Changeset 4e65af for src

Timestamp:

Aug 20, 2014, 12:58:30 PM (10 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:

45cdce6

Parents:

7f833c

git-author:

Frederik Heber <heber@…> (08/13/14 13:59:54)

git-committer:

Frederik Heber <heber@…> (08/20/14 12:58:30)

Message:

FIX: PdbParser would write coordinates 4.1000 instead of 5.000.

• we did round in printCoordinates(), without checking for overflow, resulting in 1000 for 999.9 instead of 999.
• extended ParserPdbUnitTest to test these cases.

Location:

src/Parser

Files:

• PdbParser.cpp (modified) (2 diffs)
• unittests/ParserPdbUnitTest.cpp (modified) (1 diff)

src/Parser/PdbParser.cpp

@@ -394 +394 @@
     --meaningful_bits;
   // count digits before dot (without minus and round towards zero!)
-  const int full = floor(fabs(value));
+  int full = floor(fabs(value));
   size_t bits_before_dot = 1;
   {
@@ -411 +411 @@
     if (value < 0)
       position << "-";
-    const int remainder = round((abs(value)-full)*pow(10,bits_after_dot));
+    // truncate 999.9 to 999 and not to 1000! (hence, extra check!)
+    int remainder = round((abs(value)-full)*pow(10,bits_after_dot));
+    if (remainder >= pow(10,bits_after_dot)) {
+      remainder = 0;
+      ++full;
+    }
     position << full << "." << setfill('0') << setw(bits_after_dot) << remainder;
     if (bits_after_dot == 2)

src/Parser/unittests/ParserPdbUnitTest.cpp

@@ -141 +141 @@
   CPPUNIT_ASSERT_EQUAL( 
       std::string("-1234.56"), FormatParser<pdb>::printCoordinate(-1234.56) );
+  CPPUNIT_ASSERT_EQUAL( 
+      std::string("4.990"), FormatParser<pdb>::printCoordinate(4.99) );
+  CPPUNIT_ASSERT_EQUAL( 
+      std::string("4.999"), FormatParser<pdb>::printCoordinate(4.999) );
+  CPPUNIT_ASSERT_EQUAL( 
+      std::string("5.000"), FormatParser<pdb>::printCoordinate(4.9999) );
+  CPPUNIT_ASSERT_EQUAL( 
+      std::string("5.000"), FormatParser<pdb>::printCoordinate(4.99999) );
+  CPPUNIT_ASSERT_EQUAL( 
+      std::string("5.001"), FormatParser<pdb>::printCoordinate(5.001) );
+  CPPUNIT_ASSERT_EQUAL( 
+      std::string("5.000"), FormatParser<pdb>::printCoordinate(5.0001) );
+  CPPUNIT_ASSERT_EQUAL( 
+      std::string("5.000"), FormatParser<pdb>::printCoordinate(5.00001) );
 }