Changeset 0cbad2 for tests/regression/Molecules/BondFile

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:

tests/regression/Molecules/BondFile

Files:

• post/test.pdb (added)
• pre/silica.dbond.0000 (added)
• pre/silica.pov1.0000.pdb (added)
• pre/test.dbond (modified) (1 diff)
• testsuite-molecules-bond-file.at (modified) (1 diff)

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

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

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

@@ -1 +1 @@
 ### Bonds from file
 
-AT_SETUP([Molecules - Bonds from file])
+AT_SETUP([Molecules - Fragmentation bonds file])
 AT_KEYWORDS([Molecules])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/BondFile/pre/test.* .], 0)
-AT_CHECK([../../molecuilder -i test.conf  -v 4 --select-molecule-by-id 0 -A test.dbond], 0, [stdout], [stderr])
-AT_CHECK([fgrep "Looking for atoms 2 and 9." stdout], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder -i test.conf -o pdb -v 4 --select-molecule-by-id 0 -A test.dbond --skiplines 1 --offset 0], 0, [stdout], [stderr])
+AT_CHECK([file=test.pdb; diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/BondFile/post/$file], 0, [ignore], [ignore])
 AT_CLEANUP
+
+AT_SETUP([Molecules - TREMOLO dbond file])
+AT_KEYWORDS([Molecules])
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/BondFile/pre/silica.* .], 0)
+AT_CHECK([../../molecuilder -i silica.pov1.0000.pdb -v 4 --select-molecule-by-id 0 -A silica.dbond.0000 --skiplines 2 --offset 1], 0, [stdout], [stderr])
+AT_CHECK([fgrep -c "CONECT 7153 6098 5949 5922" silica.pov1.0000.pdb], 0, [1
+], [ignore])
+AT_CLEANUP