Changeset a7b761b for src/config.cpp

Timestamp:

May 27, 2010, 10:46:54 AM (16 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

1024cb

Parents:

8f215d (diff), 05a97c (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.

Message:

Merge branch 'MoleculeStartEndSwitch' into StructureRefactoring

Conflicts:

molecuilder/src/Helpers/Assert.cpp
molecuilder/src/Helpers/Assert.hpp
molecuilder/src/Legacy/oldmenu.cpp
molecuilder/src/Makefile.am
molecuilder/src/Patterns/Cacheable.hpp
molecuilder/src/Patterns/Observer.cpp
molecuilder/src/Patterns/Observer.hpp
molecuilder/src/analysis_correlation.cpp
molecuilder/src/boundary.cpp
molecuilder/src/builder.cpp
molecuilder/src/config.cpp
molecuilder/src/helpers.hpp
molecuilder/src/molecule.cpp
molecuilder/src/molecule.hpp
molecuilder/src/molecule_dynamics.cpp
molecuilder/src/molecule_fragmentation.cpp
molecuilder/src/molecule_geometry.cpp
molecuilder/src/molecule_graph.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/tesselation.cpp
molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp
molecuilder/src/unittests/ObserverTest.cpp
molecuilder/src/unittests/ObserverTest.hpp

File:

• src/config.cpp (modified) (9 diffs)

src/config.cpp

@@ -1547 +1547 @@
   int AtomNo = -1;
   int MolNo = 0;
-  atom *Walker = NULL;
   FILE *f = NULL;
 
@@ -1560 +1559 @@
   fprintf(f, "# Created by MoleCuilder\n");
 
-  for (MoleculeList::const_iterator Runner = MolList->ListOfMolecules.begin(); Runner != MolList->ListOfMolecules.end(); Runner++) {
-    Walker = (*Runner)->start;
+  for (MoleculeList::const_iterator MolRunner = MolList->ListOfMolecules.begin(); MolRunner != MolList->ListOfMolecules.end(); MolRunner++) {
     int *elementNo = Calloc<int>(MAX_ELEMENTS, "config::SavePDB - elementNo");
     AtomNo = 0;
-    while (Walker->next != (*Runner)->end) {
-      Walker = Walker->next;
-      sprintf(name, "%2s%2d",Walker->type->symbol, elementNo[Walker->type->Z]);
-      elementNo[Walker->type->Z] = (elementNo[Walker->type->Z]+1) % 100;   // confine to two digits
+    for (molecule::const_iterator iter = (*MolRunner)->begin(); iter != (*MolRunner)->end(); ++iter) {
+      sprintf(name, "%2s%2d",(*iter)->type->symbol, elementNo[(*iter)->type->Z]);
+      elementNo[(*iter)->type->Z] = (elementNo[(*iter)->type->Z]+1) % 100;   // confine to two digits
       fprintf(f,
              "ATOM %6u %-4s %4s%c%4u    %8.3f%8.3f%8.3f%6.2f%6.2f      %4s%2s%2s\n",
-             Walker->nr,                /* atom serial number */
+             (*iter)->nr,                /* atom serial number */
              name,         /* atom name */
-             (*Runner)->name,      /* residue name */
+             (*MolRunner)->name,      /* residue name */
              'a'+(unsigned char)(AtomNo % 26),           /* letter for chain */
              MolNo,         /* residue sequence number */
-             Walker->node->at(0),                 /* position X in Angstroem */
-             Walker->node->at(1),                 /* position Y in Angstroem */
-             Walker->node->at(2),                 /* position Z in Angstroem */
-             (double)Walker->type->Valence,         /* occupancy */
-             (double)Walker->type->NoValenceOrbitals,          /* temperature factor */
+             (*iter)->node->at(0),                 /* position X in Angstroem */
+             (*iter)->node->at(1),                 /* position Y in Angstroem */
+             (*iter)->node->at(2),                 /* position Z in Angstroem */
+             (double)(*iter)->type->Valence,         /* occupancy */
+             (double)(*iter)->type->NoValenceOrbitals,          /* temperature factor */
              "0",            /* segment identifier */
-             Walker->type->symbol,    /* element symbol */
+             (*iter)->type->symbol,    /* element symbol */
              "0");           /* charge */
       AtomNo++;
@@ -1601 +1598 @@
 {
   int AtomNo = -1;
-  atom *Walker = NULL;
   FILE *f = NULL;
 
