source: tests/regression/Parser/Tremolo/pre/bio.data@ f73e06

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
Last change on this file since f73e06 was 05e2ed, checked in by Frederik Heber <heber@…>, 12 years ago

FIX: TremoloParser did not load/save imprData or torsion correctly.

  • this error was introduced when incorporating local-global-maps and conversions where this was not correctly done for the improper and torsion string:
    • conversion from local to global on load was present but went over all atoms, not just newly parsed ones. adapt.. now gets atom vector as param.
    • save did no global-local conversion. For this we generalized adaptIdDependentDataString() to get a function pointer converting ids.
  • TEST: We added a new regression test on this matter where a .data file with impropers is loaded and stored.
  • Property mode set to 100644
File size: 5.3 KB
Line 
1# ATOMDATA name Id x=3 charge type resName resSeq chainID occupancy tempFactor segID neighbors=4 imprData
2# Box 20 0 0 0 20 0 0 0 20
3N 1 177.865 178.186 36.1556 -0.3 NH3 SER 1 P 1.000000e+00 0.000000e+00 P1 2 3 4 5 -
4HT1 2 178.062 178.482 37.1418 0.33 HC SER 1 P 1.000000e+00 0.000000e+00 P1 1 0 0 0 -
5HT2 3 178.665 178.524 35.5735 0.33 HC SER 1 P 1.000000e+00 0.000000e+00 P1 1 0 0 0 -
6HT3 4 177.872 177.144 36.1476 0.33 HC SER 1 P 1.000000e+00 0.000000e+00 P1 1 0 0 0 -
7CA 5 176.49 178.741 35.6547 0.21 CT1 SER 1 P 1.000000e+00 0.000000e+00 P1 1 6 7 12 -
8HA 6 175.766 178.253 36.3038 0.1 HB SER 1 P 1.000000e+00 0.000000e+00 P1 5 0 0 0 -
9CB 7 176.451 180.351 35.9417 0.05 CT2 SER 1 P 1.000000e+00 0.000000e+00 P1 5 8 9 10 -
10HB1 8 177.246 180.893 35.3722 0.09 HA SER 1 P 1.000000e+00 0.000000e+00 P1 7 0 0 0 -
11HB2 9 175.466 180.783 35.6342 0.09 HA SER 1 P 1.000000e+00 0.000000e+00 P1 7 0 0 0 -
12OG 10 176.617 180.761 37.3191 -0.66 OH1 SER 1 P 1.000000e+00 0.000000e+00 P1 7 11 0 0 -
13HG1 11 177.06 181.621 37.3313 0.43 H SER 1 P 1.000000e+00 0.000000e+00 P1 10 0 0 0 -
14C 12 176.127 178.358 34.1262 0.51 C SER 1 P 1.000000e+00 0.000000e+00 P1 5 13 14 0 5-14-13
15O 13 176.905 178.746 33.2494 -0.51 O SER 1 P 1.000000e+00 0.000000e+00 P1 12 0 0 0 -
16N 14 174.973 177.585 33.7685 -0.47 NH1 TYR 2 P 1.000000e+00 0.000000e+00 P1 12 15 16 0 12-16-15
17HN 15 174.392 177.29 34.528 0.31 H TYR 2 P 1.000000e+00 0.000000e+00 P1 14 0 0 0 -
18CA 16 174.451 177.01 32.4237 0.07 CT1 TYR 2 P 1.000000e+00 0.000000e+00 P1 14 17 18 33 -
19HA 17 175.327 176.644 31.8972 0.09 HB TYR 2 P 1.000000e+00 0.000000e+00 P1 16 0 0 0 -
20CB 18 173.38 175.729 32.5583 -0.18 CT2 TYR 2 P 1.000000e+00 0.000000e+00 P1 16 19 20 21 -
21HB1 19 173.198 175.631 33.6471 0.09 HA TYR 2 P 1.000000e+00 0.000000e+00 P1 18 0 0 0 -
22HB2 20 172.337 175.954 32.1976 0.09 HA TYR 2 P 1.000000e+00 0.000000e+00 P1 18 0 0 0 -
23CG 21 173.718 174.221 32.1456 0.000000e+00 CA TYR 2 P 1.000000e+00 0.000000e+00 P1 18 22 29 0 -
24CD1 22 174.945 173.559 32.6206 -0.115 CA TYR 2 P 1.000000e+00 0.000000e+00 P1 21 23 24 0 -
25HD1 23 175.644 174.118 33.218 0.115 HP TYR 2 P 1.000000e+00 0.000000e+00 P1 22 0 0 0 -
26CE1 24 175.199 172.127 32.4507 -0.115 CA TYR 2 P 1.000000e+00 0.000000e+00 P1 22 25 26 0 -
