Changes in / [be848d:78ea3c]

Files:

• doc/userguide/userguide.xml (modified) (2 diffs)
• src/Actions/Action.hpp (modified) (1 diff)
• src/Actions/GlobalListOfActions.hpp (modified) (1 diff)
• src/Actions/Makefile.am (modified) (3 diffs)
• src/Actions/MoleculeAction/RotateAroundBondAction.cpp (added)
• src/Actions/MoleculeAction/RotateAroundBondAction.def (added)
• src/Actions/MoleculeAction/RotateAroundBondAction.hpp (added)
• src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) (2 diffs)
• src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def (modified) (2 diffs)
• src/Actions/PotentialAction/ParsePotentialsAction.cpp (modified) (1 diff)
• src/Actions/WorldAction/StepWorldTimeAction.cpp (modified) (3 diffs)
• src/Actions/WorldAction/StepWorldTimeAction.def (modified) (1 diff)
• src/Atom/atom.cpp (modified) (1 diff)
• src/Atom/atom_atominfo.cpp (modified) (2 diffs)
• src/Fragmentation/Exporters/HydrogenPool.cpp (modified) (1 diff)
• src/Fragmentation/Exporters/HydrogenPool.hpp (modified) (1 diff)
• src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) (3 diffs)
• src/World.cpp (modified) (3 diffs)
• tests/Python/AllActions/options.dat (modified) (3 diffs)
• tests/regression/Makefile.am (modified) (1 diff)
• tests/regression/Molecules/RotateAroundBond/post/test-195-true.pdb (added)
• tests/regression/Molecules/RotateAroundBond/post/test-90-true.pdb (added)
• tests/regression/Molecules/RotateAroundBond/post/test-95-false.pdb (added)
• tests/regression/Molecules/RotateAroundBond/pre/test.pdb (added)
• tests/regression/Molecules/RotateAroundBond/pre/test_cycle.pdb (added)
• tests/regression/Molecules/RotateAroundBond/testsuite-molecules-rotate-around-bond.at (added)
• tests/regression/Molecules/RotateToPrincipalAxisSystem/testsuite-molecules-rotate-to-principal-axis-system.at (modified) (2 diffs)
• tests/regression/Molecules/testsuite-molecules.at (modified) (1 diff)
• tests/regression/WorldTime/StepWorldTime/testsuite-worldtime-step-world-time.at (modified) (3 diffs)

doc/userguide/userguide.xml

@@ -1177 +1177 @@
         <link linkend='geometry'>Geometry</link>.</para>
         </section>
+        <section xml:id="molecule.rotate-around-bond">
+          <title xml:id="molecule.rotate-around-bond.title">Rotate around bond </title>
+          <para>This rotates parts of a molecule around a given bond, i.e. the
+          bond vector becomes the rotation axis but only atoms on the side of
+          second atom get rotated. This naturally does not work for bonds in a
+          cycle.</para>
+          <programlisting>
+  ... --rotate-around-bond &quot;90&quot; \
+      --bond-side 0\
+   </programlisting>
+        </section>
         <section xml:id="molecule.rotate-around-self">
           <title xml:id="molecule.rotate-around-self.title">Rotate around self </title>
@@ -2658 +2669 @@
       under the command-line interface and look up the function name via
       help.</para>
+      <para>You can freely mix calls to the pymolecuilder module and other python commands.</para>
+      <note>However, be aware that all Actions are executed in another thread,
+      i.e. run in parallel. That means that a pymolecuilder command is not 
+      necessarily finished when python steps on to the next line!</note>
+      <para>In order to make python wait for the Actions to finish before
+      stepping, there is the special wait() command.</para>
+      <programlisting>
+         mol.MoleculeLoad("...")
+         mol.wait()
+      </programlisting>
+      <para>This will continue first after the molecule has been fully loaded.
+      </para>
+      <warning>These wait()s will have no effect if the python script is loaded
+      via the "load-session" command inside a User Interface (command-line,
+      GUI, ...) as this would cause the queue to wait indefinitely, namely till
+      the load-session itself would have finished.</warning>
+      <para>Therefore, more complex python scripts need to be called with
+      python and a set PYTHONPATH as described above.</para>
     </section>
   </chapter>

