ff_p->AddImplicitGenborn(p);
}
@@ -107,7 +107,7 @@ ForcefieldPtr Forcefield::Load(const String& filename){
ds & num_ljs;
for(int i = 0; i < num_ljs; ++i){
ds & func_type;
- MMInteractionPtr p(new MMInteraction(FuncType(func_type)));
+ InteractionPtr p(new Interaction(FuncType(func_type)));
ds & *p;
ff_p->AddLJ(p);
}
@@ -120,7 +120,7 @@ ForcefieldPtr Forcefield::Load(const String& filename){
ds & temp_num;
for(int j = 0; j < temp_num; ++j){
ds & func_type;
- MMInteractionPtr p(new MMInteraction(FuncType(func_type)));
+ InteractionPtr p(new Interaction(FuncType(func_type)));
ds & *p;
ff_p->AddDihedral(p);
}
@@ -132,7 +132,7 @@ ForcefieldPtr Forcefield::Load(const String& filename){
ds & temp_num;
for(int j = 0; j < temp_num; ++j){
ds & func_type;
- MMInteractionPtr p(new MMInteraction(FuncType(func_type)));
+ InteractionPtr p(new Interaction(FuncType(func_type)));
ds & *p;
ff_p->AddImproper(p);
}
@@ -252,7 +252,7 @@ void Forcefield::Save(const String& filename){
int func_type;
int num_bonds = bonds_.size();
ds & num_bonds;
- for(boost::unordered_map<String,MMInteractionPtr>::iterator i = bonds_.begin();
+ for(boost::unordered_map<String,InteractionPtr>::iterator i = bonds_.begin();
i != bonds_.end(); ++i){
func_type = int(i->second->GetFuncType());
ds & func_type;
@@ -261,7 +261,7 @@ void Forcefield::Save(const String& filename){
int num_angles = angles_.size();
ds & num_angles;
- for(boost::unordered_map<String,MMInteractionPtr>::iterator i = angles_.begin();
+ for(boost::unordered_map<String,InteractionPtr>::iterator i = angles_.begin();
i != angles_.end(); ++i){
func_type = int(i->second->GetFuncType());
ds & func_type;
@@ -270,7 +270,7 @@ void Forcefield::Save(const String& filename){
int num_lj_pairs = lj_14_pairs_.size();
ds & num_lj_pairs;
- for(boost::unordered_map<String,MMInteractionPtr>::iterator i = lj_14_pairs_.begin();
+ for(boost::unordered_map<String,InteractionPtr>::iterator i = lj_14_pairs_.begin();
i != lj_14_pairs_.end(); ++i){
func_type = int(i->second->GetFuncType());
ds & func_type;
@@ -279,7 +279,7 @@ void Forcefield::Save(const String& filename){
int num_constraints = constraints_.size();
ds & num_constraints;
- for(boost::unordered_map<String,MMInteractionPtr>::iterator i = constraints_.begin();
+ for(boost::unordered_map<String,InteractionPtr>::iterator i = constraints_.begin();
i != constraints_.end(); ++i){
func_type = int(i->second->GetFuncType());
ds & func_type;
@@ -288,7 +288,7 @@ void Forcefield::Save(const String& filename){
int num_cmaps = cmaps_.size();
ds & num_cmaps;
- for(boost::unordered_map<String,MMInteractionPtr>::iterator i = cmaps_.begin();
+ for(boost::unordered_map<String,InteractionPtr>::iterator i = cmaps_.begin();
i != cmaps_.end(); ++i){
func_type = int(i->second->GetFuncType());
ds & func_type;
@@ -297,7 +297,7 @@ void Forcefield::Save(const String& filename){
int num_genborn = implicit_genborn_.size();
ds & num_genborn;
- for(boost::unordered_map<String,MMInteractionPtr>::iterator i = implicit_genborn_.begin();
+ for(boost::unordered_map<String,InteractionPtr>::iterator i = implicit_genborn_.begin();
i != implicit_genborn_.end(); ++i){
func_type = int(i->second->GetFuncType());
ds & func_type;
@@ -306,7 +306,7 @@ void Forcefield::Save(const String& filename){
int num_ljs = ljs_.size();
ds & num_ljs;
- for(boost::unordered_map<String,MMInteractionPtr>::iterator i = ljs_.begin();
+ for(boost::unordered_map<String,InteractionPtr>::iterator i = ljs_.begin();
i != ljs_.end(); ++i){
func_type = int(i->second->GetFuncType());
ds & func_type;
@@ -316,11 +316,11 @@ void Forcefield::Save(const String& filename){
int num_dihedrals = dihedrals_.size();
int vector_size;
ds & num_dihedrals;
- for(boost::unordered_map<String,std::vector<MMInteractionPtr> >::iterator i = dihedrals_.begin();
+ for(boost::unordered_map<String,std::vector<InteractionPtr> >::iterator i = dihedrals_.begin();
i != dihedrals_.end(); ++i){
vector_size = i->second.size();
ds & vector_size;
- for(std::vector<MMInteractionPtr>::iterator j = i->second.begin();
+ for(std::vector<InteractionPtr>::iterator j = i->second.begin();
j != i->second.end(); ++j){
func_type = int((*j)->GetFuncType());
ds & func_type;
@@ -330,11 +330,11 @@ void Forcefield::Save(const String& filename){
int num_impropers = improper_dihedrals_.size();
ds & num_impropers;
- for(boost::unordered_map<String,std::vector<MMInteractionPtr> >::iterator i = improper_dihedrals_.begin();
+ for(boost::unordered_map<String,std::vector<InteractionPtr> >::iterator i = improper_dihedrals_.begin();
i != improper_dihedrals_.end(); ++i){
vector_size = i->second.size();
ds & vector_size;
- for(std::vector<MMInteractionPtr>::iterator j = i->second.begin();
+ for(std::vector<InteractionPtr>::iterator j = i->second.begin();
j != i->second.end(); ++j){
func_type = int((*j)->GetFuncType());
ds & func_type;
@@ -456,29 +456,29 @@ BlockModifierPtr Forcefield::GetCTerModifier(const String& res_name, const Strin
return this->GetBlockModifier(temp);
}
-MMInteractionPtr Forcefield::GetBond(const String& type1, const String& type2) const{
+InteractionPtr Forcefield::GetBond(const String& type1, const String& type2) const{
std::vector<String> types;
types.push_back(type1);
types.push_back(type2);
- boost::unordered_map<String,MMInteractionPtr>::const_iterator i =
+ boost::unordered_map<String,InteractionPtr>::const_iterator i =
bonds_.find(this->AtomTypesToKeyword(types));
if(i != bonds_.end()) return i->second;
throw ost::Error("Forcefield does not contain bond for requested atom types!");
}
-MMInteractionPtr Forcefield::GetAngle(const String& type1, const String& type2,
+InteractionPtr Forcefield::GetAngle(const String& type1, const String& type2,
const String& type3) const{
std::vector<String> types;
types.push_back(type1);
types.push_back(type2);
types.push_back(type3);
- boost::unordered_map<String,MMInteractionPtr>::const_iterator i =
+ boost::unordered_map<String,InteractionPtr>::const_iterator i =
angles_.find(this->AtomTypesToKeyword(types));
if(i != angles_.end()) return i->second;
throw ost::Error("Forcefield does not contain angle for requested atom types!");
}
-std::vector<MMInteractionPtr> Forcefield::GetDihedrals(const String& type1,
+std::vector<InteractionPtr> Forcefield::GetDihedrals(const String& type1,
const String& type2,
const String& type3,
const String& type4) const{
@@ -488,20 +488,20 @@ std::vector<MMInteractionPtr> Forcefield::GetDihedrals(const String& type1,
types.push_back(type3);
types.push_back(type4);
- boost::unordered_map<String,std::vector<MMInteractionPtr> >::const_iterator i =
+ boost::unordered_map<String,std::vector<InteractionPtr> >::const_iterator i =
dihedrals_.find(this->AtomTypesToKeyword(types));
if(i != dihedrals_.end()) return i->second;
//if we reach this point, we have to look for all dihedrals with wildcards...
- std::vector<MMInteractionPtr> dihedrals;
+ std::vector<InteractionPtr> dihedrals;
std::vector<String> types_with_wildcards;
//lets first check single wildcards
for(int i = 0; i < 4; ++i){
types_with_wildcards = types;
types_with_wildcards[i] = "X";
- boost::unordered_map<String,std::vector<MMInteractionPtr> >::const_iterator j =
+ boost::unordered_map<String,std::vector<InteractionPtr> >::const_iterator j =
dihedrals_.find(this->AtomTypesToKeyword(types_with_wildcards));
if(j != dihedrals_.end()) dihedrals.insert(dihedrals.end(),j->second.begin(),j->second.end());
}
@@ -512,7 +512,7 @@ std::vector<MMInteractionPtr> Forcefield::GetDihedrals(const String& type1,
types_with_wildcards = types;
types_with_wildcards[i] = "X";
types_with_wildcards[j] = "X";
- boost::unordered_map<String,std::vector<MMInteractionPtr> >::const_iterator k =
+ boost::unordered_map<String,std::vector<InteractionPtr> >::const_iterator k =
dihedrals_.find(this->AtomTypesToKeyword(types_with_wildcards));
if(k != dihedrals_.end()) dihedrals.insert(dihedrals.end(),k->second.begin(),k->second.end());
}
@@ -526,7 +526,7 @@ std::vector<MMInteractionPtr> Forcefield::GetDihedrals(const String& type1,
for(int i = 0; i < 4; ++i){
types_with_wildcards = all_wildcards;
types_with_wildcards[i] = types[i];
- boost::unordered_map<String,std::vector<MMInteractionPtr> >::const_iterator j =
+ boost::unordered_map<String,std::vector<InteractionPtr> >::const_iterator j =
dihedrals_.find(this->AtomTypesToKeyword(types_with_wildcards));
if(j != dihedrals_.end()) dihedrals.insert(dihedrals.end(),j->second.begin(),j->second.end());
}
@@ -535,7 +535,7 @@ std::vector<MMInteractionPtr> Forcefield::GetDihedrals(const String& type1,
throw ost::Error("Forcefield does not contain any dihedrals for requested atom types!");
}
-std::vector<MMInteractionPtr> Forcefield::GetImpropers(const String& type1,
+std::vector<InteractionPtr> Forcefield::GetImpropers(const String& type1,
const String& type2,
const String& type3,
const String& type4) const{
@@ -545,20 +545,20 @@ std::vector<MMInteractionPtr> Forcefield::GetImpropers(const String& type1,
types.push_back(type3);
types.push_back(type4);
- boost::unordered_map<String,std::vector<MMInteractionPtr> >::const_iterator i =
+ boost::unordered_map<String,std::vector<InteractionPtr> >::const_iterator i =
improper_dihedrals_.find(this->AtomTypesToKeyword(types));
if(i != improper_dihedrals_.end()) return i->second;
//if we reach this point, we have to look for all dihedrals with wildcards...