27HE1 25 176.111 171.702 32.8588 0.115 HP TYR 2 P 1.000000e+00 0.000000e+00 P1 24 0 0 0 -
28CZ 26 174.192 171.271 31.837 0.11 CA TYR 2 P 1.000000e+00 0.000000e+00 P1 24 27 31 0 -
29OH 27 174.358 169.841 31.8182 -0.54 OH1 TYR 2 P 1.000000e+00 0.000000e+00 P1 26 28 0 0 -
30HH 28 173.583 169.421 31.4253 0.43 H TYR 2 P 1.000000e+00 0.000000e+00 P1 27 0 0 0 -
31CD2 29 172.72 173.323 31.5019 -0.115 CA TYR 2 P 1.000000e+00 0.000000e+00 P1 21 30 31 0 -
32HD2 30 171.742 173.697 31.1998 0.115 HP TYR 2 P 1.000000e+00 0.000000e+00 P1 29 0 0 0 -
33CE2 31 172.964 171.877 31.3556 -0.115 CA TYR 2 P 1.000000e+00 0.000000e+00 P1 26 29 32 0 -
34HE2 32 172.189 171.223 30.9582 0.115 HP TYR 2 P 1.000000e+00 0.000000e+00 P1 31 0 0 0 -
35C 33 173.761 178.086 31.4717 0.51 C TYR 2 P 1.000000e+00 0.000000e+00 P1 16 34 35 0 16-35-34
36O 34 173.378 179.163 31.9399 -0.51 O TYR 2 P 1.000000e+00 0.000000e+00 P1 33 0 0 0 -
37N 35 173.569 177.77 30.1148 -0.47 NH1 SER 3 P 1.000000e+00 0.000000e+00 P1 33 36 37 0 33-37-36
38HN 36 173.894 176.879 29.8026 0.31 H SER 3 P 1.000000e+00 0.000000e+00 P1 35 0 0 0 -
39CA 37 172.94 178.545 28.9841 0.07 CT1 SER 3 P 1.000000e+00 0.000000e+00 P1 35 38 39 44 -
40HA 38 172.509 179.469 29.357 0.09 HB SER 3 P 1.000000e+00 0.000000e+00 P1 37 0 0 0 -
41CB 39 174.102 179.041 27.909 0.05 CT2 SER 3 P 1.000000e+00 0.000000e+00 P1 37 40 41 42 -
42HB1 40 174.382 180.111 28.0915 0.09 HA SER 3 P 1.000000e+00 0.000000e+00 P1 39 0 0 0 -
43HB2 41 175.045 178.476 28.0923 0.09 HA SER 3 P 1.000000e+00 0.000000e+00 P1 39 0 0 0 -
44OG 42 173.877 178.942 26.4905 -0.66 OH1 SER 3 P 1.000000e+00 0.000000e+00 P1 39 43 0 0 -
45HG1 43 174.537 179.483 26.0385 0.43 H SER 3 P 1.000000e+00 0.000000e+00 P1 42 0 0 0 -
46C 44 171.714 177.686 28.4324 0.51 C SER 3 P 1.000000e+00 0.000000e+00 P1 37 45 46 0 37-46-45
47O 45 171.952 176.718 27.7049 -0.51 O SER 3 P 1.000000e+00 0.000000e+00 P1 44 0 0 0 -
48N 46 170.382 178.014 28.7741 -0.47 NH1 ILE 4 P 1.000000e+00 0.000000e+00 P1 44 47 48 0 44-48-47
49HN 47 170.235 178.767 29.4144 0.31 H ILE 4 P 1.000000e+00 0.000000e+00 P1 46 0 0 0 -
50CA 48 169.076 177.369 28.3434 0.07 CT1 ILE 4 P 1.000000e+00 0.000000e+00 P1 46 49 50 0 -
51HA 49 169.299 176.379 27.9605 0.09 HB ILE 4 P 1.000000e+00 0.000000e+00 P1 48 0 0 0 -
52CB 50 168.033 176.999 29.5686 -0.09 CT1 ILE 4 P 1.000000e+00 0.000000e+00 P1 48 51 52 56 -
53HB 51 167.602 177.949 29.9729 0.09 HA ILE 4 P 1.000000e+00 0.000000e+00 P1 50 0 0 0 -
54CG2 52 166.792 176.115 29.0477 -0.27 CT3 ILE 4 P 1.000000e+00 0.000000e+00 P1 50 53 54 55 -
55HG21 53 165.981 175.974 29.8079 0.09 HA ILE 4 P 1.000000e+00 0.000000e+00 P1 52 0 0 0 -
56HG22 54 166.268 176.544 28.1608 0.09 HA ILE 4 P 1.000000e+00 0.000000e+00 P1 52 0 0 0 -
57HG23 55 167.12 175.091 28.7604 0.09 HA ILE 4 P 1.000000e+00 0.000000e+00 P1 52 0 0 0 -
58CG1 56 168.699 176.276 30.877 -0.18 CT2 ILE 4 P 1.000000e+00 0.000000e+00 P1 50 57 58 59 -
59HG11 57 169.052 175.248 30.5973 0.09 HA ILE 4 P 1.000000e+00 0.000000e+00 P1 56 0 0 0 -
60HG12 58 169.615 176.826 31.2088 0.09 HA ILE 4 P 1.000000e+00 0.000000e+00 P1 56 0 0 0 -
61CD 59 167.852 176.118 32.2138 -0.27 CT3 ILE 4 P 1.000000e+00 0.000000e+00 P1 56 0 0 0 -
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