Changeset cdaae6

Timestamp:

Feb 17, 2012, 3:24:19 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:

52ed5b

Parents:

560bbe

git-author:

Frederik Heber <heber@…> (02/16/12 13:38:53)

git-committer:

Frederik Heber <heber@…> (02/17/12 15:24:19)

Message:

FIX: BondedParticle::OutputAdjacency() and ::OutputBonds() give uncorrected ids.

• tremolo's Id starts at 1, internal (molecular) ones however start at 0. This causes undesired behavior when parsing .dbond files.
• TESTFIX: changed ids in .dbond and .adj files of regression tests Molecules/BondFile, Molecules/SaveAdjacency, and Molecules/SaveBonds.

Files:

• src/Atom/atom_bondedparticle.cpp (modified) (2 diffs)
• tests/regression/Molecules/BondFile/pre/test.dbond (modified) (1 diff)
• tests/regression/Molecules/BondFile/testsuite-molecules-fragmentation-bond-file.at (modified) (3 diffs)
• tests/regression/Molecules/SaveAdjacency/post/test.adj (modified) (1 diff)
• tests/regression/Molecules/SaveBonds/post/test.dbond (modified) (1 diff)

src/Atom/atom_bondedparticle.cpp

@@ -72 +72 @@
 {
   const BondList& ListOfBonds = getListOfBonds();
-  *AdjacencyFile << getNr() << "\t";
+  *AdjacencyFile << getNr()+1 << "\t";
   for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); (++Runner))
-    *AdjacencyFile << (*Runner)->GetOtherAtom(this)->getNr() << "\t";
+    *AdjacencyFile << (*Runner)->GetOtherAtom(this)->getNr()+1 << "\t";
   *AdjacencyFile << endl;
 };
@@ -87 +87 @@
   for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); (++Runner))
     if (getNr() < (*Runner)->GetOtherAtom(this)->getNr())
-      *BondFile << getNr() << "\t" << (*Runner)->GetOtherAtom(this)->getNr() << "\n";
+      *BondFile << getNr()+1 << "\t" << (*Runner)->GetOtherAtom(this)->getNr()+1 << "\n";
 };
 

tests/regression/Molecules/BondFile/pre/test.dbond

@@ -1 +1 @@
 m n
-0 1
-0 3
-0 4
-0 5
 1 2
+1 4
+1 5
 1 6
-1 7
+2 3
+2 7
 2 8
-2 9
-2 10
+3 9
+3 10
+3 11

tests/regression/Molecules/BondFile/testsuite-molecules-fragmentation-bond-file.at

@@ -7 +7 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/BondFile/pre/test.conf $file], 0)
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/BondFile/pre/test.dbond .], 0)
-AT_CHECK([../../molecuilder -i $file -o pdb -v 4 --select-molecule-by-id 0 -A test.dbond --skiplines 1 --offset 0], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -o pdb -v 4 --select-molecule-by-id 0 -A test.dbond --skiplines 1 --offset 1], 0, [stdout], [stderr])
 AT_CHECK([file=test.pdb; diff -w -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Molecules/BondFile/post/test.pdb], 0, [ignore], [ignore])
 
@@ -20 +20 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/BondFile/pre/test.conf $file], 0)
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/BondFile/pre/test.dbond .], 0)
-AT_CHECK([../../molecuilder -i $file -o pdb -v 4 --select-molecule-by-id 0 -A test.dbond --skiplines 1 --offset 0 --undo], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -o pdb -v 4 --select-molecule-by-id 0 -A test.dbond --skiplines 1 --offset 1 --undo], 0, [stdout], [stderr])
 AT_CHECK([file=test.pdb; diff -w -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Molecules/BondFile/post/test.pdb], 0, [ignore], [ignore])
 
@@ -33 +33 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/BondFile/pre/test.conf $file], 0)
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/BondFile/pre/test.dbond .], 0)
-AT_CHECK([../../molecuilder -i $file -o pdb -v 4 --select-molecule-by-id 0 -A test.dbond --skiplines 1 --offset 0 --undo --redo], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -o pdb -v 4 --select-molecule-by-id 0 -A test.dbond --skiplines 1 --offset 1 --undo --redo], 0, [stdout], [stderr])
 AT_CHECK([file=test.pdb; diff -w -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Molecules/BondFile/post/test.pdb], 0, [ignore], [ignore])
 

tests/regression/Molecules/SaveAdjacency/post/test.adj

@@ -1 +1 @@
 m       n
-0       8       
-1       8       
-2       8       
+1       9       
+2       9       
 3       9       
-4       9       
+4       10      
 5       10      
-6       10      
-7       10      
-8       0       9       1       2       
-9       8       10      3       4       
-10      5       6       7       9       
+6       11      
+7       11      
+8       11      
+9       1       10      2       3       
+10      9       11      4       5       
+11      6       7       8       10      

tests/regression/Molecules/SaveBonds/post/test.dbond

@@ -1 +1 @@
 m       n
-0       8
-1       8
-2       8
+1       9
+2       9
 3       9
-4       9
+4       10
 5       10
-6       10
-7       10
-8       9
+6       11
+7       11
+8       11
 9       10
+10      11