remove all std::ends (#130)

* remove all std::ends

include/GP/RbtCell.h

@@ -60,7 +60,7 @@ class RbtCell {
         evaluated = true;
         constant = true;
         ostringstream nm;
-        nm << r << ends;
+        nm << r;
         name = nm.str();
     };
     void ResetConstant() {

include/RbtConfig.h

@@ -22,7 +22,6 @@
 using std::cerr;
 using std::cout;
 using std::endl;
-using std::ends;
 using std::ios_base;
 using std::istream;
 using std::istringstream;

include/RbtContext.h

@@ -67,7 +67,7 @@ class RbtCellContext: public RbtContext {
             vm[key]->SetValue(val);
         else {
             ostringstream s;
-            s << val << ends;
+            s << val;
             vm[key] = new RbtVble(s.str(), val);
         }
     }

include/RbtVariant.h

@@ -19,7 +19,6 @@
 
 #include <sstream>
 using std::cout;
-using std::ends;
 using std::istringstream;
 using std::ostringstream;
 
@@ -153,9 +152,6 @@ class RbtVariant {
         m_d = d;
         m_sl.clear();
         ostringstream ostr;
-        // Don't need "ends" with ostringstream apparently
-        //(was introducing a non-ASCII \0 char into log files
-        // ostr << d << ends;
         ostr << d;
         RbtString s(ostr.str());
         m_sl.push_back(s);
@@ -184,9 +180,6 @@ class RbtVariant {
         m_d = c.Length();
         m_sl.clear();
         ostringstream ostr;
-        // Don't need "ends" with ostringstream apparently
-        //(was introducing a non-ASCII \0 char into log files
-        // ostr << c << ends;
         ostr << c;
         RbtString s(ostr.str());
         m_sl.push_back(s);

include/RbtVble.h

@@ -41,7 +41,7 @@ class RbtVble {
         value = val;
         if (name == "") {
             ostringstream s;
-            s << value << ends;
+            s << value;
             name = s.str();
         }
     }

src/GP/RbtGPParser.cxx

@@ -107,9 +107,9 @@ RbtString RbtGPParser::PrintEval(RbtGPChromosomePtr chrom, RbtInt n, RbtBool num
         if (numbers) {
             nm << "(";
             nm << n << " ";
-            nm << o << ") " << ends;
+            nm << o << ") ";
         } else
-            nm << o << ends;
+            nm << o;
         chrom->Cells(n)->SetName(nm.str());
         return (nm.str());
     } else

src/exe/rbdock.cxx

@@ -482,7 +482,7 @@ int main(int argc, const char *argv[]) {
                     try {
                         if (bOutput) {
                             ostringstream histr;
-                            histr << strRunName << "_" << strMolName << nRec << "_his_" << iRun << ".sd" << ends;
+                            histr << strRunName << "_" << strMolName << nRec << "_his_" << iRun << ".sd";
                             RbtMolecularFileSinkPtr spHistoryFileSink(new RbtMdlFileSink(histr.str(), spLigand));
                             spWS->SetHistorySink(spHistoryFileSink);
                         }

src/exe/rbtether.cxx

@@ -274,5 +274,4 @@ void print_atoms(RbtAtomList &atoms, ostringstream &ost) {
         else
             ost << ",";
     }
-    ost << ends;
 }

src/lib/RbtAnnotation.cxx

@@ -76,7 +76,7 @@ RbtString RbtAnnotation::Render() const {
     }
     ostr.setf(ios_base::fixed, ios_base::floatfield);
     ostr.precision(2);
-    ostr << m_dist << "," << m_score << ends;
+    ostr << m_dist << "," << m_score;
     RbtString retVal(ostr.str());
     return retVal;
 }

src/lib/RbtAtom.cxx

@@ -352,7 +352,7 @@ RbtString Rbt::ConvertFormalChargeToString(RbtInt nCharge) {
             // For higher charges, return as +3,-3 etc
             ostringstream ostr;
             ostr.setf(ios_base::showpos);
-            ostr << nCharge << ends;
+            ostr << nCharge;
             RbtString strCharge(ostr.str());
             return strCharge;
     }

src/lib/RbtCharmmDataSource.cxx

@@ -11,7 +11,6 @@
  ***********************************************************************/
 
