Changeset 6c438f for src/Parser/TremoloParser.cpp

Timestamp:

Aug 28, 2010, 3:21:11 AM (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, 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:

a6e6b5, f8982c

Parents:

2ad482 (diff), fd4905 (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@…> (08/28/10 03:17:48)

git-committer:

Frederik Heber <heber@…> (08/28/10 03:21:11)

Message:

Merge branch 'StructureRefactoring' into Shapes

Conflicts:

src/Box.cpp
src/Box.hpp
src/Descriptors/AtomShapeDescriptor.cpp
src/Descriptors/AtomShapeDescriptor.hpp
src/Descriptors/AtomShapeDescriptor_impl.hpp
src/LinearAlgebra/Line.cpp
src/LinearAlgebra/Line.hpp
src/LinearAlgebra/Matrix.cpp
src/LinearAlgebra/Matrix.hpp
src/Makefile.am
src/Shapes/BaseShapes.cpp
src/Shapes/BaseShapes_impl.hpp
src/Shapes/Shape.cpp
src/Shapes/Shape.hpp
src/Shapes/ShapeOps_impl.hpp
src/Shapes/Shape_impl.hpp
src/unittests/ShapeUnittest.cpp

• AtomShapeDescriptor had been implemented doubly.
• LineSegment* moved to LinearAlgebra/
• BaseShapes:: Cuboid is from (0,0,0) and not from (-1,-1,-1) to (1,1,1)
  • had to fix ShapeUnittest
• some overlap in Shapes due to getHomogeneousPointsOnSurface added in stable.
• BUGFIX: Matrix::transpose() did not allocate MatrixContent::content.
• merged BaseShapesUnitTest into ShapeUnitTest.

File:

• src/Parser/TremoloParser.cpp (modified) (14 diffs)

src/Parser/TremoloParser.cpp

@@ +1 @@
+/*
+ * Project: MoleCuilder
+ * Description: creates and alters molecular systems
+ * Copyright (C)  2010 University of Bonn. All rights reserved.
+ * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
+ */
+
 /*
  * TremoloParser.cpp
@@ -6 +13 @@
  */
 
+// include config.h
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include "Helpers/MemDebug.hpp"
 
 #include "Helpers/Assert.hpp"
+#include "Helpers/Log.hpp"
+#include "Helpers/Verbose.hpp"
 #include "TremoloParser.hpp"
 #include "World.hpp"
 #include "atom.hpp"
+#include "bond.hpp"
 #include "element.hpp"
-#include "bond.hpp"
+#include "molecule.hpp"
 #include "periodentafel.hpp"
 #include "Descriptors/AtomIdDescriptor.hpp"
@@ -19 +34 @@
 #include <vector>
 
+#include <iostream>
+#include <iomanip>
 
 using namespace std;
-using namespace boost;
 