@@ -1616 +1612 @@
   fprintf(f, "# Created by MoleCuilder\n");
 
-  Walker = mol->start;
   AtomNo = 0;
-  while (Walker->next != mol->end) {
-    Walker = Walker->next;
-    sprintf(name, "%2s%2d",Walker->type->symbol, elementNo[Walker->type->Z]);
-    elementNo[Walker->type->Z] = (elementNo[Walker->type->Z]+1) % 100;   // confine to two digits
+  for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
+    sprintf(name, "%2s%2d",(*iter)->type->symbol, elementNo[(*iter)->type->Z]);
+    elementNo[(*iter)->type->Z] = (elementNo[(*iter)->type->Z]+1) % 100;   // confine to two digits
     fprintf(f,
            "ATOM %6u %-4s %4s%c%4u    %8.3f%8.3f%8.3f%6.2f%6.2f      %4s%2s%2s\n",
-           Walker->nr,                /* atom serial number */
+           (*iter)->nr,                /* atom serial number */
            name,         /* atom name */
            mol->name,      /* residue name */
            'a'+(unsigned char)(AtomNo % 26),           /* letter for chain */
            0,         /* residue sequence number */
-           Walker->node->at(0),                 /* position X in Angstroem */
-           Walker->node->at(1),                 /* position Y in Angstroem */
-           Walker->node->at(2),                 /* position Z in Angstroem */
-           (double)Walker->type->Valence,         /* occupancy */
-           (double)Walker->type->NoValenceOrbitals,          /* temperature factor */
+           (*iter)->node->at(0),                 /* position X in Angstroem */
+           (*iter)->node->at(1),                 /* position Y in Angstroem */
+           (*iter)->node->at(2),                 /* position Z in Angstroem */
+           (double)(*iter)->type->Valence,         /* occupancy */
+           (double)(*iter)->type->NoValenceOrbitals,          /* temperature factor */
            "0",            /* segment identifier */
-           Walker->type->symbol,    /* element symbol */
+           (*iter)->type->symbol,    /* element symbol */
            "0");           /* charge */
     AtomNo++;
@@ -1653 +1647 @@
 bool config::SaveTREMOLO(const char * const filename, const molecule * const mol) const
 {
-  atom *Walker = NULL;
   ofstream *output = NULL;
   stringstream * const fname = new stringstream;
@@ -1666 +1659 @@
 
