From 154a849587d5b32b5f2245310e8c89b1512d10ba Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Thu, 19 Jul 2012 10:52:37 +0200
Subject: [PATCH] Fixed several inconsistent file/class names
---
src/CLToolDriver.cpp | 5 ++---
src/{ContactMap.cpp => ColvarContactMap.cpp} | 16 ++++++++--------
src/{ColvarTarget.cpp => FunctionTarget.cpp} | 12 ++++++------
src/GenericWholeMolecules.cpp | 4 ++--
src/MultiColvar.cpp | 4 ++--
src/{MolInfo.cpp => SetupMolInfo.cpp} | 12 ++++++------
src/{MolInfo.h => SetupMolInfo.h} | 4 ++--
7 files changed, 28 insertions(+), 29 deletions(-)
rename src/{ContactMap.cpp => ColvarContactMap.cpp} (94%)
rename src/{ColvarTarget.cpp => FunctionTarget.cpp} (90%)
rename src/{MolInfo.cpp => SetupMolInfo.cpp} (94%)
rename src/{MolInfo.h => SetupMolInfo.h} (96%)
diff --git a/src/CLToolDriver.cpp b/src/CLToolDriver.cpp
index 8eac390d5..284c663ee 100644
--- a/src/CLToolDriver.cpp
+++ b/src/CLToolDriver.cpp
@@ -315,10 +315,9 @@ int CLToolDriver<real>::main(int argc,char**argv,FILE*in,FILE*out,PlumedCommunic
return 0;
}
-typedef CLToolDriver<double> Driver;
-typedef CLToolDriver<float> DriverSp;
+typedef CLToolDriver<double> CLToolDriverDouble;
-PLUMED_REGISTER_CLTOOL(Driver,"driver")
+PLUMED_REGISTER_CLTOOL(CLToolDriverDouble,"driver")
diff --git a/src/ContactMap.cpp b/src/ColvarContactMap.cpp
similarity index 94%
rename from src/ContactMap.cpp
rename to src/ColvarContactMap.cpp
index 4fc37998b..e6d96ba61 100644
--- a/src/ContactMap.cpp
+++ b/src/ColvarContactMap.cpp
@@ -51,7 +51,7 @@ PRINT ARG=f1.* FILE=colvar
*/
//+ENDPLUMEDOC
-class ContactMap : public Colvar {
+class ColvarContactMap : public Colvar {
private:
bool pbc, dosum;
NeighborList *nl;
@@ -59,16 +59,16 @@ private:
bool reduceListAtNextStep;
public:
static void registerKeywords( Keywords& keys );
- ContactMap(const ActionOptions&);
- ~ContactMap();
+ ColvarContactMap(const ActionOptions&);
+ ~ColvarContactMap();
// active methods:
virtual void calculate();
void checkFieldsAllowed(){};
};
-PLUMED_REGISTER_ACTION(ContactMap,"CONTACTMAP")
+PLUMED_REGISTER_ACTION(ColvarContactMap,"CONTACTMAP")
-void ContactMap::registerKeywords( Keywords& keys ){
+void ColvarContactMap::registerKeywords( Keywords& keys ){
Colvar::registerKeywords( keys );
keys.add("numbered","ATOMS","the atoms involved in each of the contacts you wish to calculate. "
"Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one contact will be "
@@ -78,7 +78,7 @@ void ContactMap::registerKeywords( Keywords& keys ){
keys.addFlag("SUM",false,"calculate the sum of all the contacts in the input");
}
-ContactMap::ContactMap(const ActionOptions&ao):
+ColvarContactMap::ColvarContactMap(const ActionOptions&ao):
PLUMED_COLVAR_INIT(ao),
pbc(true),
dosum(false),
@@ -143,11 +143,11 @@ reduceListAtNextStep(false)
checkRead();
}
-ContactMap::~ContactMap(){
+ColvarContactMap::~ColvarContactMap(){
delete nl;
}
-void ContactMap::calculate(){
+void ColvarContactMap::calculate(){
double ncoord=0., coord;
Tensor virial;
diff --git a/src/ColvarTarget.cpp b/src/FunctionTarget.cpp
similarity index 90%
rename from src/ColvarTarget.cpp
rename to src/FunctionTarget.cpp
index 7155ac0a0..b4cc1821c 100644
--- a/src/ColvarTarget.cpp
+++ b/src/FunctionTarget.cpp
@@ -41,26 +41,26 @@ set of collective variables.
