Changeset cc6e5c for utils/Python

Timestamp:

May 20, 2014, 8:47:10 AM (11 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:

975b83

Parents:

0d4168

git-author:

Frederik Heber <heber@…> (09/28/13 00:59:47)

git-committer:

Frederik Heber <heber@…> (05/20/14 08:47:10)

Message:

Replaced Reactions by simple function exported to pyMoleCuilder.

• Reactions are a bad idea from the start, calculations do not need to be undone. Hence, why make them into an Action that is specifically undoable?
• removed all Reaction..-related files.
• removed ActinQueue::getLastAction().
• removed CalculateBoundingBoxAction, CalculateCellVolumeAction, and CalculateMolarMassAction, replaced by small function in Python folder.
• TESTFIX: removed associated regression tests in Analysis.
• modified boxmaker.py.in as names of functions changed.
• removed Actions/pyMoleCuilder.cpp, is redunant with PythonScripting_impl.hpp.

File:

• utils/Python/boxmaker.py.in (modified) (2 diffs)

utils/Python/boxmaker.py.in

@@ -151 +151 @@
 def GetSourceMolareMass(opt, units):
     mol.SelectionAllAtoms()
-    mass_sum = mol.AnalysisCalculateMolarMass()
+    mass_sum = mol.getSelectedMolarMass()
     have = ("%f atomicmassunit" % mass_sum)
     want = ("%f*%s" % tuple(units['mass']))
@@ -279 +279 @@
 def GetSourceBBabs(opt):
     mol.WorldCenterOnEdge()
-    bb = mol.AnalysisCalculateBoundingBox()
+    bb = mol.getBoundingBox()
     bbmin = [bb[0], bb[2], bb[4]]
     bbmax = [bb[1], bb[3], bb[5]]