Changeset 8de375 for src/molecule.cpp

Timestamp:

May 19, 2010, 6:46:52 PM (15 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, 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:

0fb9f6

Parents:

eff648 (diff), bab12a (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

git-author:

Frederik Heber <heber@…> (05/19/10 18:45:23)

git-committer:

Frederik Heber <heber@…> (05/19/10 18:46:52)

Message:

Merge branch 'StructureRefactoring' into CommandLineActionMapping

Conflicts:

molecuilder/src/atom_particleinfo.cpp
molecuilder/src/builder.cpp

The following conflicts were solved:

• in atom_particleinfo constructor the bugfix could not be merged automatically
• in builder.cpp at the end of main() cleanup and memory:getstate() were still present.

File:

• src/molecule.cpp (modified) (10 diffs)

src/molecule.cpp

@@ -135 +135 @@
       if (pointer->type->Z != 1)
         NoNonHydrogen++;
-      if (pointer->Name == NULL) {
-        Free(&pointer->Name);
-        pointer->Name = Malloc<char>(6, "molecule::AddAtom: *pointer->Name");
-        sprintf(pointer->Name, "%2s%02d", pointer->type->symbol, pointer->nr+1);
+      if(pointer->getName() == "Unknown"){
+        stringstream sstr;
+        sstr << pointer->type->symbol << pointer->nr+1;
+        pointer->setName(sstr.str());
       }
     }
@@ -157 +157 @@
   if (pointer != NULL) {
     atom *walker = pointer->clone();
-    walker->Name = Malloc<char>(strlen(pointer->Name) + 1, "atom::atom: *Name");
-    strcpy (walker->Name, pointer->Name);
+    stringstream sstr;
+    sstr << pointer->getName();
+    walker->setName(sstr.str());
     walker->nr = last_atom++;  // increase number within molecule
     add(walker, end);
@@ -252 +253 @@
   BondRescale = TopOrigin->type->HBondDistance[TopBond->BondDegree-1];
   if (BondRescale == -1) {
-    DoeLog(1) && (eLog()<< Verbose(1) << "There is no typical hydrogen bond distance in replacing bond (" << TopOrigin->Name << "<->" << TopReplacement->Name << ") of degree " << TopBond->BondDegree << "!" << endl);
+    DoeLog(1) && (eLog()<< Verbose(1) << "There is no typical hydrogen bond distance in replacing bond (" << TopOrigin->getName() << "<->" << TopReplacement->getName() << ") of degree " << TopBond->BondDegree << "!" << endl);
     return false;
     BondRescale = bondlength;
@@ -275 +276 @@
       InBondvector *= BondRescale;   // rescale the distance vector to Hydrogen bond length
       FirstOtherAtom->x = TopOrigin->x; // set coordination to origin ...
-      FirstOtherAtom->x = InBondvector;  // ... and add distance vector to replacement atom
+      FirstOtherAtom->x += InBondvector;  // ... and add distance vector to replacement atom
       AllWentWell = AllWentWell && AddAtom(FirstOtherAtom);
 //      Log() << Verbose(4) << "Added " << *FirstOtherAtom << " at: ";
@@ -295 +296 @@
             SecondOtherAtom = (*Runner)->GetOtherAtom(TopOrigin);
           } else {
-            DoeLog(2) && (eLog()<< Verbose(2) << "Detected more than four bonds for atom " << TopOrigin->Name);
+            DoeLog(2) && (eLog()<< Verbose(2) << "Detected more than four bonds for atom " << TopOrigin->getName());
           }
         }
@@ -339 +340 @@
       bondangle = TopOrigin->type->HBondAngle[1];
       if (bondangle == -1) {
-        DoeLog(1) && (eLog()<< Verbose(1) << "There is no typical hydrogen bond angle in replacing bond (" << TopOrigin->Name << "<->" << TopReplacement->Name << ") of degree " << TopBond->BondDegree << "!" << endl);
+        DoeLog(1) && (eLog()<< Verbose(1) << "There is no typical hydrogen bond angle in replacing bond (" << TopOrigin->getName() << "<->" << TopReplacement->getName() << ") of degree " << TopBond->BondDegree << "!" << endl);
         return false;
         bondangle = 0;
@@ -616 +617 @@
     add(Binder, last);
   } else {
-    DoeLog(1) && (eLog()<< Verbose(1) << "Could not add bond between " << atom1->Name << " and " << atom2->Name << " as one or both are not present in the molecule." << endl);
+    DoeLog(1) && (eLog()<< Verbose(1) << "Could not add bond between " << atom1->getName() << " and " << atom2->getName() << " as one or both are not present in the molecule." << endl);
   }
   return Binder;
@@ -695 +696 @@
     AtomCount--;
   } else
-    DoeLog(1) && (eLog()<< Verbose(1) << "Atom " << pointer->Name << " is of element " << pointer->type->Z << " but the entry in the table of the molecule is 0!" << endl);
+    DoeLog(1) && (eLog()<< Verbose(1) << "Atom " << pointer->getName() << " is of element " << pointer->type->Z << " but the entry in the table of the molecule is 0!" << endl);
   if (ElementsInMolecule[pointer->type->Z] == 0)  // was last atom of this element?
     ElementCount--;
@@ -713 +714 @@
     ElementsInMolecule[pointer->type->Z]--; // decrease number of atom of this element
   else
-    DoeLog(1) && (eLog()<< Verbose(1) << "Atom " << pointer->Name << " is of element " << pointer->type->Z << " but the entry in the table of the molecule is 0!" << endl);
+    DoeLog(1) && (eLog()<< Verbose(1) << "Atom " << pointer->getName() << " is of element " << pointer->type->Z << " but the entry in the table of the molecule is 0!" << endl);
   if (ElementsInMolecule[pointer->type->Z] == 0)  // was last atom of this element?
     ElementCount--;
@@ -915 +916 @@
         if (Walker->type->Z != 1) // count non-hydrogen atoms whilst at it
           NoNonHydrogen++;
-        Free(&Walker->Name);
-        Walker->Name = Malloc<char>(6, "molecule::CountAtoms: *walker->Name");
-        sprintf(Walker->Name, "%2s%02d", Walker->type->symbol, Walker->nr+1);
-        DoLog(3) && (Log() << Verbose(3) << "Naming atom nr. " << Walker->nr << " " << Walker->Name << "." << endl);
+        stringstream sstr;
+        sstr << Walker->type->symbol << Walker->nr+1;
+        Walker->setName(sstr.str());
+        DoLog(3) && (Log() << Verbose(3) << "Naming atom nr. " << Walker->nr << " " << Walker->getName() << "." << endl);
         i++;
       }