 #include <sstream>
-using std::ends;
 using std::ostringstream;
 
 #include "RbtCharmmDataSource.h"
@@ -69,7 +68,7 @@ RbtString RbtCharmmDataSource::AtomTypeString(RbtInt nAtomType) {
         return (*iter).second;
     else {
         ostringstream ostr;
-        ostr << "CHARMm atom type #" << nAtomType << " not found in CharmmDataSource" << ends;
+        ostr << "CHARMm atom type #" << nAtomType << " not found in CharmmDataSource";
         RbtString strError(ostr.str());
         throw RbtFileMissingParameter(_WHERE_, strError);
     }

src/lib/RbtConstraint.cxx

@@ -16,7 +16,6 @@
 
 #include "RbtLigandError.h"
 
-using std::ends;
 using std::ostringstream;
 
 // initialization of the static data of RbtConstraint
@@ -206,7 +205,7 @@ void RbtHeavyConstraint::AddAtomList(RbtModelPtr lig, RbtBool bCheck) {
     m_atomList = Rbt::GetAtomList(lig->GetAtomList(), std::not1(Rbt::isAtomicNo_eq(1)));
     if (bCheck && (m_atomList.size() < counter)) {
         ostringstream ostr;
-        ostr << "The ligand has only " << m_atomList.size() << " heavy atom(s) (" << counter << " required)" << ends;
+        ostr << "The ligand has only " << m_atomList.size() << " heavy atom(s) (" << counter << " required)";
         throw RbtLigandError(_WHERE_, ostr.str());
     }
 }
@@ -218,7 +217,7 @@ void RbtHBDConstraint::AddAtomList(RbtModelPtr lig, RbtBool bCheck) {
     if (bCheck && (m_atomList.size() < counter)) {
         ostringstream ostr;
         ostr << "The ligand has only " << m_atomList.size() << " neutral H-bond donor hydrogens(s) (" << counter
-             << " required)" << ends;
+             << " required)";
         throw RbtLigandError(_WHERE_, ostr.str());
     }
 }
@@ -230,7 +229,7 @@ void RbtHBAConstraint::AddAtomList(RbtModelPtr lig, RbtBool bCheck) {
     if (bCheck && (m_atomList.size() < counter)) {
         ostringstream ostr;
         ostr << "The ligand has only " << m_atomList.size() << " neutral H-bond acceptor(s) (" << counter
-             << " required)" << ends;
+             << " required)";
         throw RbtLigandError(_WHERE_, ostr.str());
     }
 }
@@ -239,8 +238,7 @@ void RbtHydroConstraint::AddAtomList(RbtModelPtr lig, RbtBool bCheck) {
     m_atomList = Rbt::GetAtomList(lig->GetAtomList(), Rbt::isAtomLipophilic());
     if (bCheck && (m_atomList.size() < counter)) {
         ostringstream ostr;
-        ostr << "The ligand has only " << m_atomList.size() << " hydrophobic atom(s) (" << counter << " required)"
-             << ends;
+        ostr << "The ligand has only " << m_atomList.size() << " hydrophobic atom(s) (" << counter << " required)";
         throw RbtLigandError(_WHERE_, ostr.str());
     }
 }
@@ -251,7 +249,7 @@ void RbtHydroAliphaticConstraint::AddAtomList(RbtModelPtr lig, RbtBool bCheck) {
     if (bCheck && (m_atomList.size() < counter)) {
         ostringstream ostr;
         ostr << "The ligand has only " << m_atomList.size() << " hydrophobic aliphatic atom(s) (" << counter
-             << " required)" << ends;
+             << " required)";
         throw RbtLigandError(_WHERE_, ostr.str());
     }
 }
@@ -262,7 +260,7 @@ void RbtHydroAromaticConstraint::AddAtomList(RbtModelPtr lig, RbtBool bCheck) {
     if (bCheck && (m_atomList.size() < counter)) {
         ostringstream ostr;
         ostr << "The ligand has only " << m_atomList.size() << " hydrophobic aromatic atom(s) (" << counter
-             << " required)" << ends;
+             << " required)";
         throw RbtLigandError(_WHERE_, ostr.str());
     }
 }
@@ -272,7 +270,7 @@ void RbtNegChargeConstraint::AddAtomList(RbtModelPtr lig, RbtBool bCheck) {
     if (bCheck && (m_atomList.size() < counter)) {
         ostringstream ostr;
         ostr << "The ligand has only " << m_atomList.size() << " negatively charged atom(s) (" << counter
-             << " required)" << ends;
+             << " required)";
         throw RbtLigandError(_WHERE_, ostr.str());
     }
 }
@@ -282,7 +280,7 @@ void RbtPosChargeConstraint::AddAtomList(RbtModelPtr lig, RbtBool bCheck) {
     if (bCheck && (m_atomList.size() < counter)) {
         ostringstream ostr;
         ostr << "The ligand has only " << m_atomList.size() << " positively charged atom(s) (" << counter
-             << " required)" << ends;
+             << " required)";
         throw RbtLigandError(_WHERE_, ostr.str());
     }
 }
@@ -299,8 +297,7 @@ void RbtRingAromaticConstraint::AddAtomList(RbtModelPtr lig, RbtBool bCheck) {
     }
     if (bCheck && (m_atomList.size() < counter)) {
         ostringstream ostr;
-        ostr << "The ligand has only " << m_atomList.size() << " aromatic ring(s) (" << counter << " required)"
-             << ends;
+        ostr << "The ligand has only " << m_atomList.size() << " aromatic ring(s) (" << counter << " required)";
         throw RbtLigandError(_WHERE_, ostr.str());
     }
 }

