Changes in src/Parser/FormatParserStorage.cpp [cabb46:73916f]

File:

• src/Parser/FormatParserStorage.cpp (modified) (4 diffs)

src/Parser/FormatParserStorage.cpp

@@ -36 +36 @@
 
 #include "Helpers/Assert.hpp"
+
+#include "molecule.hpp"
 
 #include "Patterns/Singleton_impl.hpp"
@@ -224 +226 @@
  * \return true - parsing ok, false - suffix unknown
  */
-bool FormatParserStorage::get(std::istream &input, std::string suffix)
+bool FormatParserStorage::load(std::istream &input, std::string suffix)
 {
   if (suffix == ParserSuffixes[mpqc]) {
@@ -243 +245 @@
 }
 
+/** Stores all selected atoms in an ostream depending on its suffix
+ * \param &output output stream
+ * \param suffix
+ * \return true - storing ok, false - suffix unknown
+ */
+bool FormatParserStorage::saveSelectedAtoms(std::ostream &output, std::string suffix)
+{
+  std::vector<atom *> atoms = World::getInstance().getSelectedAtoms();
+  return save(output, suffix, atoms);
+}
+
+/** Stores all selected atoms in an ostream depending on its suffix
+ * We store in the order of the atomic ids, not in the order they appear in the molecules.
+ * Hence, we first create a vector from all selected molecules' atoms.
+ * \param &output output stream
+ * \param suffix
+ * \return true - storing ok, false - suffix unknown
+ */
+bool FormatParserStorage::saveSelectedMolecules(std::ostream &output, std::string suffix)
+{
+  std::vector<molecule *> molecules = World::getInstance().getSelectedMolecules();
+  std::map<size_t, atom *> IdAtoms;
+  for (std::vector<molecule *>::const_iterator MolIter = molecules.begin();
+      MolIter != molecules.end();
+      ++MolIter) {
+    for(molecule::atomSet::const_iterator AtomIter = (*MolIter)->begin();
+        AtomIter != (*MolIter)->end();
+        ++AtomIter) {
+      IdAtoms.insert( make_pair((*AtomIter)->getId(), (*AtomIter)) );
+    }
+  }
+  std::vector<atom *> atoms;
+  atoms.reserve(IdAtoms.size());
+  for (std::map<size_t, atom *>::const_iterator iter = IdAtoms.begin();
+      iter != IdAtoms.end();
+      ++iter) {
+    atoms.push_back(iter->second);
+  }
+  return save(output, suffix, atoms);
+}
 
 /** Stores world in an ostream depending on its suffix
@@ -249 +291 @@
  * \return true - storing ok, false - suffix unknown
  */
-bool FormatParserStorage::put(std::ostream &output, std::string suffix)
+bool FormatParserStorage::saveWorld(std::ostream &output, std::string suffix)
+{
+  std::vector<atom *> atoms = World::getInstance().getAllAtoms();
+  return save(output, suffix, atoms);
+}
+
+/** Stores a given vector of \a atoms in an ostream depending on its suffix
+ * \param &output output stream
+ * \param suffix
+ * \return true - storing ok, false - suffix unknown
+ */
+bool FormatParserStorage::save(std::ostream &output, std::string suffix, const std::vector<atom *> &atoms)
 {
   if (suffix == ParserSuffixes[mpqc]) {
-    getMpqc().save(&output);
+    getMpqc().save(&output, atoms);
   } else if (suffix == ParserSuffixes[pcp]) {
-    getPcp().save(&output);
+    getPcp().save(&output, atoms);
   } else if (suffix == ParserSuffixes[pdb]) {
-    getPdb().save(&output);
+    getPdb().save(&output, atoms);
   } else if (suffix == ParserSuffixes[tremolo]) {
-    getTremolo().save(&output);
+    getTremolo().save(&output, atoms);
   } else if (suffix == ParserSuffixes[xyz]) {
-    getXyz().save(&output);
+    getXyz().save(&output, atoms);
   } else {
     DoeLog(1) && (eLog() << Verbose(1) << "Unknown suffix " << suffix << " to for FormatParserStorage::put()." << endl);