Changeset 8ab0407

Timestamp:

Mar 18, 2010, 11:37:26 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, 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:

c7b1e7

Parents:

1f1b23

git-author:

Frederik Heber <heber@…> (03/18/10 11:34:39)

git-committer:

Frederik Heber <heber@…> (03/18/10 11:37:26)

Message:

molecule::StoreAdjacencyToFile() and molecule::StoreBondsToFile() now take additional filename.

• since ParseCommandLineOptions() has cases j and J which use the above functions, we have to generalize these functions to work also without a given path and with arbritrary filename.

Signed-off-by: Frederik Heber <heber@…>

Location:

src

Files:

• molecule.hpp (modified) (1 diff)
• molecule_fragmentation.cpp (modified) (1 diff)
• molecule_graph.cpp (modified) (4 diffs)

src/molecule.hpp

@@ -269 +269 @@
   int FragmentMolecule(int Order, config *configuration);
   bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, char *path = NULL);
-  bool StoreBondsToFile(char *path);
-  bool StoreAdjacencyToFile(char *path);
+  bool StoreBondsToFile(char *path, char *filename);
+  bool StoreAdjacencyToFile(char *path, char *filename);
   bool CheckAdjacencyFileAgainstMolecule(char *path, atom **ListOfAtoms);
   bool ParseOrderAtSiteFromFile(char *path);

src/molecule_fragmentation.cpp

@@ -703 +703 @@
 
     // store Adjacency file
-    StoreAdjacencyToFile(configuration->configpath);
+    char *filename = Malloc<char> (MAXSTRINGSIZE, "molecule::FragmentMolecule - *filename");
+    strcpy(filename, FRAGMENTPREFIX);
+    strcat(filename, ADJACENCYFILE);
+    StoreAdjacencyToFile(configuration->configpath, filename);
+    Free(&filename);
 
     // store Hydrogen saturation correction file

src/molecule_graph.cpp

@@ -978 +978 @@
 /** Storing the bond structure of a molecule to file.
  * Simply stores Atom::nr and then the Atom::nr of all bond partners per line.
- * \param *out output stream for debugging
  * \param *path path to file
+ * \param *filename name of file
  * \return true - file written successfully, false - writing failed
  */
-bool molecule::StoreAdjacencyToFile(char *path)
+bool molecule::StoreAdjacencyToFile(char *path, char *filename)
 {
   ofstream AdjacencyFile;
@@ -988 +988 @@
   bool status = true;
 
-  line << path << "/" << FRAGMENTPREFIX << ADJACENCYFILE;
+  if (path != NULL)
+    line << path << "/" << filename;
+  else
+    line << filename;
   AdjacencyFile.open(line.str().c_str(), ios::out);
   Log() << Verbose(1) << "Saving adjacency list ... ";
@@ -1007 +1010 @@
 /** Storing the bond structure of a molecule to file.
  * Simply stores Atom::nr and then the Atom::nr of all bond partners, one per line.
- * \param *out output stream for debugging
  * \param *path path to file
+ * \param *filename name of file
  * \return true - file written successfully, false - writing failed
  */
-bool molecule::StoreBondsToFile(char *path)
+bool molecule::StoreBondsToFile(char *path, char *filename)
 {
   ofstream BondFile;
@@ -1017 +1020 @@
   bool status = true;
 
-  line << path << "/" << FRAGMENTPREFIX << ADJACENCYFILE;
+  if (path != NULL)
+    line << path << "/" << filename;
+  else
+    line << filename;
   BondFile.open(line.str().c_str(), ios::out);
   Log() << Verbose(1) << "Saving adjacency list ... ";