- std::vector<MMInteractionPtr> impropers;
+ std::vector<InteractionPtr> impropers;
std::vector<String> types_with_wildcards;
//lets first check single wildcards
for(int i = 0; i < 4; ++i){
types_with_wildcards = types;
types_with_wildcards[i] = "X";
- boost::unordered_map<String,std::vector<MMInteractionPtr> >::const_iterator j =
+ boost::unordered_map<String,std::vector<InteractionPtr> >::const_iterator j =
improper_dihedrals_.find(this->AtomTypesToKeyword(types_with_wildcards));
if(j != improper_dihedrals_.end()) impropers.insert(impropers.end(),j->second.begin(),j->second.end());
}
@@ -569,7 +569,7 @@ std::vector<MMInteractionPtr> Forcefield::GetImpropers(const String& type1,
types_with_wildcards = types;
types_with_wildcards[i] = "X";
types_with_wildcards[j] = "X";
- boost::unordered_map<String,std::vector<MMInteractionPtr> >::const_iterator k =
+ boost::unordered_map<String,std::vector<InteractionPtr> >::const_iterator k =
improper_dihedrals_.find(this->AtomTypesToKeyword(types_with_wildcards));
if(k != improper_dihedrals_.end()) impropers.insert(impropers.end(),k->second.begin(),k->second.end());
}
@@ -583,7 +583,7 @@ std::vector<MMInteractionPtr> Forcefield::GetImpropers(const String& type1,
for(int i = 0; i < 4; ++i){
types_with_wildcards = all_wildcards;
types_with_wildcards[i] = types[i];
- boost::unordered_map<String,std::vector<MMInteractionPtr> >::const_iterator j =
+ boost::unordered_map<String,std::vector<InteractionPtr> >::const_iterator j =
improper_dihedrals_.find(this->AtomTypesToKeyword(types_with_wildcards));
if(j != improper_dihedrals_.end()) impropers.insert(impropers.end(),j->second.begin(),j->second.end());
}
@@ -593,7 +593,7 @@ std::vector<MMInteractionPtr> Forcefield::GetImpropers(const String& type1,
throw ost::Error("Forcefield does not contain any impropers for requested atom types!");
}
-MMInteractionPtr Forcefield::GetCMap(const String& type1, const String& type2,
+InteractionPtr Forcefield::GetCMap(const String& type1, const String& type2,
const String& type3, const String& type4,
const String& type5) const{
@@ -603,24 +603,24 @@ MMInteractionPtr Forcefield::GetCMap(const String& type1, const String& type2,
types.push_back(type3);
types.push_back(type4);
types.push_back(type5);
- boost::unordered_map<String,MMInteractionPtr>::const_iterator i =
+ boost::unordered_map<String,InteractionPtr>::const_iterator i =
cmaps_.find(this->AtomTypesToKeyword(types,false));
if(i != cmaps_.end()) return i->second;
throw ost::Error("Forcefield does not contain cmap for requested atom types!");
}
-MMInteractionPtr Forcefield::GetImplicitGenborn(const String& type) const{
+InteractionPtr Forcefield::GetImplicitGenborn(const String& type) const{
- boost::unordered_map<String,MMInteractionPtr>::const_iterator i =
+ boost::unordered_map<String,InteractionPtr>::const_iterator i =
implicit_genborn_.find(type);
if(i != implicit_genborn_.end()) return i->second;
throw ost::Error("Forcefield does not contain implicit genborn parameters for requested atom type!");
}
-MMInteractionPtr Forcefield::GetLJ(const String& type) const{
+InteractionPtr Forcefield::GetLJ(const String& type) const{
- boost::unordered_map<String,MMInteractionPtr>::const_iterator i =
+ boost::unordered_map<String,InteractionPtr>::const_iterator i =
ljs_.find(type);
if(i != ljs_.end()){
@@ -629,7 +629,7 @@ MMInteractionPtr Forcefield::GetLJ(const String& type) const{
throw ost::Error("Forcefield does not contain lennard jones parameters for requested atom types!");
}
-MMInteractionPtr Forcefield::GetLJ(const String& type1,
+InteractionPtr Forcefield::GetLJ(const String& type1,
const String& type2,
bool pair) const{
std::vector<String> types;
@@ -637,7 +637,7 @@ MMInteractionPtr Forcefield::GetLJ(const String& type1,
types.push_back(type2);
if(pair){
- boost::unordered_map<String,MMInteractionPtr>::const_iterator i =
+ boost::unordered_map<String,InteractionPtr>::const_iterator i =
lj_14_pairs_.find(this->AtomTypesToKeyword(types));
if(i == lj_14_pairs_.end()){
if(!gen_pairs_){
@@ -653,11 +653,11 @@ MMInteractionPtr Forcefield::GetLJ(const String& type1,
}
}
- MMInteractionPtr temp1, temp2;
+ InteractionPtr temp1, temp2;
temp1 = this->GetLJ(type1);
temp2 = this->GetLJ(type2);
if(temp1 && temp2){
- MMInteractionPtr return_ptr(new MMInteraction(LJPair));
+ InteractionPtr return_ptr(new Interaction(LJPair));
std::vector<Real> param1, param2, param;
param1 = temp1->GetParam();
param2 = temp2->GetParam();
@@ -672,12 +672,12 @@ MMInteractionPtr Forcefield::GetLJ(const String& type1,
}
-MMInteractionPtr Forcefield::GetConstraint(const String& type1,
+InteractionPtr Forcefield::GetConstraint(const String& type1,
const String& type2){
std::vector<String> types;
types.push_back(type1);
types.push_back(type2);
- boost::unordered_map<String,MMInteractionPtr>::const_iterator i =
+ boost::unordered_map<String,InteractionPtr>::const_iterator i =
constraints_.find(this->AtomTypesToKeyword(types));
if(i != constraints_.end()) return i->second;
throw ost::Error("Forcefield does not contain constraint for requested atom types!");
@@ -693,63 +693,63 @@ Real Forcefield::GetMass(const String& atom_type) const{
return it->second;
}
-void Forcefield::AddBond(MMInteractionPtr p){
+void Forcefield::AddBond(InteractionPtr p){
this->CheckInteractionToAdd(p,"BOND");
std::vector<String> types = p->GetTypes();
bonds_[this->AtomTypesToKeyword(types)] = p;
}
-void Forcefield::AddAngle(MMInteractionPtr p){
+void Forcefield::AddAngle(InteractionPtr p){
this->CheckInteractionToAdd(p,"ANGLE");
std::vector<String> types = p->GetTypes();
angles_[this->AtomTypesToKeyword(types)] = p;
}
-void Forcefield::AddDihedral(MMInteractionPtr p){
+void Forcefield::AddDihedral(InteractionPtr p){
this->CheckInteractionToAdd(p,"DIHEDRAL");
std::vector<String> types = p->GetTypes();
String keyword = this->AtomTypesToKeyword(types);
if(dihedrals_.find(keyword) == dihedrals_.end()){
- dihedrals_[keyword] = std::vector<MMInteractionPtr>();
+ dihedrals_[keyword] = std::vector<InteractionPtr>();
}
dihedrals_[keyword].push_back(p);
}
-void Forcefield::AddImproper(MMInteractionPtr p){
+void Forcefield::AddImproper(InteractionPtr p){
this->CheckInteractionToAdd(p,"IMPROPER");
std::vector<String> types = p->GetTypes();
String keyword = this->AtomTypesToKeyword(types);
if(improper_dihedrals_.find(keyword) == improper_dihedrals_.end()){
- improper_dihedrals_[keyword] = std::vector<MMInteractionPtr>();
+ improper_dihedrals_[keyword] = std::vector<InteractionPtr>();
}
improper_dihedrals_[keyword].push_back(p);
}
-void Forcefield::AddCMap(MMInteractionPtr p){
+void Forcefield::AddCMap(InteractionPtr p){
this->CheckInteractionToAdd(p,"CMAP");
std::vector<String> types = p->GetTypes();
cmaps_[this->AtomTypesToKeyword(types,false)] = p;
}
-void Forcefield::AddImplicitGenborn(MMInteractionPtr p){
+void Forcefield::AddImplicitGenborn(InteractionPtr p){
this->CheckInteractionToAdd(p,"IMPLICIT_GENBORN");
std::vector<String> types = p->GetTypes();
implicit_genborn_[this->AtomTypesToKeyword(types)] = p;
}
-void Forcefield::AddLJ(MMInteractionPtr p){
+void Forcefield::AddLJ(InteractionPtr p){
this->CheckInteractionToAdd(p,"LJ");
std::vector<String> types = p->GetTypes();
ljs_[types[0]] = p;
}
-void Forcefield::AddLJPair(MMInteractionPtr p){
+void Forcefield::AddLJPair(InteractionPtr p){
this->CheckInteractionToAdd(p,"LJ_PAIR");
std::vector<String> types = p->GetTypes();
lj_14_pairs_[this->AtomTypesToKeyword(types)] = p;
}
-void Forcefield::AddConstraint(MMInteractionPtr p){
+void Forcefield::AddConstraint(InteractionPtr p){
this->CheckInteractionToAdd(p,"CONSTRAINT");
std::vector<String> types = p->GetTypes();
constraints_[this->AtomTypesToKeyword(types)] = p;
@@ -955,7 +955,7 @@ String Forcefield::AtomTypesToKeyword(std::vector<String>& types, bool allow_reo
return ss.str();
}
-void Forcefield::CheckInteractionToAdd(MMInteractionPtr p, const String& interaction_type) const{
+void Forcefield::CheckInteractionToAdd(InteractionPtr p, const String& interaction_type) const{
bool valid = true;
if(p->GetTypes().empty()) valid = false;
if(!p->IsParametrized()) valid = false;
diff --git a/modules/mol/mm/src/forcefield.hh b/modules/mol/mm/src/forcefield.hh
index aba6447676e34319030bda1402d40751c2d3d881..0e9a0da64b95774ec42bedcc0b2e5fd35e21e7cc 100644
--- a/modules/mol/mm/src/forcefield.hh
+++ b/modules/mol/mm/src/forcefield.hh
@@ -10,7 +10,7 @@
#include <ost/message.hh>
#include <ost/mol/mm/buildingblock.hh>
-#include <ost/mol/mm/mm_interaction.hh>
+#include <ost/mol/mm/interaction.hh>
#include <ost/mol/mm/block_modifiers.hh>
#include <ost/mol/mm/gromacs_block_modifiers.hh>
@@ -71,38 +71,38 @@ public:
BlockModifierPtr GetCTerModifier(const String& res_name, const String& ter_name = "") const;
- MMInteractionPtr GetBond(const String& type1,
+ InteractionPtr GetBond(const String& type1,
const String& type2) const;
- MMInteractionPtr GetAngle(const String& type1,
+ InteractionPtr GetAngle(const String& type1,
const String& type2,
const String& type3) const;
- std::vector<MMInteractionPtr> GetDihedrals(const String& type1,
+ std::vector<InteractionPtr> GetDihedrals(const String& type1,
const String& type2,
const String& type3,
const String& type4) const;
- std::vector<MMInteractionPtr> GetImpropers(const String& type1,
+ std::vector<InteractionPtr> GetImpropers(const String& type1,
const String& type2,
const String& type3,
const String& type4) const;
- MMInteractionPtr GetCMap(const String& type1,
+ InteractionPtr GetCMap(const String& type1,
const String& type2,
const String& type3,
const String& type4,
const String& type5) const;
- MMInteractionPtr GetImplicitGenborn(const String& type1) const;
+ InteractionPtr GetImplicitGenborn(const String& type1) const;
- MMInteractionPtr GetLJ(const String& type1,
+ InteractionPtr GetLJ(const String& type1,
const String& type2,
bool pair=false) const;
- MMInteractionPtr GetLJ(const String& type) const;
+ InteractionPtr GetLJ(const String& type) const;
- MMInteractionPtr GetConstraint(const String& type1,
+ InteractionPtr GetConstraint(const String& type1,
const String& type2);
Real GetMass(const String& type) const;
@@ -115,23 +115,23 @@ public:
void AddBuildingBlock(const String& name, BuildingBlockPtr p) { building_blocks_[name] = p; }
- void AddBond(MMInteractionPtr p);
+ void AddBond(InteractionPtr p);
- void AddAngle(MMInteractionPtr p);
+ void AddAngle(InteractionPtr p);
- void AddDihedral(MMInteractionPtr p);
+ void AddDihedral(InteractionPtr p);
- void AddImproper(MMInteractionPtr p);
+ void AddImproper(InteractionPtr p);
- void AddCMap(MMInteractionPtr p);
+ void AddCMap(InteractionPtr p);
- void AddImplicitGenborn(MMInteractionPtr p);
+ void AddImplicitGenborn(InteractionPtr p);
- void AddLJ(MMInteractionPtr p);
+ void AddLJ(InteractionPtr p);
- void AddLJPair(MMInteractionPtr p);
+ void AddLJPair(InteractionPtr p);
- void AddConstraint(MMInteractionPtr p);
+ void AddConstraint(InteractionPtr p);
void AddMass(const String& type, Real mass) { atom_masses_[type] = mass; }
@@ -179,7 +179,7 @@ public:
private:
String AtomTypesToKeyword(std::vector<String>& types, bool allow_reordering = true) const;
- void CheckInteractionToAdd(MMInteractionPtr p, const String& interaction_type) const;
+ void CheckInteractionToAdd(InteractionPtr p, const String& interaction_type) const;
//this is all nonbonded stuff
bool gen_pairs_;
@@ -191,15 +191,15 @@ private:
boost::unordered_map<String, BlockModifierPtr> block_modifiers_;
//the standard interactions
- boost::unordered_map<String,MMInteractionPtr> bonds_;
- boost::unordered_map<String,MMInteractionPtr> angles_;
- boost::unordered_map<String,MMInteractionPtr> lj_14_pairs_;
- boost::unordered_map<String,MMInteractionPtr> constraints_;
- boost::unordered_map<String,MMInteractionPtr> cmaps_;
- boost::unordered_map<String,MMInteractionPtr> implicit_genborn_;
- boost::unordered_map<String,MMInteractionPtr> ljs_;
- boost::unordered_map<String,std::vector<MMInteractionPtr> > dihedrals_;
- boost::unordered_map<String,std::vector<MMInteractionPtr> > improper_dihedrals_;
+ boost::unordered_map<String,InteractionPtr> bonds_;
+ boost::unordered_map<String,InteractionPtr> angles_;
+ boost::unordered_map<String,InteractionPtr> lj_14_pairs_;
+ boost::unordered_map<String,InteractionPtr> constraints_;
+ boost::unordered_map<String,InteractionPtr> cmaps_;
+ boost::unordered_map<String,InteractionPtr> implicit_genborn_;
+ boost::unordered_map<String,InteractionPtr> ljs_;
+ boost::unordered_map<String,std::vector<InteractionPtr> > dihedrals_;
+ boost::unordered_map<String,std::vector<InteractionPtr> > improper_dihedrals_;
boost::unordered_map<String, std::vector<std::pair<String,String> > > atom_renaming_ff_specific_;
boost::unordered_map<String, ResidueNamesPtr> res_renaming_ff_specific_;
diff --git a/modules/mol/mm/src/gromacs_block_modifiers.cc b/modules/mol/mm/src/gromacs_block_modifiers.cc
index 083b0b84249355cea7a1233a76e8fab5e3128b32..5cad3445186d2e1197000e26d72efb590b699ad0 100644
--- a/modules/mol/mm/src/gromacs_block_modifiers.cc
+++ b/modules/mol/mm/src/gromacs_block_modifiers.cc
@@ -325,7 +325,7 @@ void GromacsBlockModifier::ApplyOnBuildingBlock(BuildingBlockPtr p){
//the bond, that connects the newly added atom to its anchor is not necessarily
//defined. Let's add it here. Note, that nothing happens, if this specific bond
//is already part of the building block.
