Changeset 9e1d01


Ignore:
Timestamp:
Mar 30, 2012, 9:16:31 AM (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:
b380ed
Parents:
c67ff9
git-author:
Frederik Heber <heber@…> (03/21/12 09:34:00)
git-committer:
Frederik Heber <heber@…> (03/30/12 09:16:31)
Message:

Added CopyAtoms structure.

  • this creates a copy of a vector of atoms with as much depth as desired by the user.
  • this is a hierarchy of functors that each add additional functionality such as also re-creating the bonds, ...
Location:
src
Files:
8 added
3 edited

Legend:

Unmodified
Added
Removed

  • src/Atom/Makefile.am

    rc67ff9 r9e1d01  
    2929  Atom/TesselPoint.hpp
    3030
     31COPYATOMSSOURCE = \
     32        Atom/CopyAtoms/CopyAtoms_SaturateDanglingBonds.cpp \
     33        Atom/CopyAtoms/CopyAtoms_withBonds.cpp
     34
     35COPYATOMSHEADER = \
     36        Atom/CopyAtoms/CopyAtoms_SaturateDanglingBonds.hpp \
     37        Atom/CopyAtoms/CopyAtoms_Simple.hpp \
     38        Atom/CopyAtoms/CopyAtoms_withBonds.hpp \
     39        Atom/CopyAtoms/CopyAtomsInterface.hpp
    3140
    3241noinst_LTLIBRARIES += libMolecuilderAtom.la
    3342libMolecuilderAtom_la_includedir = $(includedir)/MoleCuilder/Atom/
    3443
    35 nobase_libMolecuilderAtom_la_include_HEADERS = ${ATOMHEADER}
     44nobase_libMolecuilderAtom_la_include_HEADERS = $(ATOMHEADER) $(COPYATOMSHEADER)
    3645
    3746## Define the source file list for the "libexample-@MOLECUILDER_API_VERSION@.la"
    … …  
    4352## from each source file.  Note that it is not necessary to list header files
    4453## which are already listed elsewhere in a _HEADERS variable assignment.
    45 libMolecuilderAtom_la_SOURCES = ${ATOMSOURCE}
     54libMolecuilderAtom_la_SOURCES = $(ATOMSOURCE) $(COPYATOMSSOURCE)
    4655
    4756## Instruct libtool to include ABI version information in the generated shared

  • src/Atom/unittests/Makefile.am

    rc67ff9 r9e1d01  
    44ATOMTESTSSOURCES = \
    55        ../Atom/unittests/AtomObserverUnitTest.cpp \
     6        ../Atom/unittests/CopyAtomsInterfaceUnitTest.cpp \
    67        stubs/ObserverStub.cpp
    78
    89ATOMTESTSHEADERS = \
    910        ../Atom/unittests/AtomObserverUnitTest.hpp \
     11        ../Atom/unittests/CopyAtomsInterfaceUnitTest.hpp \
    1012        stubs/ObserverStub.hpp
    1113
    1214ATOMTESTS = \
    13   AtomObserverUnitTest
     15  AtomObserverUnitTest \
     16  CopyAtomsInterfaceUnitTest
    1417
    1518TESTS += $(ATOMTESTS)
    … …  
    3538AtomObserverUnitTest_LDADD = ${ATOMTESTLIBS}
    3639
     40CopyAtomsInterfaceUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     41        ../Atom/unittests/CopyAtomsInterfaceUnitTest.cpp \
     42        ../Atom/unittests/CopyAtomsInterfaceUnitTest.hpp
     43CopyAtomsInterfaceUnitTest_LDADD = ${ATOMTESTLIBS}
    3744
    3845

  • src/documentation/constructs/atoms.dox

    rc67ff9 r9e1d01  
    5656 * compatible implementation.
    5757 *
     58 * \section atoms-copy Copying atoms
    5859 *
    59  * \date 2011-10-31
     60 * Copying atoms is a frequent action. That's why there are specific functors
     61 * to get it done in more and more complex ways. The functors all inherit
     62 * the \ref CopyAtomsInterface and the more complex ones build upon the
     63 * functionality of the simpler ones:
     64 * -# CopyAtomsInterface: Internally sets to the number of desired atoms.
     65 * -# CopyAtoms_Simple: Fills the internal set with true copies.
     66 * -# CopyAtoms_withBonds: Additionally also adds bonds in between the copies
     67 *    as they exist in between the original atoms.
     68 * -# CopyAtoms_SaturateDanglingBonds: additionally checks for cut bond that
     69 *    would now become dangling bonds and inserts additional hydrogens for
     70 *    each cut bond such that the copied array of atoms is saturated.
     71 *
     72 * The CopyAtomsInterface is simple to use:
     73 * \code
     74 *   std::vector<atom *> atoms_to_copy;
     75 *   CopyAtoms_Simple copyMethod;
     76 *   copyMethod(atoms_to_copy);
     77 *   std::vector<atom *> copiedAtoms = getCopiedAtoms();
     78 * \endcode
     79 *
     80 *
     81 * \date 2012-03-30
     82 *
    6083 */
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