Changeset 0cbad2 for src/Actions

Timestamp:

Mar 1, 2011, 1:17:07 PM (14 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:

300220

Parents:

3738f0

git-author:

Frederik Heber <heber@…> (02/18/11 23:39:44)

git-committer:

Frederik Heber <heber@…> (03/01/11 13:17:07)

Message:

Moved molecule::CreateAdjacencyListFromDbondFile() over to BondGraph and made more flexible.

• extended molecule::CreateAdjacencyListFromDbondFile() to also parse TREMOLO's dbond files.
• BondFileAction now has two more options: skiplines and offset to control parsing, default values assure behavior as has been.
• same way CreateAdjacencyListFromDbondFile() has these two options added also.
• extended regression test Molecule/BondFile with unconnected PDB and dbond file.

Location:

src/Actions/MoleculeAction

Files:

• BondFileAction.cpp (modified) (2 diffs)
• BondFileAction.def (modified) (1 diff)

src/Actions/MoleculeAction/BondFileAction.cpp

@@ -20 +20 @@
 #include "CodePatterns/MemDebug.hpp"
 
+#include "bondgraph.hpp"
 #include "CodePatterns/Log.hpp"
 #include "molecule.hpp"
@@ -45 +46 @@
   if(World::getInstance().countSelectedMolecules() == 1) {
     mol = World::getInstance().beginMoleculeSelection()->second;
-    DoLog(0) && (Log() << Verbose(0) << "Parsing bonds from " << params.bondfile << "." << endl);
+    LOG(0, "STATUS: Parsing bonds from " << params.bondfile
+        << ", skipping " << params.skiplines << "lines"
+        << ", adding " << params.id_offset << " to each id.");
     ifstream input(params.bondfile.string().c_str());
-    mol->CreateAdjacencyListFromDbondFile(&input);
+    molecule::atomVector Set = mol->getAtomSet();
+    World::getInstance().getBondGraph()->CreateAdjacencyListFromDbondFile(Set, &input, params.skiplines, params.id_offset);
     input.close();
+    mol->getBondCount();
     return Action::success;
   } else

src/Actions/MoleculeAction/BondFileAction.def

@@ -12 +12 @@
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
-#define paramtypes (boost::filesystem::path)
-#define paramtokens ("bond-file")
-#define paramdescriptions ("name of the bond file")
-#undef paramdefaults
-#define paramreferences (bondfile)
+#define paramtypes (boost::filesystem::path)(int)(int)
+#define paramtokens ("bond-file")("skiplines")("offset")
+#define paramdescriptions ("name of the bond file")("number of header lines to skip")("offset to add to each id")
+#define paramdefaults (NODEFAULT)("1")("0")
+#define paramreferences (bondfile)(skiplines)(id_offset)
 
 #undef statetypes