Changeset 955b91 for src/Parser

Timestamp:

Mar 27, 2012, 3:53:35 PM (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, 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:

4d2b33

Parents:

912c40

git-author:

Frederik Heber <heber@…> (03/14/12 18:08:24)

git-committer:

Frederik Heber <heber@…> (03/27/12 15:53:35)

Message:

FIX: Removed using namespace std in Vector.hpp.

• this caused some follow-up problems in other LinearAlgebra modules,

mostly stuff from iostream not having std

prefix then.

this also caused more of them in MoleCuilder modules, mostly due to string,

stringstream, and numeric_limits with std

prefix.

Location:

src/Parser

Files:

• PdbParser.cpp (modified) (1 diff)
• PdbParser.hpp (modified) (2 diffs)
• TremoloParser.cpp (modified) (4 diffs)

src/Parser/PdbParser.cpp

@@ -84 +84 @@
  * @return token type
  */
-enum PdbKey::KnownTokens FormatParser< pdb >::getToken(string &line)
+enum PdbKey::KnownTokens FormatParser< pdb >::getToken(std::string &line)
 {
   // look for first space

src/Parser/PdbParser.hpp

@@ -60 +60 @@
 
 private:
-  enum PdbKey::KnownTokens getToken(string &line);
-  void readAtomDataLine(const unsigned int _step, string &line, molecule *newmol);
-  void parseAtomDataKeysLine(string line, int offset);
+  enum PdbKey::KnownTokens getToken(std::string &line);
+  void readAtomDataLine(const unsigned int _step, std::string &line, molecule *newmol);
+  void parseAtomDataKeysLine(std::string line, int offset);
   void readNeighbors(const unsigned int _step, std::string &line);
 //  void adaptImprData();
@@ -69 +69 @@
   bool isUsedField(std::string fieldName);
   void writeNeighbors(std::ostream* file, int numberOfNeighbors, atom* currentAtom);
-  void saveLine(ostream* file, const PdbAtomInfoContainer &atomInfo);
+  void saveLine(std::ostream* file, const PdbAtomInfoContainer &atomInfo);
 
   // internal getter and setter

src/Parser/TremoloParser.cpp

@@ -347 +347 @@
  * \param with which offset the keys begin within the line
  */
-void FormatParser< tremolo >::parseAtomDataKeysLine(string line, int offset) {
+void FormatParser< tremolo >::parseAtomDataKeysLine(std::string line, int offset) {
   std::string keyword;
   std::stringstream lineStream;
@@ -482 +482 @@
  * \param atomid world id of the atom the information belongs to
  */
-void FormatParser< tremolo >::readNeighbors(stringstream* line, int numberOfNeighbors, int atomId) {
+void FormatParser< tremolo >::readNeighbors(std::stringstream* line, int numberOfNeighbors, int atomId) {
   int neighborId = 0;
   for (int i = 0; i < numberOfNeighbors; i++) {
@@ -502 +502 @@
  * \return true if the field name is used
  */
-bool FormatParser< tremolo >::isUsedField(string fieldName) {
+bool FormatParser< tremolo >::isUsedField(std::string fieldName) {
   bool fieldNameExists = false;
   for (std::vector<std::string>::iterator usedField = usedFields.begin(); usedField != usedFields.end(); usedField++) {
@@ -559 +559 @@
  * \return input string with modified atom IDs
  */
-std::string FormatParser< tremolo >::adaptIdDependentDataString(string data) {
+std::string FormatParser< tremolo >::adaptIdDependentDataString(std::string data) {
   // there might be no IDs
   if (data == "-") {