- MMInteractionPtr b_p(new MMInteraction(p->GetBonds()[0]->GetFuncType()));
+ InteractionPtr b_p(new Interaction(p->GetBonds()[0]->GetFuncType()));
std::vector<String> bond_names;
std::vector<String> bond_types;
bond_names.push_back(anchor_atoms[0]);
@@ -345,27 +345,27 @@ void GromacsBlockModifier::ApplyOnBuildingBlock(BuildingBlockPtr p){
}
//we simply add the new interactions to the building block
- for(std::vector<MMInteractionPtr>::iterator i = bonds_.begin();
+ for(std::vector<InteractionPtr>::iterator i = bonds_.begin();
i != bonds_.end(); ++i){
p->AddBond(*i, true);
}
- for(std::vector<MMInteractionPtr>::iterator i = angles_.begin();
+ for(std::vector<InteractionPtr>::iterator i = angles_.begin();
i != angles_.end(); ++i){
p->AddAngle(*i, true);
}
- for(std::vector<MMInteractionPtr>::iterator i = dihedrals_.begin();
+ for(std::vector<InteractionPtr>::iterator i = dihedrals_.begin();
i != dihedrals_.end(); ++i){
p->AddDihedral(*i, true);
}
- for(std::vector<MMInteractionPtr>::iterator i = impropers_.begin();
+ for(std::vector<InteractionPtr>::iterator i = impropers_.begin();
i != impropers_.end(); ++i){
p->AddImproper(*i, true);
}
- for(std::vector<MMInteractionPtr>::iterator i = cmaps_.begin();
+ for(std::vector<InteractionPtr>::iterator i = cmaps_.begin();
i != cmaps_.end(); ++i){
p->AddCMap(*i, true);
}
@@ -430,7 +430,7 @@ void GromacsBlockModifier::ApplyOnResidue(ost::mol::ResidueHandle& res, ost::mol
}
-void GromacsBlockModifier::CheckInteractionToAdd(MMInteractionPtr p, const String& interaction_type) const{
+void GromacsBlockModifier::CheckInteractionToAdd(InteractionPtr p, const String& interaction_type) const{
if(p->GetNames().empty()) throw ost::Error("Expect interaction to have names properly set!");
if(interaction_type == "BOND"){
diff --git a/modules/mol/mm/src/gromacs_block_modifiers.hh b/modules/mol/mm/src/gromacs_block_modifiers.hh
index e5621f9e772b4ea3cf9d9bdb8783302695d9d7e5..9f6afd897a5e9b77729e6ebae51674a1a7fc0770 100644
--- a/modules/mol/mm/src/gromacs_block_modifiers.hh
+++ b/modules/mol/mm/src/gromacs_block_modifiers.hh
@@ -109,19 +109,19 @@ public:
const std::vector<String>& anchors,
const String& type, Real charge);
- void AddBond(MMInteractionPtr p) { this->CheckInteractionToAdd(p,"BOND");
+ void AddBond(InteractionPtr p) { this->CheckInteractionToAdd(p,"BOND");
bonds_.push_back(p); }
- void AddAngle(MMInteractionPtr p) { this->CheckInteractionToAdd(p,"ANGLE");
+ void AddAngle(InteractionPtr p) { this->CheckInteractionToAdd(p,"ANGLE");
angles_.push_back(p); }
- void AddDihedral(MMInteractionPtr p) { this->CheckInteractionToAdd(p,"DIHEDRAL");
+ void AddDihedral(InteractionPtr p) { this->CheckInteractionToAdd(p,"DIHEDRAL");
dihedrals_.push_back(p); }
- void AddImproper(MMInteractionPtr p) { this->CheckInteractionToAdd(p,"IMPROPER");
+ void AddImproper(InteractionPtr p) { this->CheckInteractionToAdd(p,"IMPROPER");
impropers_.push_back(p); }
- void AddCMap(MMInteractionPtr p) { this->CheckInteractionToAdd(p,"CMAP");
+ void AddCMap(InteractionPtr p) { this->CheckInteractionToAdd(p,"CMAP");
cmaps_.push_back(p); }
void AddDeleteAtom(const String& atom_name) { delete_atom_names_.push_back(atom_name); }
@@ -149,7 +149,7 @@ public:
int func_type;
if(ds.IsSource()){
ds & func_type;
- bonds_.push_back(MMInteractionPtr(new MMInteraction(FuncType(func_type))));
+ bonds_.push_back(InteractionPtr(new Interaction(FuncType(func_type))));
}
else{
func_type = bonds_[i]->GetFuncType();
@@ -162,7 +162,7 @@ public:
int func_type;
if(ds.IsSource()){
ds & func_type;
- angles_.push_back(MMInteractionPtr(new MMInteraction(FuncType(func_type))));
+ angles_.push_back(InteractionPtr(new Interaction(FuncType(func_type))));
}
else{
func_type = angles_[i]->GetFuncType();
@@ -175,7 +175,7 @@ public:
int func_type;
if(ds.IsSource()){
ds & func_type;
- dihedrals_.push_back(MMInteractionPtr(new MMInteraction(FuncType(func_type))));
+ dihedrals_.push_back(InteractionPtr(new Interaction(FuncType(func_type))));
}
else{
func_type = dihedrals_[i]->GetFuncType();
@@ -188,7 +188,7 @@ public:
int func_type;
if(ds.IsSource()){
ds & func_type;
- impropers_.push_back(MMInteractionPtr(new MMInteraction(FuncType(func_type))));
+ impropers_.push_back(InteractionPtr(new Interaction(FuncType(func_type))));
}
else{
func_type = impropers_[i]->GetFuncType();
@@ -201,7 +201,7 @@ public:
int func_type;
if(ds.IsSource()){
ds & func_type;
- cmaps_.push_back(MMInteractionPtr(new MMInteraction(FuncType(func_type))));
+ cmaps_.push_back(InteractionPtr(new Interaction(FuncType(func_type))));
}
else{
func_type = cmaps_[i]->GetFuncType();
@@ -272,16 +272,16 @@ public:
private:
- void CheckInteractionToAdd(MMInteractionPtr p, const String& interaction_type) const;
+ void CheckInteractionToAdd(InteractionPtr p, const String& interaction_type) const;
//Atoms, that will be added to the building block
//Interactions, that will be added to the building block
- std::vector<MMInteractionPtr> bonds_;
- std::vector<MMInteractionPtr> angles_;
- std::vector<MMInteractionPtr> dihedrals_;
- std::vector<MMInteractionPtr> impropers_;
- std::vector<MMInteractionPtr> cmaps_;
+ std::vector<InteractionPtr> bonds_;
+ std::vector<InteractionPtr> angles_;
+ std::vector<InteractionPtr> dihedrals_;
+ std::vector<InteractionPtr> impropers_;
+ std::vector<InteractionPtr> cmaps_;
//paramters we need for the replace statement
std::vector<String> replace_old_atom_name_;
diff --git a/modules/mol/mm/src/gromacs_reader.cc b/modules/mol/mm/src/gromacs_reader.cc
index e6fed54ac29ceef9bc77c325183b44d8fb54020f..7306556dbfcbb82b41d535fd5a703f5f20fb208e 100644
--- a/modules/mol/mm/src/gromacs_reader.cc
+++ b/modules/mol/mm/src/gromacs_reader.cc
@@ -437,25 +437,25 @@ void GromacsReader::ParseForcefield(std::vector<std::vector<String> >& content){
switch(keyword_id){
case 11:{
- MMInteractionPtr bond = this->ParseBond(current_line,true);
+ InteractionPtr bond = this->ParseBond(current_line,true);
ff_->AddBond(bond);
ff_bonded_types_[0] = bond->GetFuncType();
break;
}
case 12:{
- MMInteractionPtr constraint = this->ParseConstraint(current_line,true);
+ InteractionPtr constraint = this->ParseConstraint(current_line,true);
ff_->AddConstraint(constraint);
break;
}
case 13:{
- MMInteractionPtr angle = this->ParseAngle(current_line,true);
+ InteractionPtr angle = this->ParseAngle(current_line,true);
ff_->AddAngle(angle);
ff_bonded_types_[1] = angle->GetFuncType();
break;
}
case 14:{
- MMInteractionPtr p = this->ParseDihedral(current_line,true);
+ InteractionPtr p = this->ParseDihedral(current_line,true);
FuncType functype = p->GetFuncType();
if(functype == PeriodicDihedral){
@@ -469,17 +469,17 @@ void GromacsReader::ParseForcefield(std::vector<std::vector<String> >& content){
break;
}
case 15:{
- MMInteractionPtr lj = this->ParseLJ(current_line,true);
+ InteractionPtr lj = this->ParseLJ(current_line,true);
ff_->AddLJ(lj);
break;
}
case 16:{
- MMInteractionPtr genborn = this->ParseGenborn(current_line,true);
+ InteractionPtr genborn = this->ParseGenborn(current_line,true);
ff_->AddImplicitGenborn(genborn);
break;
}
case 17:{
- MMInteractionPtr lj_pair = this->ParseLJPair(current_line,true);
+ InteractionPtr lj_pair = this->ParseLJPair(current_line,true);
ff_->AddLJPair(lj_pair);
break;
}
@@ -506,7 +506,7 @@ void GromacsReader::ParseForcefield(std::vector<std::vector<String> >& content){
break;
}
case 20:{
- MMInteractionPtr cmap = this->ParseCMap(current_line,true);
+ InteractionPtr cmap = this->ParseCMap(current_line,true);
ff_->AddCMap(cmap);
break;
}
@@ -1103,7 +1103,7 @@ BuildingBlockPtr GromacsReader::BlockFromITP(const std::vector<std::vector<Strin
current_line[2] = index_name_mapper[boost::lexical_cast<int>(current_line[2])];
current_line[3] = index_name_mapper[boost::lexical_cast<int>(current_line[3])];
- MMInteractionPtr int_ptr = this->ParseDihedral(current_line,false);
+ InteractionPtr int_ptr = this->ParseDihedral(current_line,false);
FuncType functype = int_ptr->GetFuncType();
if(functype == PeriodicDihedral){
@@ -1117,7 +1117,7 @@ BuildingBlockPtr GromacsReader::BlockFromITP(const std::vector<std::vector<Strin
case 5:{
//current_line[0] = index_name_mapper[boost::lexical_cast<int>(current_line[0])];
//current_line[1] = index_name_mapper[boost::lexical_cast<int>(current_line[1])];
- //p->exclusions_.push_back(MMInteraction::ParseExclusion(current_line,false));
+ //p->exclusions_.push_back(Interaction::ParseExclusion(current_line,false));
break;
}
case 6:{
@@ -1142,9 +1142,9 @@ BuildingBlockPtr GromacsReader::BlockFromITP(const std::vector<std::vector<Strin
std::vector<String> names;
- MMInteractionPtr p1(new MMInteraction(DistanceConstraint));
- MMInteractionPtr p2(new MMInteraction(DistanceConstraint));
- MMInteractionPtr p3(new MMInteraction(DistanceConstraint));
+ InteractionPtr p1(new Interaction(DistanceConstraint));
+ InteractionPtr p2(new Interaction(DistanceConstraint));
+ InteractionPtr p3(new Interaction(DistanceConstraint));
//first constraint dist => O - H
parameters.push_back(boost::lexical_cast<Real>(current_line[2]));
@@ -1249,7 +1249,7 @@ BlockModifierPtr GromacsReader::ParseBlockModifier(const std::vector<std::vector
}
-MMInteractionPtr GromacsReader::ParseBond(const std::vector<String>& data,
+InteractionPtr GromacsReader::ParseBond(const std::vector<String>& data,
bool type_definition,
FuncType functype){
@@ -1280,7 +1280,7 @@ MMInteractionPtr GromacsReader::ParseBond(const std::vector<String>& data,
atom_definition.push_back(data[0]);
atom_definition.push_back(data[1]);
- MMInteractionPtr p(new MMInteraction(functype));
+ InteractionPtr p(new Interaction(functype));
if(type_definition) p->SetTypes(atom_definition);
else p->SetNames(atom_definition);
@@ -1299,7 +1299,7 @@ MMInteractionPtr GromacsReader::ParseBond(const std::vector<String>& data,
return p;
}
-MMInteractionPtr GromacsReader::ParseAngle(const std::vector<String>& data,
+InteractionPtr GromacsReader::ParseAngle(const std::vector<String>& data,
bool type_definition,
FuncType functype){
@@ -1330,7 +1330,7 @@ MMInteractionPtr GromacsReader::ParseAngle(const std::vector<String>& data,
atom_definition.push_back(data[1]);
atom_definition.push_back(data[2]);
- MMInteractionPtr p(new MMInteraction(functype));
+ InteractionPtr p(new Interaction(functype));
if(type_definition) p->SetTypes(atom_definition);
else p->SetNames(atom_definition);
@@ -1357,7 +1357,7 @@ MMInteractionPtr GromacsReader::ParseAngle(const std::vector<String>& data,
return p;
}
-MMInteractionPtr GromacsReader::ParseDihedral(const std::vector<String>& data,
+InteractionPtr GromacsReader::ParseDihedral(const std::vector<String>& data,
bool type_definition,
FuncType functype){
if(data.size() < 4){
@@ -1389,7 +1389,7 @@ MMInteractionPtr GromacsReader::ParseDihedral(const std::vector<String>& data,
atom_definition.push_back(data[2]);
atom_definition.push_back(data[3]);
- MMInteractionPtr p(new MMInteraction(functype));
+ InteractionPtr p(new Interaction(functype));
if(type_definition) p->SetTypes(atom_definition);
else p->SetNames(atom_definition);
@@ -1414,7 +1414,7 @@ MMInteractionPtr GromacsReader::ParseDihedral(const std::vector<String>& data,
return p;
}
-MMInteractionPtr GromacsReader::ParseCMap(const std::vector<String>& data,
+InteractionPtr GromacsReader::ParseCMap(const std::vector<String>& data,
bool type_definition,
FuncType functype){
if(data.size() < 5){
@@ -1432,7 +1432,7 @@ MMInteractionPtr GromacsReader::ParseCMap(const std::vector<String>& data,
atom_definition.push_back(data[3]);
atom_definition.push_back(data[4]);
- MMInteractionPtr p(new MMInteraction(functype));
+ InteractionPtr p(new Interaction(functype));
if(type_definition) p->SetTypes(atom_definition);
else p->SetNames(atom_definition);
@@ -1467,7 +1467,7 @@ MMInteractionPtr GromacsReader::ParseCMap(const std::vector<String>& data,
}
-MMInteractionPtr GromacsReader::ParseLJ(const std::vector<String>& data,
+InteractionPtr GromacsReader::ParseLJ(const std::vector<String>& data,
bool type_definition,
FuncType functype){
@@ -1482,7 +1482,7 @@ MMInteractionPtr GromacsReader::ParseLJ(const std::vector<String>& data,
std::vector<String> atom_definition;
atom_definition.push_back(data[0]);
- MMInteractionPtr p(new MMInteraction(functype));
+ InteractionPtr p(new Interaction(functype));
if(type_definition) p->SetTypes(atom_definition);
else p->SetNames(atom_definition);
@@ -1501,7 +1501,7 @@ MMInteractionPtr GromacsReader::ParseLJ(const std::vector<String>& data,
}
-MMInteractionPtr GromacsReader::ParseLJPair(const std::vector<String>& data,
+InteractionPtr GromacsReader::ParseLJPair(const std::vector<String>& data,
bool type_definition,
FuncType functype){
@@ -1532,7 +1532,7 @@ MMInteractionPtr GromacsReader::ParseLJPair(const std::vector<String>& data,
atom_definition.push_back(data[0]);
atom_definition.push_back(data[1]);
- MMInteractionPtr p(new MMInteraction(functype));
+ InteractionPtr p(new Interaction(functype));
if(type_definition) p->SetTypes(atom_definition);
else p->SetNames(atom_definition);
@@ -1550,7 +1550,7 @@ MMInteractionPtr GromacsReader::ParseLJPair(const std::vector<String>& data,
return p;
}
-MMInteractionPtr GromacsReader::ParseConstraint(const std::vector<String>& data,
+InteractionPtr GromacsReader::ParseConstraint(const std::vector<String>& data,
bool type_definition,
FuncType functype){
@@ -1581,7 +1581,7 @@ MMInteractionPtr GromacsReader::ParseConstraint(const std::vector<String>& data,
atom_definition.push_back(data[0]);
atom_definition.push_back(data[1]);
- MMInteractionPtr p(new MMInteraction(functype));
+ InteractionPtr p(new Interaction(functype));
if(type_definition) p->SetTypes(atom_definition);
else p->SetNames(atom_definition);
@@ -1598,7 +1598,7 @@ MMInteractionPtr GromacsReader::ParseConstraint(const std::vector<String>& data,
return p;
}
-MMInteractionPtr GromacsReader::ParseGenborn(const std::vector<String>& data,
+InteractionPtr GromacsReader::ParseGenborn(const std::vector<String>& data,
bool type_definition,
FuncType functype){
@@ -1612,7 +1612,7 @@ MMInteractionPtr GromacsReader::ParseGenborn(const std::vector<String>& data,
functype = GBSA; //bit hacky, I know, but there is only one type for gbsa anyway....