src/Actions/Action.hpp

@@ -29 +29 @@
  */
 #ifndef STATUS
-#define STATUS(msg) pushStatus(msg)
+#define STATUS(msg) \
+  pushStatus(msg); \
+  LOG(0, "STATUS: " << msg)
 #endif
 

src/Actions/GlobalListOfActions.hpp

@@ -88 +88 @@
   (MoleculeLoad) \
   (MoleculeRemove) \
+  (MoleculeRotateAroundBond) \
   (MoleculeRotateAroundSelfByAngle) \
   (MoleculeRotateToPrincipalAxisSystem) \

src/Actions/Makefile.am

@@ -339 +339 @@
   Actions/MoleculeAction/LoadAction.cpp \
   Actions/MoleculeAction/RemoveAction.cpp \
+  Actions/MoleculeAction/RotateAroundBondAction.cpp \
   Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp \
   Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp \
@@ -357 +358 @@
   Actions/MoleculeAction/LoadAction.hpp \
   Actions/MoleculeAction/RemoveAction.hpp \
+  Actions/MoleculeAction/RotateAroundBondAction.hpp \
   Actions/MoleculeAction/RotateAroundSelfByAngleAction.hpp \
   Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp \
@@ -375 +377 @@
   Actions/MoleculeAction/LoadAction.def \
   Actions/MoleculeAction/RemoveAction.def \
+  Actions/MoleculeAction/RotateAroundBondAction.def \
   Actions/MoleculeAction/RotateAroundSelfByAngleAction.def \
   Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def \

src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp

@@ -35 +35 @@
 //#include "CodePatterns/MemDebug.hpp"
 
+#include "CodePatterns/Assert.hpp"
 #include "CodePatterns/Log.hpp"
-#include "CodePatterns/Verbose.hpp"
+
+#include "Actions/UndoRedoHelpers.hpp"
+#include "Atom/AtomicInfo.hpp"
 #include "LinearAlgebra/Line.hpp"
 #include "LinearAlgebra/RealSpaceMatrix.hpp"
@@ -58 +61 @@
   molecule *mol = NULL;
 
+  std::vector<AtomicInfo> UndoInfo;
   for (World::MoleculeSelectionIterator iter = World::getInstance().beginMoleculeSelection(); iter != World::getInstance().endMoleculeSelection(); ++iter) {
     mol = iter->second;
     LOG(0, "Converting to prinicipal axis system.");
 
-    RealSpaceMatrix InertiaTensor = mol->getInertiaTensor();
+    // gather undo information: store position of all atoms of molecule
+    UndoInfo.reserve(UndoInfo.size()+mol->size());
+    {
+      for (molecule::const_iterator iter = const_cast<molecule const *>(mol)->begin();
+          iter != const_cast<molecule const *>(mol)->end();
+          ++iter) {
+        const atom * const Walker = *iter;
+        UndoInfo.push_back(AtomicInfo(*Walker));
+      }
+    }
 
+    // rotate
+//    RealSpaceMatrix InertiaTensor = mol->getInertiaTensor();
     mol->RotateToPrincipalAxisSystem(params.Axis.get());
 
     // summing anew for debugging (resulting matrix has to be diagonal!)
-    InertiaTensor = mol->getInertiaTensor();
+    RealSpaceMatrix InertiaTensor = mol->getInertiaTensor();
   }
-  return Action::success;
+
+  MoleculeRotateToPrincipalAxisSystemState *UndoState =
+      new MoleculeRotateToPrincipalAxisSystemState(UndoInfo, params);
+  return ActionState::ptr(UndoState);
 }
 
 ActionState::ptr MoleculeRotateToPrincipalAxisSystemAction::performUndo(ActionState::ptr _state) {
-//  MoleculeRotateToPrincipalAxisSystemState *state = assert_cast<MoleculeRotateToPrincipalAxisSystemState*>(_state.get());
+  MoleculeRotateToPrincipalAxisSystemState *state =
+      assert_cast<MoleculeRotateToPrincipalAxisSystemState*>(_state.get());
 
