Changeset 9131f3 for src/Parser/TremoloParser.cpp

Timestamp:

Mar 30, 2010, 1:22:20 PM (15 years ago)

Author:

Saskia Metzler <metzler@…>

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, 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:

4415da

Parents:

cb2146

Message:

WIP tremolo parser

File:

• src/Parser/TremoloParser.cpp (modified) (1 diff)

src/Parser/TremoloParser.cpp

@@ -6 +6 @@
  */
 
-void TremoloParser::load(char* fileName) {
-MatrixContainer* data = readData(fileName, getHeaderSize('#'), 0);
-store additional data
-for (each line in matrix) {
-  add atom to the world
-}
+#include "TremoloParser.hpp"
+#include "World.hpp"
+#include "atom.hpp"
+#include "element.hpp"
+#include "periodentafel.hpp"
+#include <map>
+#include <vector>
+
+using namespace std;
+
+/**
+ * Constructor.
+ */
+TremoloParser::TremoloParser() {
+  knownKeys["x"] = x;
+  knownKeys["u"] = u;
+  knownKeys["F"] = F;
+  knownKeys["stress"] = stress;
+  knownKeys["Id"] = Id;
+  knownKeys["neighbors"] = neighbors;
+  knownKeys["imprData"] = imprData;
+  knownKeys["GroupMeasureTypeNo"] = GroupMeasureTypeNo;
+  knownKeys["Type"] = Type;
+  knownKeys["extType"] = extType;
+  knownKeys["name"] = name;
+  knownKeys["resName"] = resName;
+  knownKeys["chainID"] = chainID;
+  knownKeys["resSeq"] = resSeq;
+  knownKeys["occupancy"] = occupancy;
+  knownKeys["tempFactor"] = tempFactor;
+  knownKeys["segID"] = segID;
+  knownKeys["Charge"] = Charge;
+  knownKeys["charge"] = charge;
+  knownKeys["GrpTypeNo"] = GrpTypeNo;
 }
 
-void TremoloParser::save(char* fileName) {
+/**
+ * Destructor.
+ */
+TremoloParser::~TremoloParser() {
+}
+
+/**
+ * Stores keys from the ATOMDATA line.
+ *
+ * \param line to parse the keys from
+ * \param with which offset the keys begin within the line
+ */
+void TremoloParser::parseAtomDataKeysLine(string line, int offset) {
+  string keyword;
+  stringstream lineStream;
+
+  lineStream << line.substr(offset);
+  while (lineStream.good()) {
+    lineStream >> keyword;
+    usedFields.push_back(keyword);
+  }
+}
+
+/**
+ * Reads one data line of a tremolo file and interprets it according to the keys
+ * obtained from the ATOMDATA line.
+ *
+ * \param line to parse as an atom
+ */
+void TremoloParser::readAtomDataLine(string line) {
+  vector<string>::iterator it;
+  stringstream lineStream;
+  string word;
+
+  lineStream << line;
+  for (it=usedFields.begin(); it < usedFields.end(); it++) {
+    cout << *it << " -- " << it->substr(0, it->find("=")) << " -- " << knownKeys[it->substr(0, it->find("="))] << endl;
+    switch (knownKeys[it->substr(0, it->find("="))]) {
+      case x :
+        lineStream >> word;
+        cout<< "Found an x: word: " << word << endl;
+        break;
+      default :
+        lineStream >> word;
+        cout << "Unknown key: " << *it << ", word: " << word << endl;
+        break;
+    }
+  }
+}
+
+
+/**
+ * Loads atoms from a tremolo-formatted file.
+ *
+ * \param tremolo file
+ */
+void TremoloParser::load(istream* file) {
+  string line;
+  string::size_type location;
+
+  usedFields.clear();
+  while (file->good()) {
+    std::getline(*file, line, '\n');
+    if (usedFields.empty()) {
+      location = line.find("ATOMDATA", 0);
+      if (location != string::npos) {
+       parseAtomDataKeysLine(line, location + 8);
+      }
+    }
+    if (line.length() > 0 && line.at(0) != '#') {
+      readAtomDataLine(line);
+    }
+  }
+}
+
+/*
+#ATOMDATA  <record_entry_1> ... <record_entry_n>
+# <record_entry>: <dataname>[=<n>]
+# <dataname>    : x | u | F | stress | Id | neighbors | imprData
+#               | GroupMeasureTypeNo | Type | extType
+#               | name | resName | chainID | resSeq
+#               | occupancy | tempFactor | segID | Charge
+#               | charge
+ATOMDATA name Id x=3 mass charge epsilon sigma eps14 sig14 name type protein protno neighbors=4
+*/
+
+//MatrixContainer* data = readData(fileName, getHeaderSize('#'), 0);
+
+
+/**
+ * Saves the World's current state into as a tremolo file.
+ *
+ * \param file where to save the state
+ */
+void TremoloParser::save(ostream* file) {
+/*
 write header
 for (each atom in world) {
   write coordinates and additional data
 }
+*/
 }