- MMInteractionPtr p(new MMInteraction(functype));
+ InteractionPtr p(new Interaction(functype));
if(type_definition) p->SetTypes(atom_definition);
else p->SetNames(atom_definition);
@@ -1631,7 +1631,7 @@ MMInteractionPtr GromacsReader::ParseGenborn(const std::vector<String>& data,
}
-MMInteractionPtr GromacsReader::ParseExclusion(const std::vector<String>& data,
+InteractionPtr GromacsReader::ParseExclusion(const std::vector<String>& data,
bool type_definition,
FuncType functype){
@@ -1645,7 +1645,7 @@ MMInteractionPtr GromacsReader::ParseExclusion(const std::vector<String>& data,
atom_definition.push_back(data[0]);
atom_definition.push_back(data[1]);
- MMInteractionPtr p(new MMInteraction(functype));
+ InteractionPtr p(new Interaction(functype));
if(type_definition) p->SetTypes(atom_definition);
else p->SetNames(atom_definition);
@@ -1682,7 +1682,7 @@ void GromacsReader::ParseCHARMMPRM(std::vector<std::vector<String> >& content){
break;
}
case 1:{ //bonds
- MMInteractionPtr p(new MMInteraction(HarmonicBond));
+ InteractionPtr p(new Interaction(HarmonicBond));
std::vector<String> types;
std::vector<Real> parameters;
types.push_back(current_line[0]);
@@ -1699,7 +1699,7 @@ void GromacsReader::ParseCHARMMPRM(std::vector<std::vector<String> >& content){
break;
}
case 2:{ //angles
- MMInteractionPtr p(new MMInteraction(UreyBradleyAngle));
+ InteractionPtr p(new Interaction(UreyBradleyAngle));
std::vector<String> types;
std::vector<Real> parameters;
types.push_back(current_line[0]);
@@ -1725,7 +1725,7 @@ void GromacsReader::ParseCHARMMPRM(std::vector<std::vector<String> >& content){
break;
}
case 3:{ //diherals
- MMInteractionPtr p(new MMInteraction(PeriodicDihedral));
+ InteractionPtr p(new Interaction(PeriodicDihedral));
std::vector<String> types;
std::vector<Real> parameters;
types.push_back(current_line[0]);
@@ -1745,7 +1745,7 @@ void GromacsReader::ParseCHARMMPRM(std::vector<std::vector<String> >& content){
break;
}
case 4:{ //improper
- MMInteractionPtr p(new MMInteraction(HarmonicImproper));
+ InteractionPtr p(new Interaction(HarmonicImproper));
std::vector<String> types;
std::vector<Real> parameters;
types.push_back(current_line[0]);
@@ -1787,7 +1787,7 @@ void GromacsReader::ParseCHARMMPRM(std::vector<std::vector<String> >& content){
throw ost::io::IOException(ss.str());
}
if(parameters.size() == dim*dim+1){
- MMInteractionPtr p(new MMInteraction(CMap));
+ InteractionPtr p(new Interaction(CMap));
p->SetTypes(types);
p->SetParam(parameters);
ff_->AddCMap(p);
@@ -1815,7 +1815,7 @@ void GromacsReader::ParseCHARMMPRM(std::vector<std::vector<String> >& content){
}catch(std::exception& e){
throw ost::io::IOException("Could not cast LJ parameters into real type!");
}
- MMInteractionPtr p(new MMInteraction(LJ));
+ InteractionPtr p(new Interaction(LJ));
p->SetTypes(types);
p->SetParam(parameters);
ff_->AddLJ(p);
@@ -1846,7 +1846,7 @@ void GromacsReader::ParseCHARMMPRM(std::vector<std::vector<String> >& content){
//have explicitely defined 1,4 interactions
for(uint i = 0; i < lj_14_types.size(); ++i){
for(uint j = i; j < lj_14_types.size(); ++j){
- MMInteractionPtr p(new MMInteraction(LJPair));
+ InteractionPtr p(new Interaction(LJPair));
std::vector<String> types;
std::vector<Real> parameters;
types.push_back(lj_14_types[i]);
@@ -1861,7 +1861,7 @@ void GromacsReader::ParseCHARMMPRM(std::vector<std::vector<String> >& content){
//let's add all pairwise 1,4 interactions, where only one partner has explicitely defined 1,4 interactions
for(uint i = 0; i < lj_14_types.size(); ++i){
for(uint j = 0; j < lj_types.size(); ++j){
- MMInteractionPtr p(new MMInteraction(LJPair));
+ InteractionPtr p(new Interaction(LJPair));
std::vector<String> types;
std::vector<Real> parameters;
types.push_back(lj_14_types[i]);
@@ -1914,7 +1914,7 @@ void GromacsReader::ParseCHARMMRTF(std::vector<std::vector<String> >& content){
case 17:{//bond
int num_bonds = (current_line.size()-1) / 2;
for(int i = 0; i < num_bonds; ++i){
- MMInteractionPtr p(new MMInteraction(HarmonicBond));
+ InteractionPtr p(new Interaction(HarmonicBond));
std::vector<String> names;
names.push_back(current_line[i*2+1]);
names.push_back(current_line[i*2+2]);
@@ -1927,7 +1927,7 @@ void GromacsReader::ParseCHARMMRTF(std::vector<std::vector<String> >& content){
case 18:{//angle
int num_angles = (current_line.size()-1) / 3;
for(int i = 0; i < num_angles; ++i){
- MMInteractionPtr p(new MMInteraction(UreyBradleyAngle));
+ InteractionPtr p(new Interaction(UreyBradleyAngle));
std::vector<String> names;
names.push_back(current_line[i*3+1]);
names.push_back(current_line[i*3+2]);
@@ -1941,7 +1941,7 @@ void GromacsReader::ParseCHARMMRTF(std::vector<std::vector<String> >& content){
case 19:{//dihedral
int num_dihedrals = (current_line.size()-1) / 4;
for(int i = 0; i < num_dihedrals; ++i){
- MMInteractionPtr p(new MMInteraction(PeriodicDihedral));
+ InteractionPtr p(new Interaction(PeriodicDihedral));
std::vector<String> names;
names.push_back(current_line[i*4+1]);
names.push_back(current_line[i*4+2]);
@@ -1956,7 +1956,7 @@ void GromacsReader::ParseCHARMMRTF(std::vector<std::vector<String> >& content){
case 20:{//improper
int num_impropers = (current_line.size()-1) / 4;
for(int i = 0; i < num_impropers; ++i){
- MMInteractionPtr p(new MMInteraction(HarmonicImproper));
+ InteractionPtr p(new Interaction(HarmonicImproper));
std::vector<String> names;
names.push_back(current_line[i*4+1]);
names.push_back(current_line[i*4+2]);
@@ -1971,7 +1971,7 @@ void GromacsReader::ParseCHARMMRTF(std::vector<std::vector<String> >& content){
case 5:{//cmap
int num_cmaps = (current_line.size()-1) / 8;
for(int i = 0; i < num_cmaps; ++i){
- MMInteractionPtr p(new MMInteraction(CMap));
+ InteractionPtr p(new Interaction(CMap));
std::vector<String> names;
names.push_back(current_line[i*4+1]);
names.push_back(current_line[i*4+2]);
@@ -2007,7 +2007,7 @@ void GromacsReader::ParseCHARMMRTF(std::vector<std::vector<String> >& content){
case 26:{ //double =>basically a bond
int num_bonds = (current_line.size()-1) / 2;
for(int i = 0; i < num_bonds; ++i){
- MMInteractionPtr p(new MMInteraction(HarmonicBond));
+ InteractionPtr p(new Interaction(HarmonicBond));
std::vector<String> names;
names.push_back(current_line[i*2+1]);
names.push_back(current_line[i*2+2]);
diff --git a/modules/mol/mm/src/gromacs_reader.hh b/modules/mol/mm/src/gromacs_reader.hh
index 89a2e20a45edbbb2e63c860800a80f704339eefc..31d4ddbfeac26d97d9845d25daa9be61c0be4acf 100644
--- a/modules/mol/mm/src/gromacs_reader.hh
+++ b/modules/mol/mm/src/gromacs_reader.hh
@@ -11,7 +11,7 @@
#include <ost/base.hh>
#include <ost/io/io_exception.hh>
#include <ost/mol/mm/forcefield.hh>
-#include <ost/mol/mm/mm_interaction.hh>
+#include <ost/mol/mm/interaction.hh>
#include <ost/mol/mm/gromacs_block_modifiers.hh>
@@ -103,39 +103,39 @@ public:
private:
- MMInteractionPtr ParseBond(const std::vector<String>& data,
+ InteractionPtr ParseBond(const std::vector<String>& data,
bool type_definition,
FuncType functype = Invalid);
- MMInteractionPtr ParseAngle(const std::vector<String>& data,
+ InteractionPtr ParseAngle(const std::vector<String>& data,
bool type_definition,
FuncType functype = Invalid);
- MMInteractionPtr ParseDihedral(const std::vector<String>& data,
+ InteractionPtr ParseDihedral(const std::vector<String>& data,
bool type_definition,
FuncType functype = Invalid);
- MMInteractionPtr ParseCMap(const std::vector<String>& data,
+ InteractionPtr ParseCMap(const std::vector<String>& data,
bool type_definition,
FuncType functype = Invalid);
- MMInteractionPtr ParseLJ(const std::vector<String>& data,
+ InteractionPtr ParseLJ(const std::vector<String>& data,
bool type_definition,
FuncType functype = Invalid);
- MMInteractionPtr ParseLJPair(const std::vector<String>& data,
+ InteractionPtr ParseLJPair(const std::vector<String>& data,
bool type_definition,
FuncType functype = Invalid);
- MMInteractionPtr ParseConstraint(const std::vector<String>& data,
+ InteractionPtr ParseConstraint(const std::vector<String>& data,
bool type_definition,
FuncType functype = Invalid);
- MMInteractionPtr ParseGenborn(const std::vector<String>& data,
+ InteractionPtr ParseGenborn(const std::vector<String>& data,
bool type_definition,
FuncType functype = Invalid);
- MMInteractionPtr ParseExclusion(const std::vector<String>& data,
+ InteractionPtr ParseExclusion(const std::vector<String>& data,
bool type_definition,
FuncType functype = Invalid);
diff --git a/modules/mol/mm/src/heuristic_block_modifiers.cc b/modules/mol/mm/src/heuristic_block_modifiers.cc
index 9d415088a4c688996284262994889ac44f4e936d..46b1850acbb73b0399a79ead0173d7505eaf7ba0 100644
--- a/modules/mol/mm/src/heuristic_block_modifiers.cc
+++ b/modules/mol/mm/src/heuristic_block_modifiers.cc
@@ -12,7 +12,7 @@ void HeuristicHydrogenConstructor::ApplyOnBuildingBlock(BuildingBlockPtr p){
HeuristicHydrogenConstructor::HeuristicHydrogenConstructor(BuildingBlockPtr block){
std::vector<String> atom_names = block->GetAtoms();
- std::vector<MMInteractionPtr> bonds = block->GetBonds();
+ std::vector<InteractionPtr> bonds = block->GetBonds();
for(std::vector<String>::iterator aname = atom_names.begin();
aname != atom_names.end(); ++aname){
@@ -21,7 +21,7 @@ HeuristicHydrogenConstructor::HeuristicHydrogenConstructor(BuildingBlockPtr bloc
std::vector<String> antecedent_names, hydrogen_names;
String aname_other;
- for (std::vector<MMInteractionPtr>::iterator i = bonds.begin() ;
+ for (std::vector<InteractionPtr>::iterator i = bonds.begin() ;
i != bonds.end(); ++i){
std::vector<String> bond_names=(*i)->GetNames();
diff --git a/modules/mol/mm/src/mm_interaction.cc b/modules/mol/mm/src/interaction.cc
similarity index 82%
rename from modules/mol/mm/src/mm_interaction.cc
rename to modules/mol/mm/src/interaction.cc
index 093e2d122e43773e786c1afa5b3440e109d65c2d..2831edbbce1bd45b05d168e8f0b68d5ef41b64b7 100644
