source: tests/regression/Molecules/StretchBond/post/benzene.pdb@ 3b74fa

Action_Thermostats Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision
Last change on this file since 3b74fa was 3b74fa, checked in by Frederik Heber <frederik.heber@…>, 8 years ago

Rewrite of StretchBondAction to take bondgraph into account.

  • i.e. we now look at the bond graph of the molecule to find all atoms on either side of the bond and shift each set accordingly.
  • this functionality needs to be refactored into a distinct class lateron.
  • TESTS: Added new test case on cyclic bond with benzene.
  • Property mode set to 100644
File size: 2.0 KB
Line 
1REMARK created by molecuilder on Mon May 15 12:28:27 2017, time step 0
2ATOM 1 H01 0non 01 5.000 7.145 5.002 0.00 0.00 H 0
3ATOM 2 C01 0non 01 6.080 7.145 5.001 0.00 0.00 C 0
4ATOM 3 C02 0non 01 6.781 8.145 5.004 0.00 0.00 C 0
5ATOM 4 C03 0non 01 6.781 6.144 5.004 0.00 0.00 C 0
6ATOM 5 C04 0non 01 8.161 8.345 5.004 0.00 0.00 C 0
7ATOM 6 C05 0non 01 8.161 5.945 5.004 0.00 0.00 C 0
8ATOM 7 C06 0non 01 8.849 7.145 5.001 0.00 0.00 C 0
9ATOM 8 H02 0non 01 6.245 9.290 5.006 0.00 0.00 H 0
10ATOM 9 H03 0non 01 6.245 5.000 5.007 0.00 0.00 H 0
11ATOM 10 H04 0non 01 8.705 9.278 5.005 0.00 0.00 H 0
12ATOM 11 H05 0non 01 8.704 5.012 5.006 0.00 0.00 H 0
13ATOM 12 H06 0non 01 9.929 7.145 5.000 0.00 0.00 H 0
14CONECT 1 2
15CONECT 2 1 3 4
16CONECT 3 2 5 8
17CONECT 4 2 6 9
18CONECT 5 3 7 10
19CONECT 6 4 7 11
20CONECT 7 5 6 12
21CONECT 8 3
22CONECT 9 4
23CONECT 10 5
24CONECT 11 6
25CONECT 12 7
26END
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