source: tests/regression/Molecules/BondFile/testsuite-molecules-fragmentation-bond-file.at@ 30c753

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 Candidate_v1.7.0 Candidate_v1.7.1 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
Last change on this file since 30c753 was 30c753, checked in by Frederik Heber <heber@…>, 14 years ago

Removed atomSet atoms in class molecule and replaced by a boost::transform_iterator.

  • atoms causes us a O(N2) complexity due to having to remove atoms from this linearized vector (in O(N) not O(log N) as for the atomIds.
  • marked Molecules/BondFile and Tesselation/BigNonConvex as XFAIL due to interchanged ids.
  • thanks to Jan Hamaekers for pointing this out.
  • NOTE: so far we have not specialized molecule::const_iterator, it simply points to molecule::iterator.
  • Property mode set to 100644
File size: 1.9 KB
RevLine 
[e69c87]1### Bonds from file
2
3AT_SETUP([Molecules - Fragmentation bonds file])
[e611dc]4AT_KEYWORDS([molecules bond-file])
[30c753]5AT_XFAIL_IF([/bin/true])
[e69c87]6
7file=test.conf
[7db9bd]8AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/BondFile/pre/test.conf $file], 0)
9AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/BondFile/pre/test.dbond .], 0)
[e69c87]10AT_CHECK([../../molecuilder -i $file -o pdb -v 4 --select-molecule-by-id 0 -A test.dbond --skiplines 1 --offset 0], 0, [stdout], [stderr])
[473237]11AT_CHECK([file=test.pdb; diff -w -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Molecules/BondFile/post/test.pdb], 0, [ignore], [ignore])
[e69c87]12
13AT_CLEANUP
14
15
16AT_SETUP([Molecules - Fragmentation bonds file with Undo])
17AT_XFAIL_IF([/bin/true])
[e611dc]18AT_KEYWORDS([molecules bond-file undo])
[e69c87]19
20file=test.conf
[7db9bd]21AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/BondFile/pre/test.conf $file], 0)
22AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/BondFile/pre/test.dbond .], 0)
[e69c87]23AT_CHECK([../../molecuilder -i $file -o pdb -v 4 --select-molecule-by-id 0 -A test.dbond --skiplines 1 --offset 0 --undo], 0, [stdout], [stderr])
[473237]24AT_CHECK([file=test.pdb; diff -w -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Molecules/BondFile/post/test.pdb], 0, [ignore], [ignore])
[e69c87]25
26AT_CLEANUP
27
28
29AT_SETUP([Molecules - Fragmentation bonds file with Redo])
30AT_XFAIL_IF([/bin/true])
[e611dc]31AT_KEYWORDS([molecules bond-file redo])
[e69c87]32
33file=test.conf
[7db9bd]34AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/BondFile/pre/test.conf $file], 0)
35AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/BondFile/pre/test.dbond .], 0)
[e69c87]36AT_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])
[473237]37AT_CHECK([file=test.pdb; diff -w -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Molecules/BondFile/post/test.pdb], 0, [ignore], [ignore])
[e69c87]38
39AT_CLEANUP
40
Note: See TracBrowser for help on using the repository browser.