--- a/modules/mol/mm/src/mm_interaction.cc
+++ b/modules/mol/mm/src/interaction.cc
@@ -1,14 +1,14 @@
-#include <ost/mol/mm/mm_interaction.hh>
+#include <ost/mol/mm/interaction.hh>
namespace ost { namespace mol{ namespace mm{
-MMInteraction::MMInteraction(FuncType func_type): func_type_(func_type),
- set_parameters_(false),
- has_type_wildcard_(false),
- has_name_wildcard_(false){ }
+Interaction::Interaction(FuncType func_type): func_type_(func_type),
+ set_parameters_(false),
+ has_type_wildcard_(false),
+ has_name_wildcard_(false){ }
-void MMInteraction::SetTypes(std::vector<String> types){
+void Interaction::SetTypes(std::vector<String> types){
if(!this->CheckSetNamesTypes(types)){
throw ost::Error("Tried to set invalid number of types to interaction!");
}
@@ -19,7 +19,7 @@ void MMInteraction::SetTypes(std::vector<String> types){
else has_type_wildcard_ = false;
}
-void MMInteraction::SetNames(std::vector<String> names){
+void Interaction::SetNames(std::vector<String> names){
if(!this->CheckSetNamesTypes(names)){
throw ost::Error("Tried to set invalid number of names to interaction!");
}
@@ -30,7 +30,7 @@ void MMInteraction::SetNames(std::vector<String> names){
else has_name_wildcard_ = false;
}
-void MMInteraction::SetParam(std::vector<Real>& parameters){
+void Interaction::SetParam(std::vector<Real>& parameters){
if(!this->CheckSetParam(parameters)){
throw ost::Error("Tried to set invalid number of parameters to interaction!");
}
@@ -38,7 +38,7 @@ void MMInteraction::SetParam(std::vector<Real>& parameters){
set_parameters_ = true;
}
-ost::mol::AtomHandleList MMInteraction::GetAtoms(const ost::mol::ResidueHandle& res) const{
+ost::mol::AtomHandleList Interaction::GetAtoms(const ost::mol::ResidueHandle& res) const{
ost::mol::AtomHandleList return_list;
ost::mol::ResidueHandle prev = res.GetPrev();
@@ -84,7 +84,7 @@ ost::mol::AtomHandleList MMInteraction::GetAtoms(const ost::mol::ResidueHandle&
return return_list;
}
-bool MMInteraction::MatchTypes(const std::vector<String>& atom_types) const {
+bool Interaction::MatchTypes(const std::vector<String>& atom_types) const {
if(atom_types_.size() == 0) return false;
if(atom_types.size() != atom_types_.size()) return false;
@@ -102,7 +102,7 @@ bool MMInteraction::MatchTypes(const std::vector<String>& atom_types) const {
return match || reverse_match;
}
-bool MMInteraction::MatchNames(const std::vector<String>& atom_names) const {
+bool Interaction::MatchNames(const std::vector<String>& atom_names) const {
if(atom_names_.size() == 0) return false;
if(atom_names.size() != atom_names_.size()) return false;
@@ -120,7 +120,7 @@ bool MMInteraction::MatchNames(const std::vector<String>& atom_names) const {
return match || r_match;
}
-bool MMInteraction::ReplaceAtom(const String& name, const String& new_name, const String& new_type){
+bool Interaction::ReplaceAtom(const String& name, const String& new_name, const String& new_type){
for(uint i = 0; i < atom_names_.size(); ++i){
if(atom_names_[i] == name){
@@ -135,15 +135,15 @@ bool MMInteraction::ReplaceAtom(const String& name, const String& new_name, cons
return false;
}
-bool MMInteraction::HasName(const String& name) const{
+bool Interaction::HasName(const String& name) const{
return std::find(atom_names_.begin(),atom_names_.end(),name) != atom_names_.end();
}
-bool MMInteraction::HasType(const String& type) const{
+bool Interaction::HasType(const String& type) const{
return std::find(atom_types_.begin(),atom_types_.end(),type) != atom_types_.end();
}
-bool MMInteraction::CheckSetNamesTypes(std::vector<String>& types){
+bool Interaction::CheckSetNamesTypes(std::vector<String>& types){
switch(func_type_){
case HarmonicBond: return types.size() == 2;
@@ -164,7 +164,7 @@ bool MMInteraction::CheckSetNamesTypes(std::vector<String>& types){
}
}
-bool MMInteraction::CheckSetParam(std::vector<Real>& param){
+bool Interaction::CheckSetParam(std::vector<Real>& param){
switch(func_type_){
case HarmonicBond: return param.size() == 2;
diff --git a/modules/mol/mm/src/mm_interaction.hh b/modules/mol/mm/src/interaction.hh
similarity index 95%
rename from modules/mol/mm/src/mm_interaction.hh
rename to modules/mol/mm/src/interaction.hh
index ca69e78b15117d729cc9b10e823d4cc6a66d7922..0d495b27537ff9e35d13d78e6fc021e237bf6fd6 100644
--- a/modules/mol/mm/src/mm_interaction.hh
+++ b/modules/mol/mm/src/interaction.hh
@@ -17,8 +17,8 @@
namespace ost { namespace mol{ namespace mm{
-class MMInteraction;
-typedef boost::shared_ptr<MMInteraction> MMInteractionPtr;
+class Interaction;
+typedef boost::shared_ptr<Interaction> InteractionPtr;
enum FuncType{
Invalid,
@@ -38,10 +38,10 @@ enum FuncType{
HarmonicDistanceRestraint
};
-class MMInteraction{
+class Interaction{
public:
- MMInteraction(FuncType func_type);
+ Interaction(FuncType func_type);
void SetTypes(std::vector<String> types);
@@ -141,7 +141,6 @@ private:
std::vector<String> atom_names_;
};
-
}}} //ns
#endif
diff --git a/modules/mol/mm/src/mm_modeller.cc b/modules/mol/mm/src/modeller.cc
similarity index 95%
rename from modules/mol/mm/src/mm_modeller.cc
rename to modules/mol/mm/src/modeller.cc
index 2cc9714833324a7bb92a8be3582656190d3e3a9f..9e87752bf96316426b68247da9ac002f5948c0ca 100644
--- a/modules/mol/mm/src/mm_modeller.cc
+++ b/modules/mol/mm/src/modeller.cc
@@ -1,9 +1,9 @@
-#include <ost/mol/mm/mm_modeller.hh>
+#include <ost/mol/mm/modeller.hh>
namespace ost{ namespace mol{ namespace mm{
-void MMModeller::GenerateDisulfidBonds(ost::mol::EntityHandle& handle){
+void Modeller::GenerateDisulfidBonds(ost::mol::EntityHandle& handle){
ost::mol::ResidueHandleList res_list = handle.GetResidueList();
ost::mol::XCSEditor ed = handle.EditXCS();
@@ -31,7 +31,7 @@ void MMModeller::GenerateDisulfidBonds(ost::mol::EntityHandle& handle){
}
}
-void MMModeller::GenerateCYSHEMEBonds(ost::mol::EntityHandle& handle){
+void Modeller::GenerateCYSHEMEBonds(ost::mol::EntityHandle& handle){
ost::mol::ResidueHandleList res_list = handle.GetResidueList();
ost::mol::XCSEditor ed = handle.EditXCS();
@@ -85,7 +85,7 @@ void MMModeller::GenerateCYSHEMEBonds(ost::mol::EntityHandle& handle){
}
}
-void MMModeller::GenerateHISHEMEBonds(ost::mol::EntityHandle& handle){
+void Modeller::GenerateHISHEMEBonds(ost::mol::EntityHandle& handle){
ost::mol::ResidueHandleList res_list = handle.GetResidueList();
ost::mol::XCSEditor ed = handle.EditXCS();
@@ -111,7 +111,7 @@ void MMModeller::GenerateHISHEMEBonds(ost::mol::EntityHandle& handle){
}
}
-void MMModeller::GenerateMETHEMEBonds(ost::mol::EntityHandle& handle){
+void Modeller::GenerateMETHEMEBonds(ost::mol::EntityHandle& handle){
ost::mol::ResidueHandleList res_list = handle.GetResidueList();
ost::mol::XCSEditor ed = handle.EditXCS();
@@ -136,7 +136,7 @@ void MMModeller::GenerateMETHEMEBonds(ost::mol::EntityHandle& handle){
}
}
-void MMModeller::LowerPrecision(ost::mol::EntityHandle& handle){
+void Modeller::LowerPrecision(ost::mol::EntityHandle& handle){
ost::mol::AtomHandleList atom_list = handle.GetAtomList();
ost::mol::XCSEditor ed = handle.EditXCS(ost::mol::BUFFERED_EDIT);
@@ -154,7 +154,7 @@ void MMModeller::LowerPrecision(ost::mol::EntityHandle& handle){
ed.UpdateICS();
}
-void MMModeller::AssignPDBNaming(ost::mol::EntityHandle& handle){
+void Modeller::AssignPDBNaming(ost::mol::EntityHandle& handle){
std::map<String,String> gromacs_to_pdb;
gromacs_to_pdb["ARGN"] = "ARG";
@@ -206,7 +206,7 @@ void MMModeller::AssignPDBNaming(ost::mol::EntityHandle& handle){
}
}
-void MMModeller::AssignGromacsNaming(ost::mol::EntityHandle& handle){
+void Modeller::AssignGromacsNaming(ost::mol::EntityHandle& handle){
ost::mol::XCSEditor ed = handle.EditXCS();
diff --git a/modules/mol/mm/src/mm_modeller.hh b/modules/mol/mm/src/modeller.hh
similarity index 98%
rename from modules/mol/mm/src/mm_modeller.hh
rename to modules/mol/mm/src/modeller.hh
index 682f5a885ba37e829e96a35c410923350c7081d1..814a5edaadf33f23cd02b6fa9c9ae8ea557a6933 100644
--- a/modules/mol/mm/src/mm_modeller.hh
+++ b/modules/mol/mm/src/modeller.hh
@@ -29,7 +29,7 @@
namespace ost { namespace mol{ namespace mm{
-class MMModeller{
+class Modeller{
public:
static void GenerateDisulfidBonds(ost::mol::EntityHandle& handle);
diff --git a/modules/mol/mm/src/mm_observer.cc b/modules/mol/mm/src/observer.cc
similarity index 99%
rename from modules/mol/mm/src/mm_observer.cc
rename to modules/mol/mm/src/observer.cc
index aa0d5c5ee5e24b08f7993778c795b6c1bebecc9b..5ea1cbe7292a583df2d6fa944d58d1fd10f6986a 100644
--- a/modules/mol/mm/src/mm_observer.cc
+++ b/modules/mol/mm/src/observer.cc
@@ -1,4 +1,4 @@
-#include <ost/mol/mm/mm_observer.hh>
+#include <ost/mol/mm/observer.hh>
#include <OpenMM.h>
namespace ost { namespace mol{ namespace mm{
diff --git a/modules/mol/mm/src/mm_observer.hh b/modules/mol/mm/src/observer.hh
similarity index 94%
rename from modules/mol/mm/src/mm_observer.hh
rename to modules/mol/mm/src/observer.hh
index eec055472e9500ede28edf4eb398ca2c1acd0bc4..815db37e0c3141af724c6204cf0b5f8bf65cf0e8 100644
--- a/modules/mol/mm/src/mm_observer.hh
+++ b/modules/mol/mm/src/observer.hh
@@ -21,15 +21,15 @@ namespace OpenMM{
namespace ost { namespace mol{ namespace mm{
-class MMObserver;
+class Observer;
class TrajObserver;
class TrajWriter;
-typedef boost::shared_ptr<MMObserver> MMObserverPtr;
+typedef boost::shared_ptr<Observer> ObserverPtr;
typedef boost::shared_ptr<TrajObserver> TrajObserverPtr;
typedef boost::shared_ptr<TrajWriter> TrajWriterPtr;
-class MMObserver{
+class Observer{
public:
virtual void Notify() = 0;
@@ -43,7 +43,7 @@ public:
};
-class TrajObserver : public MMObserver{
+class TrajObserver : public Observer{
public:
@@ -67,7 +67,7 @@ private:
bool registered_;
};
-class TrajWriter : public MMObserver{
+class TrajWriter : public Observer{
//Note, that this code is highly redundant to the code in io/mol/dcd_io.hh!!!
