Merge pull request #511 from plumed/v2.5-fix-h36

V2.5 fix h36

src/tools/PDB.cpp

@@ -329,11 +329,11 @@ bool PDB::readFromFilepointer(FILE *fp,bool naturalUnits,double scale) {
       AtomNumber a; unsigned resno;
       double o,b;
       Vector p;
-      Tools::convert(serial,a);
-
       {
         int result;
-        const char* errmsg = h36::hy36decode(5, serial.c_str(),5, &result);
+        auto trimmed=serial;
+        Tools::trim(trimmed);
+        const char* errmsg = h36::hy36decode(5, trimmed.c_str(),trimmed.length(), &result);
         if(errmsg) {
           std::string msg(errmsg);
           plumed_merror(msg);
@@ -535,15 +535,23 @@ void PDB::print( const double& lunits, SetupMolInfo* mymoldat, OFile& ofile, con
   if( argnames.size()>0 ) ofile.printf("\n");
   if( !mymoldat ) {
     for(unsigned i=0; i<positions.size(); ++i) {
-      ofile.printf("ATOM  %5d  X   RES  %4u    %8.3f%8.3f%8.3f%6.2f%6.2f\n",
-                   numbers[i].serial(), i,
+      std::array<char,6> at;
+      const char* msg = h36::hy36encode(5,numbers[i].serial(),&at[0]);
+      plumed_assert(msg==nullptr) << msg;
+      at[5]=0;
+      ofile.printf("ATOM  %s  X   RES  %4u    %8.3f%8.3f%8.3f%6.2f%6.2f\n",
+                   &at[0], i,
                    lunits*positions[i][0], lunits*positions[i][1], lunits*positions[i][2],
                    occupancy[i], beta[i] );
     }
   } else {
     for(unsigned i=0; i<positions.size(); ++i) {
-      ofile.printf("ATOM  %5d %-4s %3s  %4u    %8.3f%8.3f%8.3f%6.2f%6.2f\n",
-                   numbers[i].serial(), mymoldat->getAtomName(numbers[i]).c_str(),
+      std::array<char,6> at;
+      const char* msg = h36::hy36encode(5,numbers[i].serial(),&at[0]);
+      plumed_assert(msg==nullptr) << msg;
+      at[5]=0;
+      ofile.printf("ATOM  %s %-4s %3s  %4u    %8.3f%8.3f%8.3f%6.2f%6.2f\n",
+                   &at[0], mymoldat->getAtomName(numbers[i]).c_str(),
                    mymoldat->getResidueName(numbers[i]).c_str(), mymoldat->getResidueNumber(numbers[i]),
                    lunits*positions[i][0], lunits*positions[i][1], lunits*positions[i][2],
                    occupancy[i], beta[i] );