Changeset 06f41f3 for src/Graph/CheckAgainstAdjacencyFile.cpp

Timestamp:

Dec 3, 2012, 9:49:30 AM (13 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, Candidate_v1.7.0, Candidate_v1.7.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

9511c7

Parents:

b78dfd

git-author:

Frederik Heber <heber@…> (09/19/12 13:55:43)

git-committer:

Frederik Heber <heber@…> (12/03/12 09:49:30)

Message:

CheckAgainstAdjacencyFile now works on given vector of atomids.

• added helper function getGlobalIdsFromLocalIds() as we have to translate molecule's internal ids to global atomId_t to check against those in file.
• TESTFIX: Adapted CheckAgainstAdjacencyFileUnitTest to the changes, also added another test case to operatorTest().

File:

• src/Graph/CheckAgainstAdjacencyFile.cpp (modified) (12 diffs)

src/Graph/CheckAgainstAdjacencyFile.cpp

@@ -56 +56 @@
  */
 CheckAgainstAdjacencyFile::CheckAgainstAdjacencyFile(std::istream &File) :
-  status(true),
   NonMatchNumber(0)
 {
-  ParseInExternalMap(File);
+  bool status = ParseInInternalMap(File);
+  if (!status) // remove map if failed to parse
+    InternalAtomBondMap.clear();
 }
 
 CheckAgainstAdjacencyFile::~CheckAgainstAdjacencyFile()
-{
-  ExternalAtomBondMap.clear();
-  InternalAtomBondMap.clear();
-}
+{}
 
 /** Parses the bond partners of each atom from an external file into \a AtomBondMap.
@@ -73 +71 @@
  * @return true - everything ok, false - error while parsing
  */
-bool CheckAgainstAdjacencyFile::ParseInExternalMap(std::istream &File)
+bool CheckAgainstAdjacencyFile::ParseInInternalMap(std::istream &File)
 {
   if (File.fail()) {
@@ -80 +78 @@
   }
 
-  ExternalAtomBondMap.clear();
+  InternalAtomBondMap.clear();
   char buffer[MAXSTRINGSIZE];
   int tmp;
@@ -93 +91 @@
     if (AtomNr > 0) {
       const atom *Walker = World::getInstance().getAtom(AtomById(AtomNr-1));
-      ASSERT(Walker != NULL,
-          "CheckAgainstAdjacencyFile::ParseInExternalMap() - there is no atom with id "+toString(AtomNr-1)+".");
       if (Walker == NULL)
         return false;
+      const atomId_t WalkerId = Walker->getId();
       // parse bond partner ids associated to AtomNr
       while (line >> ws >> tmp) {
-        LOG(3, "INFO: Recognized bond partner " << tmp-1);
-        ExternalAtomBondMap.insert( std::make_pair(Walker->getId(), tmp-1) );
+        LOG(3, "INFO: Recognized bond partner " << tmp-1 << " for " << WalkerId << ".");
+        InternalAtomBondMap.insert( std::make_pair(WalkerId, tmp-1) );
       }
     } else {
@@ -114 +111 @@
 /** Fills the InternalAtomBondMap from the atoms given by the two iterators.
  *
- * @param AtomMapBegin iterator pointing to begin of map (think of World's SelectionIterator)
- * @param AtomMapEnd iterator pointing past end of map (think of World's SelectionIterator)
- */
-void CheckAgainstAdjacencyFile::CreateInternalMap(World::AtomSet::const_iterator AtomMapBegin, World::AtomSet::const_iterator AtomMapEnd)
-{
-  InternalAtomBondMap.clear();
+ * @param atomids set of atomic ids to check (must be global ids, i.e. from atom::getId())
+ */
+void CheckAgainstAdjacencyFile::CreateExternalMap(const atomids_t &atomids)
+{
+  ExternalAtomBondMap.clear();
   // go through each atom in the list
-  for (World::AtomSet::const_iterator iter = AtomMapBegin; iter != AtomMapEnd; ++iter) {
-    const atom *Walker = iter->second;
-    const atomId_t WalkerId = Walker->getId();
+  for (atomids_t::const_iterator iter = atomids.begin(); iter != atomids.end(); ++iter) {
+    const atomId_t WalkerId = *iter;
     ASSERT(WalkerId != (size_t)-1,
-        "CheckAgainstAdjacencyFile::CreateInternalMap() - Walker has no id.");
+        "CheckAgainstAdjacencyFile::CreateExternalMap() - Walker has no id.");
+    const atom *Walker = World::getInstance().getAtom(AtomById(WalkerId));
+    ASSERT( Walker != NULL,
+        "CheckAgainstAdjacencyFile::CreateExternalMap() - Walker id "+toString(*iter)
+        +" is not associated to any of World's atoms.");
     const BondList& ListOfBonds = Walker->getListOfBonds();
     // go through each of its bonds
@@ -133 +132 @@
       const atomId_t id = (*Runner)->GetOtherAtom(Walker)->getId();
       ASSERT(id != (size_t)-1,
-          "CheckAgainstAdjacencyFile::CreateInternalMap() - OtherAtom has not id.");
-      InternalAtomBondMap.insert( std::make_pair(WalkerId, id) );
+          "CheckAgainstAdjacencyFile::CreateExternalMap() - OtherAtom has not id.");
+      ExternalAtomBondMap.insert( std::make_pair(WalkerId, id) );
     }
   }
@@ -142 +141 @@
  * \return true - structure is equal, false - not equivalence
  */
-bool CheckAgainstAdjacencyFile::operator()(World::AtomSet::const_iterator AtomMapBegin, World::AtomSet::const_iterator AtomMapEnd)
-{
-  LOG(0, "STATUS: Looking at bond structure stored in adjacency file and comparing to present one ... ");
-
-  bool status = true;
-
-  if (InternalAtomBondMap.empty())
-    CreateInternalMap(AtomMapBegin, AtomMapEnd);
-
-  status = status && CompareInternalExternalMap();
-
+bool CheckAgainstAdjacencyFile::operator()(const atomids_t &atomids)
+{
+  LOG(0, "STATUS: Looking at bond structure of given ids and comparing against stored in adjacency file... ");
+
+  // parse in external map
+  CreateExternalMap(atomids);
+
+  bool status = CompareInternalExternalMap();
   if (status) { // if equal we parse the KeySetFile
     LOG(0, "STATUS: Equal.");
@@ -182 +178 @@
 }
 