diff --git a/modules/mol/mm/src/mm_settings.hh b/modules/mol/mm/src/settings.hh
similarity index 97%
rename from modules/mol/mm/src/mm_settings.hh
rename to modules/mol/mm/src/settings.hh
index c29ea463f0b3aa4d2e041a3b4afb888bbb489bcd..639ddc9b487b7f3d9fcdc8d7a59d4ea9ae1f5472 100644
--- a/modules/mol/mm/src/mm_settings.hh
+++ b/modules/mol/mm/src/settings.hh
@@ -16,9 +16,9 @@ namespace OpenMM{
namespace ost { namespace mol{ namespace mm{
-struct MMSettings;
+struct Settings;
class TerminiExceptions;
-typedef boost::shared_ptr<MMSettings> MMSettingsPtr;
+typedef boost::shared_ptr<Settings> SettingsPtr;
typedef boost::shared_ptr<TerminiExceptions> TerminiExceptionsPtr;
enum Platform{
@@ -64,9 +64,9 @@ private:
};
-struct MMSettings{
+struct Settings{
- MMSettings(): add_bonds(true),
+ Settings(): add_bonds(true),
add_angles(true),
add_dihedrals(true),
add_impropers(true),
diff --git a/modules/mol/mm/src/simulation.cc b/modules/mol/mm/src/simulation.cc
index 7f10f6c392964ae1220ae513a8e12cd2f2cb1400..31fd2ec47e0ecc268c2f3ad1b8efe1faec58504c 100644
--- a/modules/mol/mm/src/simulation.cc
+++ b/modules/mol/mm/src/simulation.cc
@@ -4,7 +4,7 @@
namespace ost{ namespace mol{ namespace mm{
Simulation::Simulation(const ost::mol::EntityHandle& handle,
- const MMSettingsPtr settings){
+ const SettingsPtr settings){
//note, that ent_ will be "completed" inside this function!
//(hydrogens and shit)
@@ -16,7 +16,7 @@ Simulation::Simulation(const ost::mol::EntityHandle& handle,
Simulation::Simulation(const TopologyPtr top,
const ost::mol::EntityHandle& handle,
- const MMSettingsPtr settings){
+ const SettingsPtr settings){
if(static_cast<uint>(handle.GetAtomCount()) != top->GetNumParticles()){
throw ost::Error("Number of atoms in entity must be consistent with number of particles in topology!");
@@ -119,7 +119,7 @@ void Simulation::Save(const String& filename){
context_->createCheckpoint(stream);
}
-SimulationPtr Simulation::Load(const String& filename, MMSettingsPtr settings){
+SimulationPtr Simulation::Load(const String& filename, SettingsPtr settings){
if (!boost::filesystem::exists(filename)) {
std::stringstream ss;
ss << "Could not open simulation File '"
@@ -249,7 +249,7 @@ SimulationPtr Simulation::Load(const String& filename, MMSettingsPtr settings){
void Simulation::Init(const TopologyPtr top,
- const MMSettingsPtr settings){
+ const SettingsPtr settings){
top_ = top;
@@ -449,7 +449,7 @@ Real Simulation::GetPotentialEnergy(){
return energy;
}
-void Simulation::Register(MMObserverPtr o){
+void Simulation::Register(ObserverPtr o){
observers_.push_back(o);
time_to_notify_.push_back(o->Rythm());
o->Init(context_,top_,ent_);
diff --git a/modules/mol/mm/src/simulation.hh b/modules/mol/mm/src/simulation.hh
index 8996995254017beb1b3f5e4d56c9bdbc19c3cad8..9d3a295e999cba7e4eb5a99f5ccef17d762db7d0 100644
--- a/modules/mol/mm/src/simulation.hh
+++ b/modules/mol/mm/src/simulation.hh
@@ -8,14 +8,12 @@
#include <ost/mol/mm/system_creator.hh>
#include <ost/mol/mm/topology.hh>
#include <ost/mol/mm/topology_creator.hh>
-#include <ost/mol/mm/mm_settings.hh>
-#include <ost/mol/mm/mm_modeller.hh>
+#include <ost/mol/mm/settings.hh>
+#include <ost/mol/mm/modeller.hh>
#include <ost/geom/vec3.hh>
-#include <ost/mol/mm/mm_observer.hh>
+#include <ost/mol/mm/observer.hh>
#include <ost/mol/mm/state_extractor.hh>
#include <ost/mol/mm/steep.hh>
-#include <ost/mol/mm/mm_interaction.hh>
-
#include <time.h>
@@ -40,15 +38,15 @@ class Simulation {
public:
Simulation(const ost::mol::EntityHandle& handle,
- const MMSettingsPtr settings);
+ const SettingsPtr settings);
Simulation(const ost::mol::mm::TopologyPtr top,
const ost::mol::EntityHandle& handle,
- const MMSettingsPtr settings);
+ const SettingsPtr settings);
void Save(const String& filename);
- static SimulationPtr Load(const String& filename, MMSettingsPtr settings);
+ static SimulationPtr Load(const String& filename, SettingsPtr settings);
ost::mol::EntityHandle GetEntity() { return ent_; }
@@ -78,7 +76,7 @@ public:
void Steps(int steps);
- void Register(MMObserverPtr o);
+ void Register(ObserverPtr o);
void ResetHarmonicBond(uint index, Real bond_length, Real force_constant);
@@ -124,7 +122,7 @@ private:
Simulation() { } //hidden constructor...
void Init(const ost::mol::mm::TopologyPtr top,
- const MMSettingsPtr settings);
+ const SettingsPtr settings);
int TimeToNextNotification();
@@ -132,7 +130,7 @@ private:
IntegratorPtr integrator_;
ContextPtr context_;
TopologyPtr top_;
- std::vector<MMObserverPtr> observers_;
+ std::vector<ObserverPtr> observers_;
std::vector<int> time_to_notify_;
std::map<FuncType,uint> system_force_mapper_;
ost::mol::EntityHandle ent_;
diff --git a/modules/mol/mm/src/system_creator.cc b/modules/mol/mm/src/system_creator.cc
index 4c7eabd90a3435f5ffb1423b0e925e7e61b2e338..02ec5bec27914ff093eff78c586c1a686340945a 100644
--- a/modules/mol/mm/src/system_creator.cc
+++ b/modules/mol/mm/src/system_creator.cc
@@ -4,7 +4,7 @@
namespace ost{ namespace mol{ namespace mm{
SystemPtr SystemCreator::Create(const TopologyPtr top,
- const MMSettingsPtr settings,
+ const SettingsPtr settings,
std::map<FuncType,uint>& mapper){
uint mapper_index = 0;
diff --git a/modules/mol/mm/src/system_creator.hh b/modules/mol/mm/src/system_creator.hh
index 58b06b05631a936c5ec8eb9f5f8f07993d5ec9ab..3dc507c1ad4a9cb8d4aa4123dd5b397dbf4d6626 100644
--- a/modules/mol/mm/src/system_creator.hh
+++ b/modules/mol/mm/src/system_creator.hh
@@ -12,9 +12,8 @@
#include <ost/mol/mm/forcefield.hh>
#include <ost/mol/mm/buildingblock.hh>
#include <ost/mol/mm/block_modifiers.hh>
-#include <ost/mol/mm/mm_interaction.hh>
-#include <ost/mol/mm/mm_settings.hh>
-#include <ost/mol/mm/mm_modeller.hh>
+#include <ost/mol/mm/settings.hh>
+#include <ost/mol/mm/modeller.hh>
#include <ost/mol/mm/index.hh>
#include <ost/mol/mm/topology.hh>
@@ -35,7 +34,7 @@ typedef boost::shared_ptr<OpenMM::System> SystemPtr;
class SystemCreator {
public:
static SystemPtr Create(const TopologyPtr top,
- const MMSettingsPtr settings,
+ const SettingsPtr settings,
std::map<FuncType,uint>& mapper);
};
diff --git a/modules/mol/mm/src/topology.cc b/modules/mol/mm/src/topology.cc
index 99dc19c47e0bf35c0157cd47f1d1f5849ae324a0..e4771197da32383b39b18022d92a724dd31fd11b 100644
--- a/modules/mol/mm/src/topology.cc
+++ b/modules/mol/mm/src/topology.cc
@@ -1,5 +1,4 @@
#include <ost/mol/mm/topology.hh>
-#include <ost/mol/mm/mm_modeller.hh>
namespace ost{ namespace mol{ namespace mm{
diff --git a/modules/mol/mm/src/topology.hh b/modules/mol/mm/src/topology.hh
index 0c9b800d906f2d3dc6deef1c212b9a7e63349067..bc2f2bdcf6e365f98a97a665aaaf79bb6b2cc18c 100644
--- a/modules/mol/mm/src/topology.hh
+++ b/modules/mol/mm/src/topology.hh
@@ -15,9 +15,7 @@
#include <ost/mol/mm/buildingblock.hh>
#include <ost/mol/mm/block_modifiers.hh>
#include <ost/mol/mm/forcefield.hh>
-#include <ost/mol/mm/mm_settings.hh>
#include <ost/mol/mm/index.hh>
-#include <ost/mol/mm/mm_interaction.hh>
#include <ost/mol/xcs_editor.hh>
#include <ost/mol/bond_handle.hh>
#include <ost/mol/residue_prop.hh>
diff --git a/modules/mol/mm/src/topology_creator.cc b/modules/mol/mm/src/topology_creator.cc
index 6cdf0e15d5f61a0efd244d5a17253ff56bd4472f..fcf9af58200f857e9402815d555e8f9ebd7277ea 100644
--- a/modules/mol/mm/src/topology_creator.cc
+++ b/modules/mol/mm/src/topology_creator.cc
@@ -53,14 +53,14 @@ int GetAtomIndex(uint residue_index,
namespace ost{ namespace mol{ namespace mm{
TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
- const MMSettingsPtr settings){
+ const SettingsPtr settings){
ost::mol::ResidueHandleList res_list = ent.GetResidueList();
ost::mol::XCSEditor ed = ent.EditXCS(ost::mol::BUFFERED_EDIT);
//rename all the stuff to the gromacs naming...
- MMModeller::AssignGromacsNaming(ent);
+ Modeller::AssignGromacsNaming(ent);
//even if not reconnected yet, it gets assumed, that
//peptide or nucleotide bonds are correctly set in the input entity
@@ -130,7 +130,7 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
ed.UpdateICS();
if(settings->generate_disulfid_bonds){
- MMModeller::GenerateDisulfidBonds(ent);
+ Modeller::GenerateDisulfidBonds(ent);
}
ff->AssignFFSpecificNames(ent);
@@ -268,8 +268,8 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
std::set<Index<2> > pairs_14;
std::set<Index<2> > distance_constraints;
//per atom parameters
- std::vector<MMInteractionPtr> ljs;
- std::vector<MMInteractionPtr> gbsa;
+ std::vector<InteractionPtr> ljs;
+ std::vector<InteractionPtr> gbsa;
//extract all bonded interactions directly from the structure itself,
//except the impropers, cmaps and exclusions. Those two get read from the building
//blocks.
@@ -336,13 +336,13 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
}
}
//impropers exclusions and cmaps get read from residuetemplates!