*/
//+ENDPLUMEDOC
-class TargetFrame : public Function {
+class FunctionTarget : public Function {
private:
TargetDist target;
std::vector<double> derivs;
public:
- TargetFrame(const ActionOptions&);
+ FunctionTarget(const ActionOptions&);
virtual void calculate();
static void registerKeywords(Keywords& keys );
};
-PLUMED_REGISTER_ACTION(TargetFrame,"TARGET")
+PLUMED_REGISTER_ACTION(FunctionTarget,"TARGET")
-void TargetFrame::registerKeywords(Keywords& keys){
+void FunctionTarget::registerKeywords(Keywords& keys){
Function::registerKeywords(keys);
keys.use("ARG");
keys.add("compulsory","REFERENCE","a file in pdb format containing the reference structure. " + PDB::documentation() );
keys.add("optional","REFERENCE_VEC","the vector of values for the CVs at the reference point (if you use this you don't need REFERENCE)");
}
-TargetFrame::TargetFrame(const ActionOptions&ao):
+FunctionTarget::FunctionTarget(const ActionOptions&ao):
Action(ao),
Function(ao),
target(log)
@@ -82,7 +82,7 @@ target(log)
addValueWithDerivatives(); setNotPeriodic();
}
-void TargetFrame::calculate(){
+void FunctionTarget::calculate(){
double r=target.calculate( derivs );
setValue(r);
for(unsigned i=0;i<derivs.size();i++) setDerivative(i,derivs[i]);
diff --git a/src/GenericWholeMolecules.cpp b/src/GenericWholeMolecules.cpp
index 5fd6c7e47..844acece3 100644
--- a/src/GenericWholeMolecules.cpp
+++ b/src/GenericWholeMolecules.cpp
@@ -28,7 +28,7 @@
#include "Atoms.h"
#include "PlumedMain.h"
#include "ActionSet.h"
-#include "MolInfo.h"
+#include "SetupMolInfo.h"
#include <vector>
#include <string>
@@ -131,7 +131,7 @@ ActionAtomistic(ao)
if( resstrings.size()>0 ){
vector<string> backnames; parseVector("RES_ATOMS",backnames);
if(backnames.size()==0) error("Found RESIDUES keyword without any specification of the atoms that should be in a residue - use RES_ATOMS");
- std::vector<MolInfo*> moldat=plumed.getActionSet().select<MolInfo*>();
+ std::vector<SetupMolInfo*> moldat=plumed.getActionSet().select<SetupMolInfo*>();
if( moldat.size()==0 ) error("Unable to find MOLINFO in input");
std::vector< std::vector<AtomNumber> > backatoms;
moldat[0]->getBackbone( resstrings, backnames, backatoms );
diff --git a/src/MultiColvar.cpp b/src/MultiColvar.cpp
index ca312450c..50239b4f7 100644
--- a/src/MultiColvar.cpp
+++ b/src/MultiColvar.cpp
@@ -23,7 +23,7 @@
#include "PlumedMain.h"
#include "DistributionFunctions.h"
#include "ActionSet.h"
-#include "MolInfo.h"
+#include "SetupMolInfo.h"
#include <vector>
#include <string>
@@ -237,7 +237,7 @@ void MultiColvar::readBackboneAtoms( const std::vector<std::string>& backnames,
plumed_massert( keywords.exists("RESIDUES"), "To read in the backbone atoms the keyword RESIDUES must be registered");
readatoms=true;
- std::vector<MolInfo*> moldat=plumed.getActionSet().select<MolInfo*>();
+ std::vector<SetupMolInfo*> moldat=plumed.getActionSet().select<SetupMolInfo*>();
if( moldat.size()==0 ) error("Unable to find MOLINFO in input");
std::vector<std::string> resstrings; parseVector( "RESIDUES", resstrings );