-/** Counts the number of mismatching items in each set.
- *
- * @param firstset first set
- * @param secondset second set
- * @return number of items that don't match between first and second set
+/** Counts the number of items in the second set not present in the first set.
+ *
+ * \note We assume that the sets are sorted.
+ *
+ * @param firstset check set
+ * @param secondset reference set
+ * @return number of items in the first set that are missing in the second
  */
 template <class T>
-size_t getMismatchingItems(const T &firstset, const T &secondset)
+size_t getMissingItems(const T &firstset, const T &secondset)
 {
   size_t Mismatch = 0;
   typename T::const_iterator firstiter = firstset.begin();
   typename T::const_iterator seconditer = secondset.begin();
-  for (; (firstiter != firstset.end()) && (seconditer != secondset.end());
-      ++firstiter, ++seconditer) {
-    if (*firstiter != *seconditer)
-      ++Mismatch;
+  for (; (firstiter != firstset.end()) && (seconditer != secondset.end());) {
+    if (*firstiter > *seconditer)
+      ++seconditer;
+    else {
+      if (*firstiter < *seconditer)
+        ++Mismatch;
+      ++firstiter;
+    }
   }
   return Mismatch;
@@ -209 +211 @@
 {
   NonMatchNumber = 0;
-  // check whether sizes match
-  if (ExternalAtomBondMap.size() != InternalAtomBondMap.size()) {
-    NonMatchNumber = abs((int)ExternalAtomBondMap.size() - (int)InternalAtomBondMap.size());
-    LOG(2, "INFO: " << NonMatchNumber << " entries don't match.");
-    return false;
-  }
   // extract keys and check whether they match
   const AtomBondRange Intrange(InternalAtomBondMap.begin(), InternalAtomBondMap.end());
@@ -225 +221 @@
 
   // check for same amount of keys
-  if (InternalKeys.size() != ExternalKeys.size()) {
-    NonMatchNumber = abs((int)ExternalKeys.size() - (int)InternalKeys.size());
-    LOG(2, "INFO: Number of keys don't match: "
-        << InternalKeys.size() << " != " << ExternalKeys.size());
-    return false;
-  }
-
-  // check items against one another
-  NonMatchNumber = getMismatchingItems(InternalKeys, ExternalKeys);
+  if (ExternalKeys.size() > InternalKeys.size()) {
+    NonMatchNumber = (int)ExternalKeys.size() - (int)InternalKeys.size();
+    LOG(2, "INFO: Number of external keys exceeds internal one by " << NonMatchNumber << ".");
+    return false;
+  }
+
+  // check which keys are missing in the internal set
+  NonMatchNumber = getMissingItems(ExternalKeys, InternalKeys);
 
   if (NonMatchNumber != 0) {
@@ -241 +236 @@
 
   // now check each map per key
-  for (KeysSet::const_iterator keyIter = InternalKeys.begin();
-      keyIter != InternalKeys.end();
+  for (KeysSet::const_iterator keyIter = ExternalKeys.begin();
+      keyIter != ExternalKeys.end();
       ++keyIter) {
 //    std::cout << "Current key is " << *keyIter << std::endl;
@@ -249 +244 @@
     ValuesSet InternalValues( getValues(IntRange) );
     ValuesSet ExternalValues( getValues(ExtRange) );
+    // throw out all values not present in ExternalKeys
+    ValuesSet ExternalValues_temp( ExternalValues );
+    for(KeysSet::const_iterator iter = ExternalKeys.begin();
+        iter != ExternalKeys.end(); ++iter)
+      ExternalValues_temp.erase(*iter);
+    // all remaining values must be masked out
+    for (ValuesSet::const_iterator iter = ExternalValues_temp.begin();
+        iter != ExternalValues_temp.end(); ++iter)
+      ExternalValues.erase(*iter);
 //    std::cout << "InternalValues: " << InternalValues << std::endl;
 //    std::cout << "ExternalValues: " << ExternalValues << std::endl;
-    NonMatchNumber += getMismatchingItems(InternalValues, ExternalValues);
+    NonMatchNumber += getMissingItems(ExternalValues, InternalValues);
   }
   if (NonMatchNumber != 0) {