- std::vector<MMInteractionPtr> interaction_list;
+ std::vector<InteractionPtr> interaction_list;
std::vector<String> interaction_atom_names;
if(settings->add_impropers){
for(uint i = 0; i < building_blocks.size(); ++i){
interaction_list = building_blocks[i]->GetImpropers();
- for(std::vector<MMInteractionPtr>::iterator j = interaction_list.begin();
+ for(std::vector<InteractionPtr>::iterator j = interaction_list.begin();
j != interaction_list.end(); ++j){
interaction_atom_names = (*j)->GetNames();
Index<4> improper_index;
@@ -357,7 +357,7 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
if(settings->add_cmaps){
for(uint i = 0; i < building_blocks.size(); ++i){
interaction_list = building_blocks[i]->GetCMaps();
- for(std::vector<MMInteractionPtr>::iterator j = interaction_list.begin();
+ for(std::vector<InteractionPtr>::iterator j = interaction_list.begin();
j != interaction_list.end(); ++j){
interaction_atom_names = (*j)->GetNames();
Index<5> cmap_index;
@@ -372,7 +372,7 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
if(settings->add_nonbonded && settings->add_exclusions){
for(uint i = 0; i < building_blocks.size(); ++i){
interaction_list = building_blocks[i]->GetExclusions();
- for(std::vector<MMInteractionPtr>::iterator j = interaction_list.begin();
+ for(std::vector<InteractionPtr>::iterator j = interaction_list.begin();
j != interaction_list.end(); ++j){
interaction_atom_names = (*j)->GetNames();
uint one = GetAtomIndex(i,res_list,atom_indices,interaction_atom_names[0]);
@@ -419,7 +419,7 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
//only the first is added to avoid contradicting constraints
for(uint i = 0; i < building_blocks.size(); ++i){
interaction_list = building_blocks[i]->GetConstraints();
- for(std::vector<MMInteractionPtr>::iterator j = interaction_list.begin();
+ for(std::vector<InteractionPtr>::iterator j = interaction_list.begin();
j != interaction_list.end(); ++j){
interaction_atom_names = (*j)->GetNames();
uint one = GetAtomIndex(i,res_list,atom_indices,interaction_atom_names[0]);
@@ -452,7 +452,7 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
distance_constraints.insert(*i);
Real distance;
if(settings->ideal_bond_length_constraints){
- MMInteractionPtr bond_ptr = ff->GetBond(atom_types[(*i)[0]],atom_types[(*i)[1]]);
+ InteractionPtr bond_ptr = ff->GetBond(atom_types[(*i)[0]],atom_types[(*i)[1]]);
parameters = bond_ptr->GetParam();
distance = parameters[0];
}
@@ -466,7 +466,7 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
distance_constraints.insert(*i);
Real distance;
if(settings->ideal_bond_length_constraints){
- MMInteractionPtr bond_ptr = ff->GetBond(atom_types[(*i)[0]],atom_types[(*i)[1]]);
+ InteractionPtr bond_ptr = ff->GetBond(atom_types[(*i)[0]],atom_types[(*i)[1]]);
parameters = bond_ptr->GetParam();
distance = parameters[0];
}
@@ -530,7 +530,7 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
//handle bonds
for(uint i = 0; i < res_list.size(); ++i){
interaction_list = building_blocks[i]->GetBonds();
- for(std::vector<MMInteractionPtr>::iterator j = interaction_list.begin();
+ for(std::vector<InteractionPtr>::iterator j = interaction_list.begin();
j != interaction_list.end(); ++j){
if((*j)->IsParametrized()){
interaction_atom_names = (*j)->GetNames();
@@ -549,7 +549,7 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
for(std::set<Index<2> >::iterator i = bonds.begin();
i!=bonds.end(); ++i){
- MMInteractionPtr bond_ptr;
+ InteractionPtr bond_ptr;
try{
bond_ptr = ff->GetBond(atom_types[(*i)[0]],atom_types[(*i)[1]]);
} catch(ost::Error& e){
@@ -573,7 +573,7 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
//handle angles
for(uint i = 0; i < res_list.size(); ++i){
interaction_list = building_blocks[i]->GetAngles();
- for(std::vector<MMInteractionPtr>::iterator j = interaction_list.begin();
+ for(std::vector<InteractionPtr>::iterator j = interaction_list.begin();
j != interaction_list.end(); ++j){
if((*j)->IsParametrized()){
interaction_atom_names = (*j)->GetNames();
@@ -613,7 +613,7 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
for(std::set<Index<3> >::iterator i = angles.begin();
i!=angles.end(); ++i){
- MMInteractionPtr angle_ptr;
+ InteractionPtr angle_ptr;
try{
angle_ptr = ff->GetAngle(atom_types[(*i)[0]],
atom_types[(*i)[1]],
@@ -655,7 +655,7 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
std::set<Index<4> > dihedrals_to_delete;
for(uint i = 0; i < res_list.size(); ++i){
interaction_list = building_blocks[i]->GetDihedrals();
- for(std::vector<MMInteractionPtr>::iterator j = interaction_list.begin();
+ for(std::vector<InteractionPtr>::iterator j = interaction_list.begin();
j != interaction_list.end(); ++j){
if((*j)->IsParametrized()){
interaction_atom_names = (*j)->GetNames();
@@ -702,7 +702,7 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
for(std::set<Index<4> >::iterator i = dihedrals.begin();
i!=dihedrals.end(); ++i){
- std::vector<MMInteractionPtr> dihedral_ptr;
+ std::vector<InteractionPtr> dihedral_ptr;
try{
dihedral_ptr = ff->GetDihedrals(atom_types[(*i)[0]],
@@ -722,7 +722,7 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
continue; // ignore it and continue with next interaction
}
- for(std::vector<MMInteractionPtr>::iterator j = dihedral_ptr.begin();
+ for(std::vector<InteractionPtr>::iterator j = dihedral_ptr.begin();
j != dihedral_ptr.end(); ++j){
parameters = (*j)->GetParam();
top->AddPeriodicDihedral((*i)[0],(*i)[1],(*i)[2],(*i)[3],
@@ -736,7 +736,7 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
std::set<Index<4> > impropers_to_delete;
for(uint i = 0; i < building_blocks.size(); ++i){
interaction_list = building_blocks[i]->GetImpropers();
- for(std::vector<MMInteractionPtr>::iterator j = interaction_list.begin();
+ for(std::vector<InteractionPtr>::iterator j = interaction_list.begin();
j != interaction_list.end(); ++j){
if((*j)->IsParametrized()){
//we do not have to care about the ordering, since we extracted the
@@ -780,7 +780,7 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
for(std::set<Index<4> >::iterator i = impropers.begin();
i!=impropers.end(); ++i){
- std::vector<MMInteractionPtr> improper_ptr;
+ std::vector<InteractionPtr> improper_ptr;
try{
improper_ptr = ff->GetImpropers(atom_types[(*i)[0]],
@@ -800,7 +800,7 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
continue; // ignore it and continue with next interaction
}
- for(std::vector<MMInteractionPtr>::iterator j = improper_ptr.begin();
+ for(std::vector<InteractionPtr>::iterator j = improper_ptr.begin();
j != improper_ptr.end(); ++j){
parameters = (*j)->GetParam();
switch((*j)->GetFuncType()){
@@ -826,7 +826,7 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
//handle cmaps
for(uint i = 0; i < res_list.size(); ++i){
interaction_list = building_blocks[i]->GetCMaps();
- for(std::vector<MMInteractionPtr>::iterator j = interaction_list.begin();
+ for(std::vector<InteractionPtr>::iterator j = interaction_list.begin();
j != interaction_list.end(); ++j){
if((*j)->IsParametrized()){
//we do not have to care about the ordering, since we extracted the
@@ -854,7 +854,7 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
for(std::set<Index<5> >::iterator i = cmaps.begin();
i!=cmaps.end(); ++i){
- MMInteractionPtr cmap_ptr;
+ InteractionPtr cmap_ptr;
try{
cmap_ptr = ff->GetCMap(atom_types[(*i)[0]],
@@ -883,7 +883,7 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
if(settings->add_nonbonded){
- MMInteractionPtr lj_interaction;
+ InteractionPtr lj_interaction;
std::vector<Real> sigmas;
std::vector<Real> epsilons;
@@ -925,7 +925,7 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
std::vector<Real> radii;
std::vector<Real> scaling;
for(uint i = 0; i < atom_list.size(); ++i){
- MMInteractionPtr gbsa_ptr = ff->GetImplicitGenborn(atom_types[i]);
+ InteractionPtr gbsa_ptr = ff->GetImplicitGenborn(atom_types[i]);
if(!gbsa_ptr){
std::stringstream ss;
ss << "Structure contains atom of type " << types[i] << " which is not";
@@ -948,9 +948,9 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
//first, we rename to the gromacs standars...
ff->AssignFFSpecificNames(ent,true);
//still call the assign gromacs names function...
- MMModeller::AssignGromacsNaming(ent);
+ Modeller::AssignGromacsNaming(ent);
//let's finally do the renaming to PDB standard
- MMModeller::AssignPDBNaming(ent);
+ Modeller::AssignPDBNaming(ent);
}
diff --git a/modules/mol/mm/src/topology_creator.hh b/modules/mol/mm/src/topology_creator.hh
index 160590755bdb528c675cd28774e51debeb616130..7d95ac1bd63186bcaf10cc98037c09392c1fc65b 100644
--- a/modules/mol/mm/src/topology_creator.hh
+++ b/modules/mol/mm/src/topology_creator.hh
@@ -13,9 +13,9 @@
#include <ost/mol/mm/forcefield.hh>
#include <ost/mol/mm/buildingblock.hh>
#include <ost/mol/mm/block_modifiers.hh>
-#include <ost/mol/mm/mm_interaction.hh>
-#include <ost/mol/mm/mm_settings.hh>
-#include <ost/mol/mm/mm_modeller.hh>
+#include <ost/mol/mm/interaction.hh>
+#include <ost/mol/mm/settings.hh>
+#include <ost/mol/mm/modeller.hh>
#include <ost/mol/mm/index.hh>
#include <ost/mol/mm/topology.hh>
@@ -28,7 +28,7 @@ typedef boost::shared_ptr<TopologyCreator> TopologyCreatorPtr;
class TopologyCreator {
public:
static TopologyPtr Create(ost::mol::EntityHandle& ent,
- const MMSettingsPtr settings);
+ const SettingsPtr settings);
};
diff --git a/modules/mol/mm/tests/test_block.cc b/modules/mol/mm/tests/test_block.cc
index 45732b4131e3d4732ef2cba57169ee8ed294ccb8..ce2a9d8768aeefdbd32983455c1f94e22450e231 100644
--- a/modules/mol/mm/tests/test_block.cc
+++ b/modules/mol/mm/tests/test_block.cc
@@ -1,6 +1,6 @@
#include <boost/test/unit_test.hpp>
#include <boost/test/auto_unit_test.hpp>
-#include <ost/mol/mm/mm_interaction.hh>
+#include <ost/mol/mm/interaction.hh>
#include <ost/mol/mm/buildingblock.hh>
#include <ost/mol/mol.hh>
#include <ost/mol/builder.hh>
@@ -18,7 +18,7 @@ BOOST_AUTO_TEST_CASE(test_block_basics)
BuildingBlock block = BuildingBlock();
block.AddAtom("A","a",0.5);
block.AddAtom("B","b",1.0);
- MMInteractionPtr bond(new MMInteraction(HarmonicBond));
+ InteractionPtr bond(new Interaction(HarmonicBond));
std::vector<String> names;
names.push_back("A");
names.push_back("B");
@@ -32,7 +32,7 @@ BOOST_AUTO_TEST_CASE(test_block_basics)
BOOST_CHECK(block.GetType("X") == "x");
BOOST_CHECK(block.GetCharge("X")==42.0);
BOOST_CHECK(block.GetAtoms().size() == 2);
- std::vector<MMInteractionPtr> bonds = block.GetBonds();
+ std::vector<InteractionPtr> bonds = block.GetBonds();
BOOST_CHECK(bonds[0]->HasName("X"));
block.RemoveAtom("X");
BOOST_CHECK_THROW(block.GetType("X"),ost::Error);
@@ -45,8 +45,8 @@ BOOST_AUTO_TEST_CASE(test_block_basics)
param_one.push_back(1.0);
param_two.push_back(2.0);
param_two.push_back(2.0);
- MMInteractionPtr bond_one(new MMInteraction(HarmonicBond));
- MMInteractionPtr bond_two(new MMInteraction(HarmonicBond));
+ InteractionPtr bond_one(new Interaction(HarmonicBond));
+ InteractionPtr bond_two(new Interaction(HarmonicBond));
bond_one->SetNames(names);
bond_one->SetParam(param_one);
bond_two->SetNames(names);
@@ -93,9 +93,9 @@ BOOST_AUTO_TEST_CASE(test_connect)
block.AddAtom("A","a",0.0);
block.AddAtom("B","b",0.0);
- MMInteractionPtr bond_one(new MMInteraction(HarmonicBond));
- MMInteractionPtr bond_two(new MMInteraction(HarmonicBond));
- MMInteractionPtr bond_three(new MMInteraction(HarmonicBond));
+ InteractionPtr bond_one(new Interaction(HarmonicBond));
+ InteractionPtr bond_two(new Interaction(HarmonicBond));
+ InteractionPtr bond_three(new Interaction(HarmonicBond));
std::vector<String> two_string;
two_string.push_back("A");
two_string.push_back("B");
@@ -125,7 +125,7 @@ BOOST_AUTO_TEST_CASE(test_connect)