src/lib/RbtCrdFileSink.cxx

@@ -67,7 +67,7 @@ void RbtCrdFileSink::Render() {
 
             // 2. Write number of atoms
             ostringstream ostr;
-            ostr << setw(5) << spModel->GetNumAtoms() << ends;
+            ostr << setw(5) << spModel->GetNumAtoms();
             AddLine(ostr.str());
             // Remember the line number containing the number of atoms
             // as we'll need to update the total num atoms after each Render when we are in multiconf mode
@@ -131,15 +131,15 @@ void RbtCrdFileSink::Render() {
             ostr << setw(0) << " " << setw(4)
                  << spAtom->GetSubunitId().c_str();  // This subunit ID is unique in the segment
             ostr.setf(ios_base::right, ios_base::adjustfield);
-            ostr << setw(10) << 0.0 << ends;
+            ostr << setw(10) << 0.0;
             AddLine(ostr.str());
         }
 
         // In multiconf mode, we need to update the total number of atoms in the cache
         // then write the file without clearing the cache
         if (GetMultiConf()) {
             ostringstream ostr;
-            ostr << setw(5) << m_nAtomId << ends;
+            ostr << setw(5) << m_nAtomId;
             ReplaceLine(ostr.str(), m_numAtomsLineRec);
             Write(false);
         } else

src/lib/RbtElementFileSource.cxx

@@ -11,7 +11,6 @@
  ***********************************************************************/
 
 #include <sstream>
-using std::ends;
 using std::istringstream;
 using std::ostringstream;
 
@@ -93,7 +92,7 @@ RbtElementData RbtElementFileSource::GetElementData(RbtInt nAtomicNumber) {
         return (*iter).second;
     else {
         ostringstream ostr;
-        ostr << "Atomic number " << nAtomicNumber << " not found in " << GetFileName() << ends;
+        ostr << "Atomic number " << nAtomicNumber << " not found in " << GetFileName();
         RbtString strError(ostr.str());
         throw RbtFileMissingParameter(_WHERE_, strError);
     }

src/lib/RbtFilter.cxx

@@ -11,7 +11,6 @@
  ***********************************************************************/
 