 /**
@@ -75 +91 @@
 
   usedFields.clear();
+  molecule *newmol = World::getInstance().createMolecule();
   while (file->good()) {
     std::getline(*file, line, '\n');
@@ -84 +101 @@
     }
     if (line.length() > 0 && line.at(0) != '#') {
-      readAtomDataLine(line);
+      readAtomDataLine(line, newmol);
     }
   }
@@ -99 +116 @@
  */
 void TremoloParser::save(ostream* file) {
+  DoLog(0) && (Log() << Verbose(0) << "Saving changes to tremolo." << std::endl);
+
   vector<atom*>::iterator atomIt;
   vector<string>::iterator it;
@@ -140 +159 @@
       case TremoloKey::x :
         // for the moment, assume there are always three dimensions
-        *file << currentAtom->x[0] << "\t";
-        *file << currentAtom->x[1] << "\t";
-        *file << currentAtom->x[2] << "\t";
+        *file << currentAtom->at(0) << "\t";
+        *file << currentAtom->at(1) << "\t";
+        *file << currentAtom->at(2) << "\t";
         break;
       case TremoloKey::u :
         // for the moment, assume there are always three dimensions
-        *file << currentAtom->v[0] << "\t";
-        *file << currentAtom->v[1] << "\t";
-        *file << currentAtom->v[2] << "\t";
+        *file << currentAtom->AtomicVelocity[0] << "\t";
+        *file << currentAtom->AtomicVelocity[1] << "\t";
+        *file << currentAtom->AtomicVelocity[2] << "\t";
         break;
       case TremoloKey::Type :
@@ -154 +173 @@
         break;
       case TremoloKey::Id :
-        *file << currentAtom->getId() << "\t";
+        *file << currentAtom->getId()+1 << "\t";
         break;
       case TremoloKey::neighbors :
         writeNeighbors(file, atoi(it->substr(it->find("=") + 1, 1).c_str()), currentAtom);
         break;
+      case TremoloKey::resSeq :
+        if (additionalAtomData.find(currentAtom->getId()) != additionalAtomData.end()) {
+          *file << additionalAtomData[currentAtom->getId()].get(currentField);
+        } else if (currentAtom->getMolecule() != NULL) {
+          *file << setw(4) << currentAtom->getMolecule()->getId()+1;
+        } else {
+          *file << defaultAdditionalData.get(currentField);
+        }
+        *file << "\t";
+      break;
       default :
-        *file << (additionalAtomData.find(currentAtom->getId()) != additionalAtomData.end()
-          ? additionalAtomData[currentAtom->getId()].get(currentField)
-          : defaultAdditionalData.get(currentField));
+        if (additionalAtomData.find(currentAtom->getId()) != additionalAtomData.end()) {
+          *file << additionalAtomData[currentAtom->getId()].get(currentField);
+        } else if (additionalAtomData.find(currentAtom->GetTrueFather()->getId()) != additionalAtomData.end()) {
+          *file << additionalAtomData[currentAtom->GetTrueFather()->getId()].get(currentField);
+        } else {
+          *file << defaultAdditionalData.get(currentField);
+        }
         *file << "\t";
         break;
@@ -182 +215 @@
   for (int i = 0; i < numberOfNeighbors; i++) {
     *file << (currentBond != currentAtom->ListOfBonds.end()
-        ? (*currentBond)->GetOtherAtom(currentAtom)->getId() : 0) << "\t";
+        ? (*currentBond)->GetOtherAtom(currentAtom)->getId()+1 : 0) << "\t";
+    if (currentBond != currentAtom->ListOfBonds.end())
+      currentBond++;
   }
 }
@@ -214 +249 @@
  *
  * \param line to parse as an atom
- */
-void TremoloParser::readAtomDataLine(string line) {
+ * \param *newmol molecule to add atom to
+ */
+void TremoloParser::readAtomDataLine(string line, molecule *newmol = NULL) {
   vector<string>::iterator it;
   stringstream lineStream;
@@ -225 +261 @@
   string word;
   int oldId;
+  double tmp;
 
   lineStream << line;
@@ -232 +269 @@
       case TremoloKey::x :
         // for the moment, assume there are always three dimensions
-        lineStream >> newAtom->x[0];
-        lineStream >> newAtom->x[1];
-        lineStream >> newAtom->x[2];
+        for (int i=0;i<NDIM;i++) {
+          lineStream >> tmp;
+          newAtom->set(i, tmp);
+        }
         break;
       case TremoloKey::u :
         // for the moment, assume there are always three dimensions
-        lineStream >> newAtom->v[0];
-        lineStream >> newAtom->v[1];
-        lineStream >> newAtom->v[2];
+        lineStream >> newAtom->AtomicVelocity[0];
+        lineStream >> newAtom->AtomicVelocity[1];
+        lineStream >> newAtom->AtomicVelocity[2];
         break;
       case TremoloKey::Type :
@@ -262 +300 @@
     }
   }
+  if (newmol != NULL)
+    newmol->AddAtom(newAtom);
 }
 
@@ -385 +425 @@
 
 
-TremoloAtomInfoContainer::TremoloAtomInfoContainer() {
-  F = "0";
-  stress = "0";
-  imprData = "-";
-  GroupMeasureTypeNo = "0";
-  extType = "-";
-  name = "-";
-  resName = "-";
-  chainID = "0";
-  resSeq = "0";
-  occupancy = "0";
-  tempFactor = "0";
-  segID = "0";
-  Charge = "0";
-  charge = "0";
-  GrpTypeNo = "0";
-  torsion = "-";
-  neighbors = vector<int>(0, 5);
-}
+TremoloAtomInfoContainer::TremoloAtomInfoContainer() :
+  F("0"),
+  stress("0"),
+  imprData("-"),
+  GroupMeasureTypeNo("0"),
+  extType("-"),
+  name("-"),
+  resName("-"),
+  chainID("0"),
+  resSeq("0"),
+  occupancy("0"),
+  tempFactor("0"),
+  segID("0"),
+  Charge("0"),
+  charge("0"),
+  GrpTypeNo("0"),
+  torsion("-"),
+  neighbors(vector<int>(0, 5))
+{}
 
 void TremoloAtomInfoContainer::set(TremoloKey::atomDataKey key, string value) {