-//  string newName = state->mol->getName();
-//  state->mol->setName(state->lastName);
+  // set stored old state
+  SetAtomsFromAtomicInfo(state->undoinfo);
 
-  STATUS("Undo of MoleculeRotateToPrincipalAxisSystemAction not implemented.");
-  return Action::failure;
+  return ActionState::ptr(_state);
 }
 
 ActionState::ptr MoleculeRotateToPrincipalAxisSystemAction::performRedo(ActionState::ptr _state){
-  STATUS("Redo of MoleculeRotateToPrincipalAxisSystemAction not implemented.");
-  return Action::failure;
+  MoleculeRotateToPrincipalAxisSystemState *state =
+      assert_cast<MoleculeRotateToPrincipalAxisSystemState*>(_state.get());
+
+  for (World::MoleculeSelectionIterator iter = World::getInstance().beginMoleculeSelection();
+      iter != World::getInstance().endMoleculeSelection(); ++iter) {
+    molecule * const mol = iter->second;
+    mol->RotateToPrincipalAxisSystem(state->params.Axis.get());
+  }
+
+  return ActionState::ptr(_state);
 }
 

src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def

@@ -7 +7 @@
 
 // all includes and forward declarations necessary for non-integral types below
+#include <vector>
+
 #include "Actions/Values.hpp"
+#include "Atom/AtomicInfo.hpp"
 #include "LinearAlgebra/Vector.hpp"
 
@@ -23 +26 @@
 (VectorNotZeroValidator())
 
-#undef statetypes
-#undef statereferences
+#define statetypes (std::vector<AtomicInfo>)
+#define statereferences (undoinfo)
 
 // some defines for all the names, you may use ACTION, STATE and PARAMS

src/Actions/PotentialAction/ParsePotentialsAction.cpp

@@ -73 +73 @@
         deserialize();
       } catch (SerializerMissingValueException &e) {
-        if (const std::string *key = boost::get_error_info<SerializerKey>(e))
+        if (const std::string *key = boost::get_error_info<SerializerKey>(e)) {
           STATUS("Missing value when parsing information for potential "+*key+".");
-        else
+        } else
           STATUS("Missing value parsing information for potential with unknown key.");
         return Action::failure;
       } catch (SerializerIllegalKeyException &e) {
-        if (const std::string *key = boost::get_error_info<SerializerKey>(e))
+        if (const std::string *key = boost::get_error_info<SerializerKey>(e)) {
           STATUS("Illegal key parsing information for potential "+*key+".");
-        else
+        } else {
           STATUS("Illegal key parsing information for potential with unknown key.");
+        }
         return Action::failure;
       }

src/Actions/WorldAction/StepWorldTimeAction.cpp

@@ -47 +47 @@
 using namespace MoleCuilder;
 
-// if both are given, we use backwards
-static int getSteps(const unsigned int _forward, const unsigned int _backward)
-{
-  int steps = 0;
-  if (_backward > 0)
-    steps = -_backward;
-  else
-    steps = _forward;
-
-  return steps;
-}
-
 // and construct the stuff
 #include "StepWorldTimeAction.def"
@@ -69 +57 @@
   WorldStepWorldTimeState *UndoState = new WorldStepWorldTimeState(oldtime, params);
 
-  const int steps = getSteps(params.steps_forward.get(), params.steps_backward.get());
-
-  if ((oldtime + steps) < 0) {
+  if ((oldtime + params.steps.get()) < 0) {
     ELOG(1, "Cannot step back before time step #0.");
     delete UndoState;
     return Action::failure;
   }
-  World::getInstance().setTime(oldtime+steps);
+  World::getInstance().setTime(oldtime+params.steps.get());
   LOG(0, "Current time step is now: " << WorldTime::getTime() << ".");
   return ActionState::ptr(UndoState);
@@ -93 +79 @@
   WorldStepWorldTimeState *state = assert_cast<WorldStepWorldTimeState*>(_state.get());
 
