Changeset 788dce


Ignore:
Timestamp:
Jun 20, 2017, 7:58:36 PM (8 years ago)
Author:
Frederik Heber <frederik.heber@…>
Branches:
Action_Thermostats, Add_AtomRandomPerturbation, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_StructOpt_integration_tests, AutomationFragmentation_failures, Candidate_v1.6.1, ChangeBugEmailaddress, ChemicalSpaceEvaluator, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph_documentation, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, ForceAnnealing_oldresults, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, Gui_displays_atomic_force_velocity, IndependentFragmentGrids_IntegrationTest, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, RotateToPrincipalAxisSystem_UndoRedo, StoppableMakroAction, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps
Children:
5e17bf
Parents:
9a9f847
git-author:
Frederik Heber <heber@…> (03/22/17 15:42:35)
git-committer:
Frederik Heber <frederik.heber@…> (06/20/17 19:58:36)
Message:

Added RotateAroundBondAction.

  • TESTS: added regression test.
  • DOCU: added explanation to userguide.
Files:
8 added
6 edited

Legend:

Unmodified
Added
Removed

  • doc/userguide/userguide.xml

    r9a9f847 r788dce  
    10551055          <para>As before, this is actually just an operation on all of the molecule&apos;s atoms, namely translating them.</para>
    10561056        </section>
     1057        <section xml:id="molecule.rotate-around-bond">
     1058          <title xml:id="molecule.rotate-around-bond.title">Rotate around bond </title>
     1059          <para>This rotates parts of a molecule around a given bond, i.e. the
     1060          bond vector becomes the rotation axis but only atoms on the side of
     1061          second atom get rotated. This naturally does not work for bonds in a
     1062          cycle.</para>
     1063          <programlisting>
     1064  ... --rotate-around-bond &quot;90&quot; \
     1065      --bond-side 0\
     1066   </programlisting>
     1067        </section>
    10571068        <section xml:id="molecule.rotate-around-self">
    10581069          <title xml:id="molecule.rotate-around-self.title">Rotate around self </title>

  • src/Actions/GlobalListOfActions.hpp

    r9a9f847 r788dce  
    8383  (MoleculeLoad) \
    8484  (MoleculeRemove) \
     85  (MoleculeRotateAroundBond) \
    8586  (MoleculeRotateAroundSelfByAngle) \
    8687  (MoleculeRotateToPrincipalAxisSystem) \

  • src/Actions/Makefile.am

    r9a9f847 r788dce  
    317317  Actions/MoleculeAction/LoadAction.cpp \
    318318  Actions/MoleculeAction/RemoveAction.cpp \
     319  Actions/MoleculeAction/RotateAroundBondAction.cpp \
    319320  Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp \
    320321  Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp \
    … …  
    335336  Actions/MoleculeAction/LoadAction.hpp \
    336337  Actions/MoleculeAction/RemoveAction.hpp \
     338  Actions/MoleculeAction/RotateAroundBondAction.hpp \
    337339  Actions/MoleculeAction/RotateAroundSelfByAngleAction.hpp \
    338340  Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp \
    … …  
    353355  Actions/MoleculeAction/LoadAction.def \
    354356  Actions/MoleculeAction/RemoveAction.def \
     357  Actions/MoleculeAction/RotateAroundBondAction.def \
    355358  Actions/MoleculeAction/RotateAroundSelfByAngleAction.def \
    356359  Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def \

  • tests/Python/AllActions/options.dat

    r9a9f847 r788dce  
    3333bond-degree     "1"
    3434bond-file       "bond.dat"
     35bondside        "1"
    3536bond-table      "table.dat"
    3637calculate-bounding-box  ""
    … …  
    159160repeat-box      "1 1 1"
    160161reset   1
     162rotate-around-bond      "90."
    161163rotate-around-origin    "180."
    162164rotate-around-origin    "20."

  • tests/regression/Makefile.am

    r9a9f847 r788dce  
    133133        $(srcdir)/Molecules/LinearInterpolationofTrajectories/testsuite-molecules-linear-interpolation-of-trajectories.at \
    134134        $(srcdir)/Molecules/Remove/testsuite-molecules-remove.at \
     135        $(srcdir)/Molecules/RotateAroundBond/testsuite-molecules-rotate-around-bond.at \
    135136        $(srcdir)/Molecules/RotateAroundOrigin/testsuite-molecules-rotate-around-origin.at \
    136137        $(srcdir)/Molecules/RotateAroundSelf/testsuite-molecules-rotate-around-self.at \

  • tests/regression/Molecules/testsuite-molecules.at

    r9a9f847 r788dce  
    6060m4_include([Molecules/RotateToPrincipalAxisSystem/testsuite-molecules-rotate-to-principal-axis-system.at])
    6161
     62# rotate around one of its bond
     63m4_include([Molecules/RotateAroundBond/testsuite-molecules-rotate-around-bond.at])
     64
    6265# Rotate around origin
    6366m4_include([Molecules/RotateAroundOrigin/testsuite-molecules-rotate-around-origin.at])
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