 #include <sstream>
-using std::ends;
 using std::ostringstream;
 
 #include "RbtFilter.h"
@@ -202,7 +201,7 @@ RbtBool RbtFilter::Terminate() {
         } else {
             ostringstream error;
             error << "Wrong output: " << val;
-            error << "; Termination filters should return 0,1 or -1" << ends;
+            error << "; Termination filters should return 0,1 or -1";
             throw RbtError(_WHERE_, error.str());
         }
     } else

src/lib/RbtMdlFileSink.cxx

@@ -71,7 +71,7 @@ void RbtMdlFileSink::Render() {
         ostr << setw(3) << modelAtomList.size() + solventAtomList.size() << setw(3)
              << modelBondList.size() + solventBondList.size() << setw(3) << 0 << setw(3) << 0 << setw(3) << 0
              << setw(3) << 0 << setw(3) << 0 << setw(3) << 0 << setw(3) << 0 << setw(3) << 0 << setw(3) << 999
-             << " V2000" << ends;
+             << " V2000";
         AddLine(ostr.str());
 
         // DM 19 June 2006 - clear the map of logical atom IDs each time
@@ -125,8 +125,8 @@ void RbtMdlFileSink::RenderAtomList(const RbtAtomList& atomList) {
              << setw(3) << 0              // atom stereo parity
              << setw(3) << 0              // hydrogen count+1 (query CTABs only)
              << setw(3) << 0              // stereo care box (query CTABs only)
-             << setw(3) << 0              // valence (0 = no marking)
-             << ends;                     // Mass diff, formal charge, stereo parity, num hydrogens, center
+             << setw(3) << 0;             // valence (0 = no marking)
+                                          // Mass diff, formal charge, stereo parity, num hydrogens, center
         AddLine(ostr.str());
     }
 }
@@ -147,8 +147,8 @@ void RbtMdlFileSink::RenderBondList(const RbtBondList& bondList) {
             ostringstream ostr;
             ostr.setf(ios_base::right, ios_base::adjustfield);
             ostr << setw(3) << id1 << setw(3) << id2 << setw(3) << spBond->GetFormalBondOrder() << setw(3) << 0
-                 << setw(3) << 0 << setw(3) << 0
-                 << ends;  // Atom1, Atom2, bond order, stereo designator, unused, topology code
+                 << setw(3) << 0 << setw(3) << 0;
+            // Atom1, Atom2, bond order, stereo designator, unused, topology code
             AddLine(ostr.str());
         } else {
             // Should never happen. Probably best to throw an error at this point.

src/lib/RbtMdlFileSource.cxx

@@ -113,7 +113,7 @@ void RbtMdlFileSource::Parse() {
                 // Compose the atom name from element+atomID (i.e. C1, N2, C3 etc)
                 nAtomId++;
                 ostringstream ostr;
-                ostr << strElementName << nAtomId << ends;
+                ostr << strElementName << nAtomId;
                 RbtString strAtomName(ostr.str());
 
                 // Construct a new atom (constructor only accepts the 2D params)
@@ -728,7 +728,7 @@ void RbtMdlFileSource::AddHydrogen(RbtAtomPtr spAtom) {
     // Construct the new hydrogen atom (constructor only accepts the 2D params)
     RbtInt nAtomId = m_atomList.size() + 1;
     ostringstream ostr;
-    ostr << "H" << nAtomId << ends;
+    ostr << "H" << nAtomId;
     RbtString strAtomName(ostr.str());
     RbtAtomPtr spHAtom(new RbtAtom(
         nAtomId,
@@ -940,7 +940,7 @@ void RbtMdlFileSource::SetupSegmentNames() {
          nSeg++, seed = Rbt::FindAtom(m_atomList, Rbt::isSegmentName_eq("H"))) {
         // New segment name (H1, H2 etc)
         ostringstream ostr;
-        ostr << "H" << nSeg << ends;
+        ostr << "H" << nSeg;
         RbtString strSegName(ostr.str());
         // Temporary atom list containing atoms to be processed
         // Note: this is a true list (not a vector) as we will be making numerous insertions and deletions