BOOST_CHECK_THROW(block.Connect(res_list[0],ed),ost::Error);
BOOST_CHECK_THROW(block.Connect(res_list[2],ed),ost::Error);
- MMInteractionPtr bond_four(new MMInteraction(HarmonicBond));
+ InteractionPtr bond_four(new Interaction(HarmonicBond));
two_string[1] = "X";
bond_four->SetNames(two_string);
block.AddBond(bond_four);
@@ -170,9 +170,9 @@ BOOST_AUTO_TEST_CASE(test_match)
BOOST_CHECK(!block.Match(res_list[1],true,info_string));
- MMInteractionPtr bond_one(new MMInteraction(HarmonicBond));
- MMInteractionPtr bond_two(new MMInteraction(HarmonicBond));
- MMInteractionPtr bond_three(new MMInteraction(HarmonicBond));
+ InteractionPtr bond_one(new Interaction(HarmonicBond));
+ InteractionPtr bond_two(new Interaction(HarmonicBond));
+ InteractionPtr bond_three(new Interaction(HarmonicBond));
std::vector<String> names_one;
names_one.push_back("A");
@@ -201,7 +201,7 @@ BOOST_AUTO_TEST_CASE(test_match)
block.RemoveAtom("A");
block.AddAtom("A","a",0.0);
- MMInteractionPtr constraint(new MMInteraction(DistanceConstraint));
+ InteractionPtr constraint(new Interaction(DistanceConstraint));
constraint->SetNames(names_one);
BOOST_CHECK(!block.Match(res_list[1],true,info_string));
block.AddConstraint(constraint);
diff --git a/modules/mol/mm/tests/test_block_modifiers.cc b/modules/mol/mm/tests/test_block_modifiers.cc
index 901ae4c6fa8e30a26f632a97475d7da6a50f820b..0baa79d28c0bd78fbc8d3562323077033647fd07 100644
--- a/modules/mol/mm/tests/test_block_modifiers.cc
+++ b/modules/mol/mm/tests/test_block_modifiers.cc
@@ -1,6 +1,6 @@
#include <boost/test/unit_test.hpp>
#include <boost/test/auto_unit_test.hpp>
-#include <ost/mol/mm/mm_interaction.hh>
+#include <ost/mol/mm/interaction.hh>
#include <ost/mol/mm/buildingblock.hh>
#include <ost/mol/mol.hh>
#include <ost/mol/builder.hh>
@@ -19,13 +19,13 @@ BOOST_AUTO_TEST_CASE(test_gromacs_block_modifier_basics){
GromacsBlockModifier mod;
//let's create some interactions
- MMInteractionPtr harmonic_bond(new MMInteraction(HarmonicBond));
- MMInteractionPtr urey_bradley_angle(new MMInteraction(UreyBradleyAngle));
- MMInteractionPtr harmonic_angle(new MMInteraction(HarmonicAngle));
- MMInteractionPtr periodic_dihedral(new MMInteraction(PeriodicDihedral));
- MMInteractionPtr periodic_improper(new MMInteraction(PeriodicImproper));
- MMInteractionPtr harmonic_improper(new MMInteraction(HarmonicImproper));
- MMInteractionPtr cmap(new MMInteraction(CMap));
+ InteractionPtr harmonic_bond(new Interaction(HarmonicBond));
+ InteractionPtr urey_bradley_angle(new Interaction(UreyBradleyAngle));
+ InteractionPtr harmonic_angle(new Interaction(HarmonicAngle));
+ InteractionPtr periodic_dihedral(new Interaction(PeriodicDihedral));
+ InteractionPtr periodic_improper(new Interaction(PeriodicImproper));
+ InteractionPtr harmonic_improper(new Interaction(HarmonicImproper));
+ InteractionPtr cmap(new Interaction(CMap));
//check whether error gets thrown, when names of interactions are not set
BOOST_CHECK_THROW(mod.AddBond(harmonic_bond),ost::Error);
@@ -78,20 +78,7 @@ BOOST_AUTO_TEST_CASE(test_gromacs_block_modifier_basics){
BOOST_CHECK_THROW(mod.AddDihedral(harmonic_bond),ost::Error);
BOOST_CHECK_THROW(mod.AddImproper(periodic_dihedral),ost::Error);
BOOST_CHECK_THROW(mod.AddCMap(periodic_improper),ost::Error);
-
-
-
-
-
-
-
-
-
-
}
-
-
-
BOOST_AUTO_TEST_SUITE_END();
diff --git a/modules/mol/mm/tests/test_forcefield.cc b/modules/mol/mm/tests/test_forcefield.cc
index a2fec9865249a2f2ba9a629352516824ad3542e1..e8c649354efcfb0c3baa7b6d0d98f1585b957212 100644
--- a/modules/mol/mm/tests/test_forcefield.cc
+++ b/modules/mol/mm/tests/test_forcefield.cc
@@ -1,8 +1,8 @@
#include <boost/test/unit_test.hpp>
#include <boost/test/auto_unit_test.hpp>
-#include <ost/mol/mm/mm_settings.hh>
+#include <ost/mol/mm/settings.hh>
#include <ost/mol/mm/forcefield.hh>
-#include <ost/mol/mm/mm_interaction.hh>
+#include <ost/mol/mm/interaction.hh>
#include <ost/mol/mm/buildingblock.hh>
#include <ost/mol/mm/gromacs_block_modifiers.hh>
#include <ost/message.hh>
@@ -85,17 +85,17 @@ BOOST_AUTO_TEST_CASE(test_forcefield_basics){
five_real.push_back(5.0);
- MMInteractionPtr harmonic_bond(new MMInteraction(HarmonicBond));
- MMInteractionPtr urey_bradley_angle(new MMInteraction(UreyBradleyAngle));
- MMInteractionPtr harmonic_angle(new MMInteraction(HarmonicAngle));
- MMInteractionPtr periodic_dihedral(new MMInteraction(PeriodicDihedral));
- MMInteractionPtr periodic_improper(new MMInteraction(PeriodicImproper));
- MMInteractionPtr harmonic_improper(new MMInteraction(HarmonicImproper));
- MMInteractionPtr cmap(new MMInteraction(CMap));
- MMInteractionPtr lj(new MMInteraction(LJ));
- MMInteractionPtr lj_pair(new MMInteraction(LJPair));
- MMInteractionPtr gbsa(new MMInteraction(GBSA));
- MMInteractionPtr distance_constraint(new MMInteraction(DistanceConstraint));
+ InteractionPtr harmonic_bond(new Interaction(HarmonicBond));
+ InteractionPtr urey_bradley_angle(new Interaction(UreyBradleyAngle));
+ InteractionPtr harmonic_angle(new Interaction(HarmonicAngle));
+ InteractionPtr periodic_dihedral(new Interaction(PeriodicDihedral));
+ InteractionPtr periodic_improper(new Interaction(PeriodicImproper));
+ InteractionPtr harmonic_improper(new Interaction(HarmonicImproper));
+ InteractionPtr cmap(new Interaction(CMap));
+ InteractionPtr lj(new Interaction(LJ));
+ InteractionPtr lj_pair(new Interaction(LJPair));
+ InteractionPtr gbsa(new Interaction(GBSA));
+ InteractionPtr distance_constraint(new Interaction(DistanceConstraint));
//check whether errors get thrown when incorrectly parametrized interactions are added
diff --git a/modules/mol/mm/tests/test_interaction.cc b/modules/mol/mm/tests/test_interaction.cc
index b30080e8c0e924efbe102c3ecd0389bc2489dcc7..4e2f645faf517823e7baf4497a5d6264f7e50a6f 100644
--- a/modules/mol/mm/tests/test_interaction.cc
+++ b/modules/mol/mm/tests/test_interaction.cc
@@ -1,6 +1,6 @@
#include <boost/test/unit_test.hpp>
#include <boost/test/auto_unit_test.hpp>
-#include <ost/mol/mm/mm_interaction.hh>
+#include <ost/mol/mm/interaction.hh>
#include <ost/mol/mol.hh>
#include <ost/mol/builder.hh>
@@ -14,20 +14,20 @@ BOOST_AUTO_TEST_SUITE( mol_mm );
BOOST_AUTO_TEST_CASE(test_set_stuff)
{
- MMInteraction harmonic_bond = MMInteraction(HarmonicBond);
- MMInteraction harmonic_angle = MMInteraction(HarmonicAngle);
- MMInteraction urey_bradley = MMInteraction(UreyBradleyAngle);
- MMInteraction periodic_dihedral = MMInteraction(PeriodicDihedral);
- MMInteraction periodic_improper = MMInteraction(PeriodicImproper);
- MMInteraction harmonic_improper = MMInteraction(HarmonicImproper);
- MMInteraction cmap = MMInteraction(CMap);
- MMInteraction lj = MMInteraction(LJ);
- MMInteraction lj_pair = MMInteraction(LJPair);
- MMInteraction gbsa = MMInteraction(GBSA);
- MMInteraction distance_constraint = MMInteraction(DistanceConstraint);
- MMInteraction exclusion = MMInteraction(Exclusion);
- MMInteraction harmonic_distance_restraint = MMInteraction(HarmonicDistanceRestraint);
- MMInteraction harmonic_position_restraint = MMInteraction(HarmonicPositionRestraint);
+ Interaction harmonic_bond = Interaction(HarmonicBond);
+ Interaction harmonic_angle = Interaction(HarmonicAngle);
+ Interaction urey_bradley = Interaction(UreyBradleyAngle);
+ Interaction periodic_dihedral = Interaction(PeriodicDihedral);
+ Interaction periodic_improper = Interaction(PeriodicImproper);
+ Interaction harmonic_improper = Interaction(HarmonicImproper);
+ Interaction cmap = Interaction(CMap);
+ Interaction lj = Interaction(LJ);
+ Interaction lj_pair = Interaction(LJPair);
+ Interaction gbsa = Interaction(GBSA);
+ Interaction distance_constraint = Interaction(DistanceConstraint);
+ Interaction exclusion = Interaction(Exclusion);
+ Interaction harmonic_distance_restraint = Interaction(HarmonicDistanceRestraint);
+ Interaction harmonic_position_restraint = Interaction(HarmonicPositionRestraint);
//std::vector<String> one_string, two_string, three_string, four_string, five_string;
//std::vector<Real> one_real, two_real, three_real, four_real, five_real, zero_real;
@@ -152,7 +152,7 @@ BOOST_AUTO_TEST_CASE(test_set_stuff)
BOOST_CHECK_NO_THROW(cmap.SetParam(valid_cmap_parameters));
BOOST_CHECK(harmonic_bond.IsParametrized());
- MMInteraction new_bond = MMInteraction(HarmonicBond);
+ Interaction new_bond = Interaction(HarmonicBond);
std::vector<String> with_wildcard, without_wildcard;
with_wildcard.push_back("A");
without_wildcard.push_back("A");
@@ -183,7 +183,7 @@ BOOST_AUTO_TEST_CASE(test_set_stuff)
BOOST_AUTO_TEST_CASE(test_match_stuff)
{
- MMInteraction dihedral = MMInteraction(PeriodicDihedral);
+ Interaction dihedral = Interaction(PeriodicDihedral);
std::vector<String> with_wildcard, without_wildcard;
with_wildcard.push_back("X");
@@ -212,7 +212,7 @@ BOOST_AUTO_TEST_CASE(test_match_stuff)
}
BOOST_AUTO_TEST_CASE(test_replace_atom){
- MMInteraction bond = MMInteraction(HarmonicBond);
+ Interaction bond = Interaction(HarmonicBond);
std::vector<String> strings;
strings.push_back("A");
strings.push_back("B");
@@ -245,7 +245,7 @@ BOOST_AUTO_TEST_CASE(test_getatoms){
ost::mol::AtomHandleList atom_list_two = res_list[1].GetAtomList();
ost::mol::AtomHandleList atom_list_three = res_list[2].GetAtomList();
- MMInteraction bond = MMInteraction(HarmonicBond);
+ Interaction bond = Interaction(HarmonicBond);
std::vector<String> strings;
strings.push_back("A");
strings.push_back("B");
diff --git a/modules/mol/mm/tests/test_simulation.cc b/modules/mol/mm/tests/test_simulation.cc
index f0e362e4b7fb08e682ff815f6c5f5435fc4537da..9c08182a4c63ca96a1ae7dd3d7cffbce068b226b 100644
--- a/modules/mol/mm/tests/test_simulation.cc
+++ b/modules/mol/mm/tests/test_simulation.cc
@@ -1,8 +1,8 @@
#include <boost/test/unit_test.hpp>
#include <boost/test/auto_unit_test.hpp>
-#include <ost/mol/mm/mm_settings.hh>
+#include <ost/mol/mm/settings.hh>
#include <ost/mol/mm/forcefield.hh>
-#include <ost/mol/mm/mm_interaction.hh>
+#include <ost/mol/mm/interaction.hh>
#include <ost/mol/mm/buildingblock.hh>
#include <ost/mol/mm/gromacs_block_modifiers.hh>
#include <ost/message.hh>
@@ -29,7 +29,7 @@ BOOST_AUTO_TEST_CASE(test_simulation_basics){
ost::conop::ProcessorPtr processor(new ost::conop::HeuristicProcessor);
processor->Process(test_ent);
- MMSettingsPtr settings(new MMSettings);
+ SettingsPtr settings(new Settings);
ForcefieldPtr forcefield = Forcefield::Load("CHARMM27.dat");
settings->forcefield = forcefield;
settings->add_gbsa = true;
@@ -123,7 +123,7 @@ BOOST_AUTO_TEST_CASE(test_simulation_energy_calculations){
ost::conop::ProcessorPtr processor(new ost::conop::HeuristicProcessor);
processor->Process(test_ent);
- MMSettingsPtr settings(new MMSettings);
+ SettingsPtr settings(new Settings);
ForcefieldPtr forcefield = Forcefield::Load("CHARMM27.dat");
settings->forcefield = forcefield;
diff --git a/modules/mol/mm/tests/test_topology.cc b/modules/mol/mm/tests/test_topology.cc
index 59de803c02a02aabe90b635a881c6b4cc7be6461..09636628d94a96141bc0c5410e428db3867697ca 100644
--- a/modules/mol/mm/tests/test_topology.cc
+++ b/modules/mol/mm/tests/test_topology.cc
@@ -2,7 +2,7 @@
#include <boost/test/auto_unit_test.hpp>
#include <ost/mol/mm/topology.hh>
#include <ost/mol/mm/topology_creator.hh>
-#include <ost/mol/mm/mm_settings.hh>
+#include <ost/mol/mm/settings.hh>
#include <ost/mol/mm/forcefield.hh>
#include <ost/io/mol/pdb_reader.hh>
#include <ost/conop/heuristic.hh>
@@ -297,7 +297,7 @@ BOOST_AUTO_TEST_CASE(test_topology_merge){
reader.Import(test_ent);
ForcefieldPtr ff = Forcefield::Load("CHARMM27.dat");
- MMSettingsPtr settings = MMSettingsPtr(new MMSettings);
+ SettingsPtr settings = SettingsPtr(new Settings);
settings->add_gbsa = true;
settings->forcefield = ff;