-  const int steps = getSteps(
-      state->params.steps_forward.get(),
-      state->params.steps_backward.get());
-
-  World::getInstance().setTime(state->oldtime+steps);
+  World::getInstance().setTime(state->oldtime+state->params.steps.get());
   LOG(0, "Current time step is now: " << WorldTime::getTime() << ".");
 

src/Actions/WorldAction/StepWorldTimeAction.def

@@ -14 +14 @@
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
-#define paramtypes (unsigned int)(unsigned int)
-#define paramtokens ("steps-forward")("steps-backward")
-#define paramdescriptions ("how many steps to take forward or backward")("how many steps to take forward or backward")
-#define paramdefaults (PARAM_DEFAULT(1))(PARAM_DEFAULT(0))
-#define paramreferences (steps_forward)(steps_backward)
+#define paramtypes (int)
+#define paramtokens ("step-world-time")
+#define paramdescriptions ("how many steps to take forward (positive) or backward (negative)")
+#define paramdefaults (PARAM_DEFAULT(1))
+#define paramreferences (steps)
 #define paramvalids \
-(DummyValidator< unsigned int >()) \
-(DummyValidator< unsigned int >())
+(DummyValidator< int >())
 
 #define statetypes (unsigned int)

src/Atom/atom.cpp

@@ -103 +103 @@
   LOG(4,"atom::UpdateStep() called.");
   // append to position, velocity and force vector
-  AtomInfo::AppendTrajectoryStep(WorldTime::getTime()+1);
+  AtomInfo::AppendTrajectoryStep(WorldTime::getTime());
   // append to ListOfBonds vector
-  BondedParticleInfo::AppendTrajectoryStep(WorldTime::getTime()+1);
+  BondedParticleInfo::AppendTrajectoryStep(WorldTime::getTime());
 }
 

src/Atom/atom_atominfo.cpp

@@ -91 +91 @@
 void AtomInfo::AppendTrajectoryStep(const unsigned int _step)
 {
-  ASSERT (WorldTime::getTime() != _step,
-      "AtomInfo::AppendTrajectoryStep() - cannot append current time step.");
   NOTIFY(TrajectoryChanged);
   AtomicPosition.insert( std::make_pair(_step, zeroVec) );
@@ -105 +103 @@
 void AtomInfo::removeTrajectoryStep(const unsigned int _step)
 {
-  ASSERT (WorldTime::getTime() != _step,
-      "AtomInfo::removeTrajectoryStep() - cannot remove current time step.");
   NOTIFY(TrajectoryChanged);
   AtomicPosition.erase(_step);

src/Fragmentation/Exporters/HydrogenPool.cpp

@@ -91 +91 @@
       +" from pool is already in use.");
   LOG(3, "DEBUG: Leasing " << *Walker << ".");
-  UpdateSteps(Walker);
   HydrogenInUse.insert( std::make_pair( Walker->getId(), Walker) );
   HydrogenQueue.pop_front();
 
   return Walker;
-}
-
-void HydrogenPool::UpdateSteps(atom * _atom) const
-{
-  // make sure we are up to current time step
-  const size_t CurrentTime = WorldTime::getTime();
-  for (size_t step = _atom->getTrajectorySize(); step <= CurrentTime; ++step)
-    _atom->UpdateStep(step);
 }
 

src/Fragmentation/Exporters/HydrogenPool.hpp

@@ -73 +73 @@
   void cleanup();
 
-  /** Helper function to make sure \a _atom is up to current time step.
-   *
-   * \param _atom atom to bring trajectory size up to speed
-   */
-  void UpdateSteps(atom * _atom) const;
-
-
 private:
   //!> typedef for the deque of available hydrogens.

src/UIElements/CommandLineUI/CommandLineParser.cpp

@@ -36 +36 @@
 
 #include <boost/filesystem.hpp>
+#include <boost/lexical_cast.hpp>
+#include <boost/program_options/option.hpp>
+#include <boost/program_options/value_semantic.hpp>
 #include <boost/program_options.hpp>
 #include <fstream>
@@ -463 +466 @@
 }
 
