Changed behaviour on > 99999 atoms: now ***** is always used. Fixed PDB...

Changed behaviour on > 99999 atoms: now ***** is always used. Fixed PDB writer, reader, added unit test.

Signed-off-by: Stefan Bienert <stefan.bienert@unibas.ch>

modules/io/src/mol/pdb_reader.cc

@@ -602,16 +602,6 @@ bool PDBReader::ParseAtomIdent(const StringRef& line, int line_num,
     }    
   }
 
-  std::pair<bool, int> a_num=line.substr(6, 5).ltrim().to_int();
-  if (!a_num.first) {
-    if (!(profile_.fault_tolerant)) {
-      throw IOException(str(format("invalid atom number on line %d") %line_num));      
-    }
-    if (!(charmm_style_)) {
-      LOG_WARNING("invalid atom number on line " << line_num);
-    }
-  }
-
   alt_loc=line[16];
   res_name=line.substr(17, charmm_style_ ? 4 : 3).trim();
   std::pair<bool, int> res_num=line.substr(22, 4).ltrim().to_int();;

modules/io/src/mol/pdb_writer.cc

@@ -80,12 +80,7 @@ void write_atom(std::ostream& ostr, FormattedLine& line,
   line( 0, 6)=record_name;
   // Avoid writing out atomnumbers larger than 5 digits
   if (atomnum > 99999) {
-    if (charmm_style) {
-      line( 6, 5)=fmt::LPadded("*****");
-    } else {
-      throw IOException("Atom number is too long for PDB output." 
-                        " At most 5 digits are allowed");
-    }
+    line( 6, 5)=fmt::LPadded("*****");
   } else {
     line( 6, 5)=fmt::LPaddedInt(atomnum);
   }

modules/io/tests/test_io_pdb.cc

@@ -457,6 +457,64 @@ BOOST_AUTO_TEST_CASE(write_atom)
                     "  1.00128.00           C  ");
 }
 
+BOOST_AUTO_TEST_CASE(write_atom_100000)
+{
+  char c_names[] = "ABCDEFGHIJ";
+  std::stringstream out;
+  PDBWriter writer(out, IOProfile());
+  
+  mol::EntityHandle ent=mol::CreateEntity();
+  mol::XCSEditor edi=ent.EditXCS();
+  mol::ChainHandle ch;
+  mol::ResidueHandle r;
+  mol::AtomHandle a;
+
+  for (unsigned long i = 0; i < 10; ++i) {
+    ch=edi.InsertChain(String(1, c_names[i]));
+    for (unsigned long j = 1; j < 1000; ++j) {
+      r=edi.AppendResidue(ch, "ARG");
+      a=edi.InsertAtom(r,"N",   geom::Vec3(26.861, 50.841, 38.803), "N");
+      a.SetOccupancy(1.0);
+      a.SetBFactor(128.0);
+      a=edi.InsertAtom(r,"CA",  geom::Vec3(27.437, 49.969, 37.786), "C");
+      a.SetOccupancy(1.0);
+      a.SetBFactor(128.0);
+      a=edi.InsertAtom(r,"C",   geom::Vec3(26.336, 48.959, 37.429), "C");
+      a.SetOccupancy(1.0);
+      a.SetBFactor(128.0);
+      a=edi.InsertAtom(r,"O",   geom::Vec3(25.745, 48.313, 38.312), "O");
+      a.SetOccupancy(1.0);
+      a.SetBFactor(128.0);
+      a=edi.InsertAtom(r,"CB",  geom::Vec3(28.653, 49.266, 38.349), "C");
+      a.SetOccupancy(1.0);
+      a.SetBFactor(128.0);
+      a=edi.InsertAtom(r,"CG",  geom::Vec3(29.870, 50.188, 38.416), "C");
+      a.SetOccupancy(1.0);
+      a.SetBFactor(128.0);
+      a=edi.InsertAtom(r,"CD",  geom::Vec3(31.033, 49.532, 39.173), "C");
+      a.SetOccupancy(1.0);
+      a.SetBFactor(128.0);
+      a=edi.InsertAtom(r,"NE",  geom::Vec3(32.318, 50.244, 39.125), "N");
+      a.SetOccupancy(1.0);
+      a.SetBFactor(128.0);
+      a=edi.InsertAtom(r,"CZ",  geom::Vec3(33.462, 49.750, 39.679), "C");
+      a.SetOccupancy(1.0);
+      a.SetBFactor(128.0);
+      a=edi.InsertAtom(r,"NH1", geom::Vec3(33.522, 48.572, 40.308), "N");
+      a.SetOccupancy(1.0);
+      a.SetBFactor(128.0);
+      a=edi.InsertAtom(r,"NH2", geom::Vec3(34.610, 50.427, 39.597), "N");
+      a.SetOccupancy(1.0);
+      a.SetBFactor(128.0);
+    }
+  }
+
+  writer.Write(ent);
+  String s=out.str();
+  BOOST_CHECK_EQUAL(s.substr(8099844, 5), "99999");
+  BOOST_CHECK_EQUAL(s.substr(8099925, 5), "*****");
+}
+
 BOOST_AUTO_TEST_CASE(write_hetatom)
 {
   std::stringstream out;