Changeset 105b72 for src/Parser/PdbParser.cpp

Timestamp:

Mar 18, 2013, 1:31:46 PM (12 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:

1f5e97

Parents:

e9bdef

git-author:

Frederik Heber <heber@…> (02/26/13 09:45:40)

git-committer:

Frederik Heber <heber@…> (03/18/13 13:31:46)

Message:

FIX: PdbParser skipped when coordinate exceeded 9999.999.

• the problem is that with fixed, setprecision controls the digits after the dot only and it is not possible to get the desired behavior with a combination of setfill, setw, and setprecision alone. Hence, we wrote our own static printCoordinate() helper for that.
• Added regression test for printCoordinate() to ParserPdbUnitTest.

File:

• src/Parser/PdbParser.cpp (modified) (4 diffs)

src/Parser/PdbParser.cpp

@@ -51 +51 @@
 #include "WorldTime.hpp"
 
+#include <algorithm>
+#include <cmath>
 #include <map>
 #include <vector>
@@ -276 +278 @@
         for (size_t i=0; i<NDIM;++i) {
           stringstream position;
-          position << setw(8) << fixed << setprecision(3) << (*atomIt)->getPositionAtStep(step).at(i);
+          position << setprecision(7) << (*atomIt)->getPositionAtStep(step).at(i);
           atomInfo.set(PositionEnumMap[i], position.str());
         }
@@ -368 +370 @@
   }
   return additionalAtomData[_atom->getId()];
+}
+
+/** Tiny helper function to print a float with a most 8 digits.
+ *
+ * A few examples best give the picture:
+ * 1234.678
+ *    1.234
+ *    0.001
+ *    0.100
+ * 1234567.
+ * 123456.7
+ * -1234.56
+ *
+ * \param value
+ * \return string representation
+ */
+const std::string FormatParser< pdb >::printCoordinate(
+    const double value)
+{
+  size_t meaningful_bits=7; // one for decimal dot
+  if (value < 0) //one for the minus sign
+    --meaningful_bits;
+  // count digits before dot (without minus and round towards zero!)
+  const int full = floor(fabs(value));
+  size_t bits_before_dot = 1;
+  {
+    int tmp = full;
+    for (;bits_before_dot < meaningful_bits;++bits_before_dot) {
+      // even if value is 0...somethingish, we still must start at one digit
+      tmp = tmp/10;
+      if (tmp == 0)
+        break;
+    }
+  }
+  // this fixes bits available after dot
+  const size_t bits_after_dot = std::min((int)meaningful_bits - (int)bits_before_dot, 3);
+  stringstream position;
+  if (bits_after_dot > 0) {
+    if (value < 0)
+      position << "-";
+    const int remainder = round((abs(value)-full)*pow(10,bits_after_dot));
+    position << full << "." << setfill('0') << setw(bits_after_dot) << remainder;
+    if (bits_after_dot == 2)
+      ELOG(2, "PdbParser is writing coordinates with just a two decimal places.");
+    if (bits_after_dot == 1)
+      ELOG(1, "PdbParser is writing coordinates with just a single decimal places.");
+  } else {
+    ELOG(0, "PdbParser is writing coordinates without any decimal places.");
+    position << full << ".";
+  }
+  return position.str();
 }
 
@@ -406 +459 @@
   // only act on these
   for (size_t i=0;i<NDIM;++i) {
-    stringstream position;
-    position << fixed << setprecision(3) << showpoint
-        << atomInfo.get<double>(PositionEnumMap[i]);
-    *file << setfill(' ') << right << setw(8) << position.str();
+    *file << setfill(' ') << right << setw(8)
+        << printCoordinate(atomInfo.get<double>(PositionEnumMap[i]));
   }
   {