diff --git a/modules/mol/mm/pymod/CMakeLists.txt b/modules/mol/mm/pymod/CMakeLists.txt
index 2738a0d5a9f76ea6efe412a402895f52ed8c36e2..3156429e1c24cf25b6c7685fd6507254a02e0f8f 100644
--- a/modules/mol/mm/pymod/CMakeLists.txt
+++ b/modules/mol/mm/pymod/CMakeLists.txt
@@ -4,7 +4,7 @@ set(OST_MOL_MM_PYMOD_SOURCES
export_simulation.cc
export_openmm.cc
export_observers.cc
- export_gromacs_reader.cc
+ export_ff_reader.cc
export_interaction.cc
export_buildingblock.cc
export_block_modifiers.cc
diff --git a/modules/mol/mm/pymod/export_gromacs_reader.cc b/modules/mol/mm/pymod/export_ff_reader.cc
similarity index 56%
rename from modules/mol/mm/pymod/export_gromacs_reader.cc
rename to modules/mol/mm/pymod/export_ff_reader.cc
index fe41bfccb8ae798815d09c676a967fb8a0a849b9..ea77c2e4b5b6fd9b24241277d346974d28f7e856 100644
--- a/modules/mol/mm/pymod/export_gromacs_reader.cc
+++ b/modules/mol/mm/pymod/export_ff_reader.cc
@@ -17,25 +17,25 @@
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
#include <boost/python.hpp>
-#include <ost/mol/mm/gromacs_reader.hh>
+#include <ost/mol/mm/ff_reader.hh>
#include <ost/mol/residue_handle.hh>
using namespace boost::python;
using namespace ost::mol::mm;
-void export_GromacsReader()
+void export_FFReader()
{
- class_<ost::mol::mm::GromacsReader>("GromacsReader",init<String>())
- .def("ReadGromacsForcefield",&ost::mol::mm::GromacsReader::ReadGromacsForcefield)
- .def("SetPreprocessorDefinition",&ost::mol::mm::GromacsReader::SetPreprocessorDefinition)
- .def("GetForcefield",&ost::mol::mm::GromacsReader::GetForcefield)
- .def("SetForcefield",&ost::mol::mm::GromacsReader::SetForcefield)
- .def("ReadResidueDatabase",&ost::mol::mm::GromacsReader::ReadResidueDatabase)
- .def("ReadITP",&ost::mol::mm::GromacsReader::ReadITP)
- .def("ReadCHARMMPRM",&ost::mol::mm::GromacsReader::ReadCHARMMPRM)
- .def("ReadCHARMMRTF",&ost::mol::mm::GromacsReader::ReadCHARMMRTF)
+ class_<ost::mol::mm::FFReader>("FFReader",init<String>())
+ .def("ReadGromacsForcefield",&ost::mol::mm::FFReader::ReadGromacsForcefield)
+ .def("SetPreprocessorDefinition",&ost::mol::mm::FFReader::SetPreprocessorDefinition)
+ .def("GetForcefield",&ost::mol::mm::FFReader::GetForcefield)
+ .def("SetForcefield",&ost::mol::mm::FFReader::SetForcefield)
+ .def("ReadResidueDatabase",&ost::mol::mm::FFReader::ReadResidueDatabase)
+ .def("ReadITP",&ost::mol::mm::FFReader::ReadITP)
+ .def("ReadCHARMMPRM",&ost::mol::mm::FFReader::ReadCHARMMPRM)
+ .def("ReadCHARMMRTF",&ost::mol::mm::FFReader::ReadCHARMMRTF)
;
- boost::python::register_ptr_to_python<ost::mol::mm::GromacsReaderPtr>();
+ boost::python::register_ptr_to_python<ost::mol::mm::FFReaderPtr>();
}
\ No newline at end of file
diff --git a/modules/mol/mm/pymod/wrap_mol_mm.cc b/modules/mol/mm/pymod/wrap_mol_mm.cc
index 9ddcec57e166bd34b2a88af8c10ede960de50d3e..3c174d7db541b29d45bd0d75e3082812efbf3892 100644