diff --git a/src/MolInfo.cpp b/src/SetupMolInfo.cpp
similarity index 94%
rename from src/MolInfo.cpp
rename to src/SetupMolInfo.cpp
index 63447f69e..8ffdab74c 100644
--- a/src/MolInfo.cpp
+++ b/src/SetupMolInfo.cpp
@@ -19,7 +19,7 @@
You should have received a copy of the GNU Lesser General Public License
along with PLUMED. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#include "MolInfo.h"
+#include "SetupMolInfo.h"
#include "Atoms.h"
#include "ActionRegister.h"
#include "ActionSet.h"
@@ -59,21 +59,21 @@ ALPHARMSD BACKBONE=all TYPE=DRMSD LESS_THAN=(RATIONAL R_0=0.08 NN=8 MM=12) LABEL
//+ENDPLUMEDOC
-PLUMED_REGISTER_ACTION(MolInfo,"MOLINFO")
+PLUMED_REGISTER_ACTION(SetupMolInfo,"MOLINFO")
-void MolInfo::registerKeywords( Keywords& keys ){
+void SetupMolInfo::registerKeywords( Keywords& keys ){
ActionSetup::registerKeywords(keys);
keys.add("compulsory","STRUCTURE","a file in pdb format containing a reference structure. "
"This is used to defines the atoms in the various residues, chains, etc . " + PDB::documentation() );
keys.add("atoms","CHAIN","(for masochists ( a.k.a. Davide Branduardi ) ) The atoms involved in each of the chains of interest in the structure.");
}
-MolInfo::MolInfo( const ActionOptions&ao ):
+SetupMolInfo::SetupMolInfo( const ActionOptions&ao ):
Action(ao),
ActionSetup(ao),
ActionAtomistic(ao)
{
- std::vector<MolInfo*> moldat=plumed.getActionSet().select<MolInfo*>();
+ std::vector<SetupMolInfo*> moldat=plumed.getActionSet().select<SetupMolInfo*>();
if( moldat.size()!=0 ) error("cannot use more than one MOLINFO action in input");
std::vector<AtomNumber> backbone;
@@ -106,7 +106,7 @@ ActionAtomistic(ao)
pdb.renameAtoms("HA1","CB"); // This is a hack to make this work with GLY residues
}
-void MolInfo::getBackbone( std::vector<std::string>& restrings, const std::vector<std::string>& atnames, std::vector< std::vector<AtomNumber> >& backbone ){
+void SetupMolInfo::getBackbone( std::vector<std::string>& restrings, const std::vector<std::string>& atnames, std::vector< std::vector<AtomNumber> >& backbone ){
if( read_backbone.size()!=0 ){
if( restrings.size()!=1 ) error("cannot interpret anything other than all for residues when using CHAIN keywords");
if( restrings[0]!="all" ) error("cannot interpret anything other than all for residues when using CHAIN keywords");
diff --git a/src/MolInfo.h b/src/SetupMolInfo.h
similarity index 96%
rename from src/MolInfo.h
rename to src/SetupMolInfo.h
index 0378506c2..57712c1f3 100644
--- a/src/MolInfo.h
+++ b/src/SetupMolInfo.h
@@ -30,7 +30,7 @@
namespace PLMD {
-class MolInfo :
+class SetupMolInfo :
public ActionSetup,
public ActionAtomistic {
private:
@@ -38,7 +38,7 @@ private:
std::vector< std::vector<AtomNumber> > read_backbone;
public:
static void registerKeywords( Keywords& keys );
- MolInfo(const ActionOptions&ao);
+ SetupMolInfo(const ActionOptions&ao);
void getBackbone( std::vector<std::string>& resstrings, const std::vector<std::string>& atnames, std::vector< std::vector<AtomNumber> >& backbone );
};
--
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