Changeset d1134d

Timestamp:

Jul 12, 2017, 7:10:32 PM (7 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

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

Children:

92d0e6

Parents:

4a6ef3

git-author:

Frederik Heber <frederik.heber@…> (05/18/17 19:10:25)

git-committer:

Frederik Heber <frederik.heber@…> (07/12/17 19:10:32)

Message:

FIX: rotate-around-bond now rotates only one side of mol's bond graph.

• TESTS: Added regression test on almost complete circle where bond rotation only works because of the new functionality.

Files:

• src/Actions/MoleculeAction/RotateAroundBondAction.cpp (modified) (4 diffs)
• tests/regression/Molecules/RotateAroundBond/post/benzene_90degree.pdb (added)
• tests/regression/Molecules/RotateAroundBond/pre/benzene.pdb (added)
• tests/regression/Molecules/RotateAroundBond/testsuite-molecules-rotate-around-bond.at (modified) (1 diff)

src/Actions/MoleculeAction/RotateAroundBondAction.cpp

@@ -46 +46 @@
 #include "Graph/CyclicStructureAnalysis.hpp"
 #include "Graph/DepthFirstSearchAnalysis.hpp"
+#include "Graph/BoostGraphCreator.hpp"
+#include "Graph/BoostGraphHelpers.hpp"
+#include "Graph/BreadthFirstSearchGatherer.hpp"
 
 #include "Atom/atom.hpp"
@@ -74 +77 @@
 }
 
+static bool addEdgePredicate(
+    const bond &_bond,
+    const std::vector<atomId_t> &_atomids)
+{
+  ASSERT(_atomids.size() == (size_t)2,
+      "addEdgePredicate() - atomids must contain exactly two ids.");
+  // do not add selected edge
+  return ((_bond.leftatom->getId() != _atomids[0])
+      || (_bond.rightatom->getId() != _atomids[1]));
+}
+
 ActionState::ptr MoleculeRotateAroundBondAction::performCall()
 {
@@ -109 +123 @@
   }
 
+  // gather sorted ids
+  std::vector<atomId_t> atomids(2);
+  atomids[0] = atoms[0]->getId();
+  atomids[1] = atoms[1]->getId();
+  std::sort(atomids.begin(), atomids.end());
+  LOG(1, "DEBUG: Selected nodes are " << atomids);
+
+  // get nodes on either side of selected bond via BFS discovery
+  BoostGraphCreator BGcreator;
+  BGcreator.createFromMolecule(*mol,
+      boost::bind(addEdgePredicate, _1, boost::ref(atomids)));
+  BreadthFirstSearchGatherer NodeGatherer(BGcreator);
+  BoostGraphHelpers::Nodeset_t bondside_sets =
+      NodeGatherer(params.bondside.get() ? atoms[0]->getId() : atoms[1]->getId());
+  std::sort(bondside_sets.begin(), bondside_sets.end());
+
   // convert from degrees to radian
   const double angle_radian = params.angle.get() * M_PI/180.;
@@ -118 +148 @@
   Plane bondplane(NormalVector, OffsetVector);
   Line RotationAxis(OffsetVector, NormalVector);
+
   // go through the molecule and rotate each atom relative two plane
   for (molecule::iterator iter = mol->begin(); iter != mol->end(); ++iter) {
     const Vector &position = (*iter)->getPosition();
     const double signed_distance = bondplane.SignedDistance(position);
+    // for each atom determine in which set of nodes it is and shift accordingly
+    const atomId_t &atomid = (*iter)->getId();
     LOG(3, "DEBUG: Inspecting atom " << **iter << " at " << position);
-    if ((params.bondside.get() && (signed_distance > 0)) ||
-        (!params.bondside.get() && (signed_distance < 0))) {
+    if (std::binary_search(bondside_sets.begin(), bondside_sets.end(), atomid)) {
       LOG(4, "DEBUG: Rotating atom " << **iter << " by " << angle_radian
           << " rad around " << RotationAxis);

tests/regression/Molecules/RotateAroundBond/testsuite-molecules-rotate-around-bond.at

@@ -86 +86 @@
 
 AT_CLEANUP
+
+AT_SETUP([Molecules - Rotate around bond on almost complete cycle])
+AT_KEYWORDS([molecules rotate-around-bond])
+
+file=benzene_90degree.pdb
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/RotateAroundBond/pre/benzene.pdb $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder -i $file --select-atom-by-order -1 -6 --remove-atom --select-atom-by-id 3 5 --rotate-around-bond 90.], 0, [stdout], [stderr])
+AT_CHECK([diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Molecules/RotateAroundBond/post/$file], 0, [ignore], [ignore])
+
+AT_CLEANUP