Changeset 568be7 for src/builder.cpp

Timestamp:

Nov 7, 2009, 12:16:57 PM (16 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:

b9947d

Parents:

96c961

git-author:

Frederik Heber <heber@…> (11/07/09 09:48:07)

git-committer:

Frederik Heber <heber@…> (11/07/09 12:16:57)

Message:

Added config::SavePDB() and config::SaveMPQC().

• note: for CODICE we need to know about the different connected subgraphs created by the DFSAnalysis(). Hence, we write a pdb file which contains a resid number to discern in VMD between the molecules. Also, we need neighbour construction from a simple xyz file for TREMOLO in order to measure MSDs per water molecule.
• new function in config.cpp: config::SavePDB() gets molecule or MoleculeListClass and writes PDB file
• new function in config.cpp: config::SaveTREMOLO() gets molecule or MoleculeListClass and writes TREMOLO data file (with neighbours, mapped to global ids, and resid and resname)
• new function in moleculelist.cpp: MoleculeListClass::CountAllAtoms() - counts all atoms.
• BUGFIX: In MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs() we did not shift the chained bond list from mol into the connected subgraphs. Thus, they were free'd on delete(mol) and no bonds were present afterwards. This is fixed, now we unlink() in mol and re-link() in the respective subgraph

File:

• src/builder.cpp (modified) (2 diffs)

src/builder.cpp

@@ -1249 +1249 @@
   molecule *mol = new molecule(periode);
 
+  if (!strcmp(configuration->configpath, configuration->GetDefaultPath())) {
+    eLog() << Verbose(0) << "WARNING: config is found under different path then stated in config file::defaultpath!" << endl;
+  }
+
+
+  // first save as PDB data
+  if (ConfigFileName != NULL)
+    strcpy(filename, ConfigFileName);
+  if (output == NULL)
+    strcpy(filename,"main_pcp_linux");
+  Log() << Verbose(0) << "Saving as pdb input ";
+  if (configuration->SavePDB(filename, molecules))
+    Log() << Verbose(0) << "done." << endl;
+  else
+    Log() << Verbose(0) << "failed." << endl;
+
+  // then save as tremolo data file
+  if (ConfigFileName != NULL)
+    strcpy(filename, ConfigFileName);
+  if (output == NULL)
+    strcpy(filename,"main_pcp_linux");
+  Log() << Verbose(0) << "Saving as tremolo data input ";
+  if (configuration->SaveTREMOLO(filename, molecules))
+    Log() << Verbose(0) << "done." << endl;
+  else
+    Log() << Verbose(0) << "failed." << endl;
+
   // translate each to its center and merge all molecules in MoleculeListClass into this molecule
   int N = molecules->ListOfMolecules.size();
@@ -1329 +1356 @@
     eLog() << Verbose(0) << "WARNING: config is found under different path then stated in config file::defaultpath!" << endl;
   }
+
   delete(mol);
 };