--- a/modules/mol/mm/pymod/wrap_mol_mm.cc
+++ b/modules/mol/mm/pymod/wrap_mol_mm.cc
@@ -8,7 +8,7 @@ void export_Settings();
void export_Simulation();
void export_OpenMM();
void export_Observers();
-void export_GromacsReader();
+void export_FFReader();
void export_Interaction();
void export_Buildingblock();
void export_Forcefield();
@@ -24,7 +24,7 @@ BOOST_PYTHON_MODULE(_ost_mol_mm)
export_Simulation();
export_OpenMM();
export_Observers();
- export_GromacsReader();
+ export_FFReader();
export_Interaction();
export_Buildingblock();
export_BlockModifiers();
diff --git a/modules/mol/mm/src/CMakeLists.txt b/modules/mol/mm/src/CMakeLists.txt
index 6fc560ef2a2f31e148a22e978c0845972b795391..5751ca88379cc84827d209cfc87960bd27363ce0 100644
--- a/modules/mol/mm/src/CMakeLists.txt
+++ b/modules/mol/mm/src/CMakeLists.txt
@@ -1,6 +1,6 @@
set(OST_MOL_MM_HEADERS
forcefield.hh
- gromacs_reader.hh
+ ff_reader.hh
buildingblock.hh
block_modifiers.hh
gromacs_block_modifiers.hh
@@ -21,7 +21,7 @@ set(OST_MOL_MM_HEADERS
set(OST_MOL_MM_SOURCES
forcefield.cc
- gromacs_reader.cc
+ ff_reader.cc
buildingblock.cc
gromacs_block_modifiers.cc
heuristic_block_modifiers.cc
diff --git a/modules/mol/mm/src/gromacs_reader.cc b/modules/mol/mm/src/ff_reader.cc
similarity index 96%
rename from modules/mol/mm/src/gromacs_reader.cc
rename to modules/mol/mm/src/ff_reader.cc
index 7306556dbfcbb82b41d535fd5a703f5f20fb208e..6196cc2886e6c75d450d316711035baca28b27d9 100644
--- a/modules/mol/mm/src/gromacs_reader.cc
+++ b/modules/mol/mm/src/ff_reader.cc
@@ -1,4 +1,4 @@
-#include <ost/mol/mm/gromacs_reader.hh>
+#include <ost/mol/mm/ff_reader.hh>
namespace ost { namespace mol{ namespace mm {
@@ -147,10 +147,6 @@ CHARMMDataPtr CHARMMData::Instance(){
CHARMMDataPtr CHARMMData::instance_ = CHARMMDataPtr();
-
-
-
-
std::vector<std::vector<String> > MMPreprocessor::Process(const String& filename){
std::vector<std::vector<String> > file_content = this->ReadFile(filename);
@@ -348,7 +344,7 @@ std::vector<std::vector<String> > MMPreprocessor::ReadFile(const String& filenam
return split_file_content;
}
-GromacsReader::GromacsReader(const String& base_dir): preprocessor_(base_dir),
+FFReader::FFReader(const String& base_dir): preprocessor_(base_dir),
ff_(new Forcefield)
{
for(int i = 0; i < 4; ++i){
@@ -357,7 +353,7 @@ GromacsReader::GromacsReader(const String& base_dir): preprocessor_(base_dir),
}
}
-void GromacsReader::ReadGromacsForcefield(){
+void FFReader::ReadGromacsForcefield(){
//read in the forcefield
if(!boost::filesystem::exists(preprocessor_.GetBasedir() / "forcefield.itp")){
@@ -372,7 +368,7 @@ void GromacsReader::ReadGromacsForcefield(){
this->ParseAtomTypes(content);
}
-void GromacsReader::ReadResidueDatabase(const String& basename){
+void FFReader::ReadResidueDatabase(const String& basename){