   // scan maximum number of neighbours
-  Walker = mol->start;
   int MaxNeighbours = 0;
-  while (Walker->next != mol->end) {
-    Walker = Walker->next;
-    const int count = Walker->ListOfBonds.size();
+  for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
+    const int count = (*iter)->ListOfBonds.size();
     if (MaxNeighbours < count)
       MaxNeighbours = count;
   }
-  *output << "# ATOMDATA Id name resName resSeq x=3 charge type neighbors=" << MaxNeighbours << endl;
-
-  Walker = mol->start;
-  while (Walker->next != mol->end) {
-    Walker = Walker->next;
-    *output << Walker->nr << "\t";
-    *output << Walker->getName() << "\t";
+  *output << "# ATOMDATA Id name resName resSeq x=3 Charge type neighbors=" << MaxNeighbours << endl;
+
+  for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
+    *output << (*iter)->nr << "\t";
+    *output << (*iter)->getName() << "\t";
     *output << mol->name << "\t";
     *output << 0 << "\t";
-    *output << Walker->node->at(0) << "\t" << Walker->node->at(1) << "\t" << Walker->node->at(2) << "\t";
-    *output << static_cast<double>(Walker->type->Valence) << "\t";
-    *output << Walker->type->symbol << "\t";
-    for (BondList::iterator runner = Walker->ListOfBonds.begin(); runner != Walker->ListOfBonds.end(); runner++)
-      *output << (*runner)->GetOtherAtom(Walker)->nr << "\t";
-    for(int i=Walker->ListOfBonds.size(); i < MaxNeighbours; i++)
+    *output << (*iter)->node->at(0) << "\t" << (*iter)->node->at(1) << "\t" << (*iter)->node->at(2) << "\t";
+    *output << static_cast<double>((*iter)->type->Valence) << "\t";
+    *output << (*iter)->type->symbol << "\t";
+    for (BondList::iterator runner = (*iter)->ListOfBonds.begin(); runner != (*iter)->ListOfBonds.end(); runner++)
+      *output << (*runner)->GetOtherAtom(*iter)->nr << "\t";
+    for(int i=(*iter)->ListOfBonds.size(); i < MaxNeighbours; i++)
       *output << "-\t";
     *output << endl;
@@ -1708 +1697 @@
 bool config::SaveTREMOLO(const char * const filename, const MoleculeListClass * const MolList) const
 {
-  atom *Walker = NULL;
   ofstream *output = NULL;
   stringstream * const fname = new stringstream;
@@ -1723 +1711 @@
   int MaxNeighbours = 0;
   for (MoleculeList::const_iterator MolWalker = MolList->ListOfMolecules.begin(); MolWalker != MolList->ListOfMolecules.end(); MolWalker++) {
-    Walker = (*MolWalker)->start;
-    while (Walker->next != (*MolWalker)->end) {
-      Walker = Walker->next;
-      const int count = Walker->ListOfBonds.size();
+    for (molecule::const_iterator iter = (*MolWalker)->begin(); iter != (*MolWalker)->end(); ++iter) {
+      const int count = (*iter)->ListOfBonds.size();
       if (MaxNeighbours < count)
         MaxNeighbours = count;
     }
   }
-  *output << "# ATOMDATA Id name resName resSeq x=3 charge type neighbors=" << MaxNeighbours << endl;
+  *output << "# ATOMDATA Id name resName resSeq x=3 Charge type neighbors=" << MaxNeighbours << endl;
 
   // create global to local id map
@@ -1752 +1738 @@
     int AtomNo = 0;
     for (MoleculeList::const_iterator MolWalker = MolList->ListOfMolecules.begin(); MolWalker != MolList->ListOfMolecules.end(); MolWalker++) {
-      Walker = (*MolWalker)->start;
-      while (Walker->next != (*MolWalker)->end) {
-        Walker = Walker->next;
+      for (molecule::const_iterator iter = (*MolWalker)->begin(); iter != (*MolWalker)->end(); ++iter) {
         *output << AtomNo+1 << "\t";
-        *output << Walker->getName() << "\t";
+        *output << (*iter)->getName() << "\t";
         *output << (*MolWalker)->name << "\t";
         *output << MolCounter+1 << "\t";
-        *output << Walker->node->at(0) << "\t" << Walker->node->at(1) << "\t" << Walker->node->at(2) << "\t";
-        *output << (double)Walker->type->Valence << "\t";
-        *output << Walker->type->symbol << "\t";
-        for (BondList::iterator runner = Walker->ListOfBonds.begin(); runner != Walker->ListOfBonds.end(); runner++)
-          *output << LocalNotoGlobalNoMap[MolCounter][ (*runner)->GetOtherAtom(Walker)->nr ]+1 << "\t";
-        for(int i=Walker->ListOfBonds.size(); i < MaxNeighbours; i++)
+        *output << (*iter)->node->at(0) << "\t" << (*iter)->node->at(1) << "\t" << (*iter)->node->at(2) << "\t";
+        *output << (double)(*iter)->type->Valence << "\t";
+        *output << (*iter)->type->symbol << "\t";
+        for (BondList::iterator runner = (*iter)->ListOfBonds.begin(); runner != (*iter)->ListOfBonds.end(); runner++)
+          *output << LocalNotoGlobalNoMap[MolCounter][ (*runner)->GetOtherAtom(*iter)->nr ]+1 << "\t";
+        for(int i=(*iter)->ListOfBonds.size(); i < MaxNeighbours; i++)
           *output << "-\t";
         *output << endl;