src/lib/RbtPRMFactory.cxx

@@ -121,7 +121,7 @@ RbtModelPtr RbtPRMFactory::CreateReceptor() {
         }
         for (RbtInt i = 1; i <= n; i++) {
             ostringstream ostr;
-            ostr << _REC_COORD_FILE << "_" << i << ends;
+            ostr << _REC_COORD_FILE << "_" << i;
             RbtString paramName(ostr.str());
             RbtString strCoordFile = m_pParamSource->GetParameterValueAsString(paramName);
             if (m_iTrace > 0) {

src/lib/RbtPsfFileSink.cxx

@@ -55,7 +55,7 @@ void RbtPsfFileSink::Render() {
         AddLine("");
         RbtStringList titleList(spModel->GetTitleList());
         ostringstream ostr;
-        ostr << setw(8) << titleList.size() << setw(0) << " " << strTitleKey << ends;
+        ostr << setw(8) << titleList.size() << setw(0) << " " << strTitleKey;
         AddLine(ostr.str());
         for (RbtStringListConstIter iter = titleList.begin(); iter != titleList.end(); iter++) {
             // Add an initial star if the title does not already commence with a star
@@ -68,7 +68,7 @@ void RbtPsfFileSink::Render() {
 
         // 2. Write number of atoms
         ostringstream ostr2;
-        ostr2 << setw(8) << spModel->GetNumAtoms() << setw(0) << " " << strAtomKey << ends;
+        ostr2 << setw(8) << spModel->GetNumAtoms() << setw(0) << " " << strAtomKey;
         AddLine(ostr2.str());
         // delete ostr2.str();
 
@@ -97,7 +97,7 @@ void RbtPsfFileSink::Render() {
         delete[] line;
         // 4. Write number of bonds
         ostringstream ostr3;
-        ostr3 << setw(8) << spModel->GetNumBonds() << setw(0) << " " << strBondKey << ends;
+        ostr3 << setw(8) << spModel->GetNumBonds() << setw(0) << " " << strBondKey;
         AddLine("");
         AddLine(ostr3.str());
         // delete ostr3.str();
@@ -117,7 +117,7 @@ void RbtPsfFileSink::Render() {
             bIter++;
             ostr << setw(8) << (*bIter)->GetAtom1Ptr()->GetAtomId() << setw(8) << (*bIter)->GetAtom2Ptr()->GetAtomId();
             bIter++;
-            ostr << ends;
+            ostr;
             AddLine(ostr.str());
         }
         // Remaining bonds on final incomplete line
@@ -127,7 +127,7 @@ void RbtPsfFileSink::Render() {
                 ostr << setw(8) << (*bIter)->GetAtom1Ptr()->GetAtomId() << setw(8)
                      << (*bIter)->GetAtom2Ptr()->GetAtomId();
             }
-            ostr << ends;
+            ostr;
             AddLine(ostr.str());
         }
 

src/lib/rbcavity/rbcavity_main.cxx

@@ -91,7 +91,7 @@ void RBCavity::RBCavity(const RBCavity::RBCavityConfig &config) {
         RbtCavityList cavList = spDockSite->GetCavityList();
         for (RbtUInt i = 0; i < cavList.size(); i++) {
             ostringstream filename;
-            filename << wsName << "_cav" << i + 1 << ".grd" << ends;
+            filename << wsName << "_cav" << i + 1 << ".grd";
             ofstream dumpFile(filename.str());
             if (dumpFile) {
                 cavList[i]->GetGrid()->PrintInsightGrid(dumpFile);