std::vector<std::vector<String> > data = preprocessor_.Process(basename+".rtp");
this->ParseRTP(data);
@@ -407,17 +403,17 @@ void GromacsReader::ReadResidueDatabase(const String& basename){
}catch(ost::io::IOException e) { }
}
-void GromacsReader::ReadCHARMMPRM(const String& filename){
+void FFReader::ReadCHARMMPRM(const String& filename){
std::vector<std::vector<String> > data = preprocessor_.Process(filename);
this->ParseCHARMMPRM(data);
}
-void GromacsReader::ReadCHARMMRTF(const String& filename){
+void FFReader::ReadCHARMMRTF(const String& filename){
std::vector<std::vector<String> > data = preprocessor_.Process(filename);
this->ParseCHARMMRTF(data);
}
-void GromacsReader::ParseForcefield(std::vector<std::vector<String> >& content){
+void FFReader::ParseForcefield(std::vector<std::vector<String> >& content){
int keyword_id = -1;
std::vector<String> current_line;
@@ -515,14 +511,14 @@ void GromacsReader::ParseForcefield(std::vector<std::vector<String> >& content){
}
}
-void GromacsReader::ParseAtomTypes(std::vector<std::vector<String> >& content){
+void FFReader::ParseAtomTypes(std::vector<std::vector<String> >& content){
for(std::vector<std::vector<String> >::iterator i = content.begin();
i!=content.end(); ++i){
ff_->AddMass((*i)[0],boost::lexical_cast<Real>((*i)[1]));
}
}
-void GromacsReader::ParseRTP(std::vector<std::vector<String> >& content){
+void FFReader::ParseRTP(std::vector<std::vector<String> >& content){
read_residues_.clear();
@@ -622,7 +618,7 @@ void GromacsReader::ParseRTP(std::vector<std::vector<String> >& content){
}
-void GromacsReader::ParseARN(std::vector<std::vector<String> >& content){
+void FFReader::ParseARN(std::vector<std::vector<String> >& content){
String res_name, a_one, a_two;
for(std::vector<std::vector<String> >::iterator i = content.begin();
@@ -643,7 +639,7 @@ void GromacsReader::ParseARN(std::vector<std::vector<String> >& content){
}
}
-void GromacsReader::ParseHDB(std::vector<std::vector<String> >& content){
+void FFReader::ParseHDB(std::vector<std::vector<String> >& content){
std::vector<std::vector<String> > residue_data;
String residue_name;
@@ -674,7 +670,7 @@ void GromacsReader::ParseHDB(std::vector<std::vector<String> >& content){
}
}
-void GromacsReader::ParseHydrogenRule(const std::vector<String>& data,
+void FFReader::ParseHydrogenRule(const std::vector<String>& data,
GromacsHydrogenConstructor& constructor){
if(data.size() < 4){
@@ -716,7 +712,7 @@ void GromacsReader::ParseHydrogenRule(const std::vector<String>& data,
}
-void GromacsReader::ParseTerminiReplaceRule(const std::vector<String>& data,
+void FFReader::ParseTerminiReplaceRule(const std::vector<String>& data,
GromacsBlockModifier& modifier){
String name;
@@ -740,7 +736,7 @@ void GromacsReader::ParseTerminiReplaceRule(const std::vector<String>& data,
//we neglect the mass! This will be read from the forcefield itself!
}
-void GromacsReader::ParseTerminiAddRule(const std::vector<String>& data1,
+void FFReader::ParseTerminiAddRule(const std::vector<String>& data1,
const std::vector<String>& data2,
GromacsBlockModifier& modifier){
@@ -788,7 +784,7 @@ void GromacsReader::ParseTerminiAddRule(const std::vector<String>& data1,
}
-void GromacsReader::ParseNTDB(std::vector<std::vector<String> >& content){
+void FFReader::ParseNTDB(std::vector<std::vector<String> >& content){
//Besided general termini constructors, there are also residue
//specific constructors => custom constructors
@@ -853,7 +849,7 @@ void GromacsReader::ParseNTDB(std::vector<std::vector<String> >& content){
}
}
-void GromacsReader::ParseCTDB(std::vector<std::vector<String> >& content){
+void FFReader::ParseCTDB(std::vector<std::vector<String> >& content){
//Besided general termini constructors, there are also residue
//specific constructors => custom constructors
@@ -918,11 +914,11 @@ void GromacsReader::ParseCTDB(std::vector<std::vector<String> >& content){
}
}
-void GromacsReader::ParseVSD(std::vector<std::vector<String> >& content){
+void FFReader::ParseVSD(std::vector<std::vector<String> >& content){
}
-void GromacsReader::ParseRtoB(std::vector<std::vector<String> >& content){
+void FFReader::ParseRtoB(std::vector<std::vector<String> >& content){
//there are two versions of this file, either with two or five
//columns further instructions can be found in the gromacs manual
@@ -953,12 +949,12 @@ void GromacsReader::ParseRtoB(std::vector<std::vector<String> >& content){
}
}
-void GromacsReader::ReadITP(const String& basename){
+void FFReader::ReadITP(const String& basename){
std::vector<std::vector<String> > content = preprocessor_.Process(basename + ".itp");
this->ParseITP(content);
}
-void GromacsReader::ParseITP(std::vector<std::vector<String> >& content){
+void FFReader::ParseITP(std::vector<std::vector<String> >& content){
std::vector<std::vector<String> > residue_data;
String residue_name;
@@ -984,7 +980,7 @@ void GromacsReader::ParseITP(std::vector<std::vector<String> >& content){
}
}
-BuildingBlockPtr GromacsReader::BlockFromRTP(const std::vector<std::vector<String> >& data){
+BuildingBlockPtr FFReader::BlockFromRTP(const std::vector<std::vector<String> >& data){
if(bonded_types_.size()<4){
std::stringstream ss;
@@ -1051,7 +1047,7 @@ BuildingBlockPtr GromacsReader::BlockFromRTP(const std::vector<std::vector<Strin
return p;
}
-BuildingBlockPtr GromacsReader::BlockFromITP(const std::vector<std::vector<String> >& data){
+BuildingBlockPtr FFReader::BlockFromITP(const std::vector<std::vector<String> >& data){
int keyword_index;
@@ -1180,7 +1176,7 @@ BuildingBlockPtr GromacsReader::BlockFromITP(const std::vector<std::vector<Strin
}
-BlockModifierPtr GromacsReader::ParseBlockModifier(const std::vector<std::vector<String> >& data){
+BlockModifierPtr FFReader::ParseBlockModifier(const std::vector<std::vector<String> >& data){
int keyword_index = -1;
@@ -1249,7 +1245,7 @@ BlockModifierPtr GromacsReader::ParseBlockModifier(const std::vector<std::vector
}
-InteractionPtr GromacsReader::ParseBond(const std::vector<String>& data,
+InteractionPtr FFReader::ParseBond(const std::vector<String>& data,
bool type_definition,
FuncType functype){
@@ -1299,7 +1295,7 @@ InteractionPtr GromacsReader::ParseBond(const std::vector<String>& data,
return p;
}
-InteractionPtr GromacsReader::ParseAngle(const std::vector<String>& data,
+InteractionPtr FFReader::ParseAngle(const std::vector<String>& data,
bool type_definition,
FuncType functype){
@@ -1357,7 +1353,7 @@ InteractionPtr GromacsReader::ParseAngle(const std::vector<String>& data,
return p;
}
-InteractionPtr GromacsReader::ParseDihedral(const std::vector<String>& data,
+InteractionPtr FFReader::ParseDihedral(const std::vector<String>& data,
bool type_definition,
FuncType functype){
if(data.size() < 4){
@@ -1414,7 +1410,7 @@ InteractionPtr GromacsReader::ParseDihedral(const std::vector<String>& data,
return p;
}
-InteractionPtr GromacsReader::ParseCMap(const std::vector<String>& data,
+InteractionPtr FFReader::ParseCMap(const std::vector<String>& data,
bool type_definition,
FuncType functype){
if(data.size() < 5){
@@ -1467,7 +1463,7 @@ InteractionPtr GromacsReader::ParseCMap(const std::vector<String>& data,
}
-InteractionPtr GromacsReader::ParseLJ(const std::vector<String>& data,
+InteractionPtr FFReader::ParseLJ(const std::vector<String>& data,
bool type_definition,
FuncType functype){
@@ -1501,7 +1497,7 @@ InteractionPtr GromacsReader::ParseLJ(const std::vector<String>& data,
}
-InteractionPtr GromacsReader::ParseLJPair(const std::vector<String>& data,
+InteractionPtr FFReader::ParseLJPair(const std::vector<String>& data,
bool type_definition,
FuncType functype){
@@ -1550,7 +1546,7 @@ InteractionPtr GromacsReader::ParseLJPair(const std::vector<String>& data,
return p;
}
-InteractionPtr GromacsReader::ParseConstraint(const std::vector<String>& data,
+InteractionPtr FFReader::ParseConstraint(const std::vector<String>& data,
bool type_definition,
FuncType functype){
@@ -1598,7 +1594,7 @@ InteractionPtr GromacsReader::ParseConstraint(const std::vector<String>& data,
return p;
}
-InteractionPtr GromacsReader::ParseGenborn(const std::vector<String>& data,
+InteractionPtr FFReader::ParseGenborn(const std::vector<String>& data,
bool type_definition,
FuncType functype){
@@ -1631,7 +1627,7 @@ InteractionPtr GromacsReader::ParseGenborn(const std::vector<String>& data,
}
-InteractionPtr GromacsReader::ParseExclusion(const std::vector<String>& data,
+InteractionPtr FFReader::ParseExclusion(const std::vector<String>& data,
bool type_definition,
FuncType functype){
@@ -1653,7 +1649,7 @@ InteractionPtr GromacsReader::ParseExclusion(const std::vector<String>& data,
return p;
}
-void GromacsReader::ParseCHARMMPRM(std::vector<std::vector<String> >& content){
+void FFReader::ParseCHARMMPRM(std::vector<std::vector<String> >& content){
int keyword_id = -1;
@@ -1877,7 +1873,7 @@ void GromacsReader::ParseCHARMMPRM(std::vector<std::vector<String> >& content){
}
-void GromacsReader::ParseCHARMMRTF(std::vector<std::vector<String> >& content){
+void FFReader::ParseCHARMMRTF(std::vector<std::vector<String> >& content){
bool in_block = false;
diff --git a/modules/mol/mm/src/gromacs_reader.hh b/modules/mol/mm/src/ff_reader.hh
similarity index 97%
rename from modules/mol/mm/src/gromacs_reader.hh
rename to modules/mol/mm/src/ff_reader.hh
index 31d4ddbfeac26d97d9845d25daa9be61c0be4acf..f166f5f2404aaaec93bb9053f412620a5f85c773 100644
--- a/modules/mol/mm/src/gromacs_reader.hh
+++ b/modules/mol/mm/src/ff_reader.hh
@@ -19,9 +19,9 @@ namespace ost { namespace mol{ namespace mm{
class GromacsData;
class CHARMMData;
-class GromacsReader;
+class FFReader;
typedef boost::shared_ptr<GromacsData> GromacsDataPtr;
-typedef boost::shared_ptr<GromacsReader> GromacsReaderPtr;
+typedef boost::shared_ptr<FFReader> FFReaderPtr;
typedef boost::shared_ptr<CHARMMData> CHARMMDataPtr;
class GromacsData{
@@ -80,10 +80,10 @@ private:
};
-class GromacsReader {
+class FFReader {
public:
- GromacsReader(const String& base_dir);
+ FFReader(const String& base_dir);
void SetPreprocessorDefinition(const String& def) { preprocessor_.SetDefinition(def); }