+/** This is due to the answer by Aleksey Vitebskiy
+ * in http://stackoverflow.com/questions/4107087/accepting-negative-doubles-with-boostprogram-options
+ *
+ */
+std::vector<po::option> ignore_numbers(std::vector<std::string>& args)
+{
+    std::vector<po::option> result;
+    int pos = 0;
+    while(!args.empty()) {
+        const std::string& arg = args[0];
+        bool isNumber = true;
+        try {
+          boost::lexical_cast<double>(arg);
+        } catch(boost::bad_lexical_cast) {
+          isNumber = false;
+        }
+        if (isNumber) {
+            result.push_back(po::option());
+            po::option& opt = result.back();
+
+            opt.position_key = pos++;
+            opt.value.push_back(arg);
+            opt.original_tokens.push_back(arg);
+
+            args.erase(args.begin());
+        } else {
+            break;
+        }
+    }
+
+    return result;
+}
+
 /** Parses the command line arguments.
  * Calls program_options::store() and program_options::notify()
@@ -473 +509 @@
   bool status = true;
   try {
-    po::store(po::command_line_parser(argc,argv).options(cmdline_options).run(), vm);
+    po::store(po::command_line_parser(argc,argv).extra_style_parser(&ignore_numbers).options(cmdline_options).run(), vm);
   } catch (std::exception &e) {
     std::cerr << "Something went wrong with parsing the command-line arguments: " 

src/World.cpp

@@ -221 +221 @@
 }
 
-bool areBondsPresent(const unsigned int _step)
+static bool areBondsPresent(const unsigned int _step)
 {
   bool status = false;
@@ -234 +234 @@
 }
 
-void copyBondgraph(const unsigned int _srcstep, const unsigned int _deststep)
+static bool areAtomsPresent(const unsigned int _step)
+{
+  bool status = false;
+
+  for (World::AtomConstIterator iter = const_cast<const World &>(World::getInstance()).getAtomIter();
+      (!status) && (iter != const_cast<const World &>(World::getInstance()).atomEnd()); ++iter) {
+    const atom * const Walker = *iter;
+    status |= (Walker->getTrajectorySize() >= _step);
+  }
+
+  return status;
+}
+
+static void copyBondgraph(const unsigned int _srcstep, const unsigned int _deststep)
 {
   // gather all bonds from _srcstep
@@ -259 +272 @@
 }
 
+//static void copyAtoms(const unsigned int _srcstep, const unsigned int _deststep)
+//{
+//  for (World::AtomIterator iter = World::getInstance().getAtomIter();
+//      iter != World::getInstance().atomEnd(); ++iter) {
+//    atom * const Walker = *iter;
+//    Walker->UpdateStep(_deststep);
+//    Walker->setPositionAtStep(_deststep, Walker->getPositionAtStep(_srcstep));
+//    Walker->setAtomicVelocityAtStep(_deststep, Walker->getAtomicVelocityAtStep(_srcstep));
+//    Walker->setAtomicForceAtStep(_deststep, Walker->getAtomicForceAtStep(_srcstep));
+//  }
+//}
+
 void World::setTime(const unsigned int _step)
 {
   if (_step != WorldTime::getTime()) {
     const unsigned int oldstep = WorldTime::getTime();
+
+//    if (!areAtomsPresent(_step))
+//      copyAtoms(oldstep, _step);
 
     // 1. copy bond graph (such not each addBond causes GUI update)

tests/Python/AllActions/options.dat

@@ -33 +33 @@
 bond-degree     "1"
 bond-file       "bond.dat"
+bondside        "1"
 bond-table      "table.dat"
 calculate-bounding-box  ""
@@ -166 +167 @@
 reset   1
 reverse "0"
+rotate-around-bond      "90."
 rotate-around-origin    "180."
 rotate-around-origin    "20."
@@ -233 +235 @@
 skiplines       "2"
 start-step      "0"
-steps-forward   "1"
-steps-backward  "0"
 steps   "5"
+step-world-time "1"
 store-grids     "0"
 store-saturated-fragment        "BondFragment"

tests/regression/Makefile.am

@@ -140 +140 @@
         $(srcdir)/Molecules/LinearInterpolationofTrajectories/testsuite-molecules-linear-interpolation-of-trajectories.at \
         $(srcdir)/Molecules/Remove/testsuite-molecules-remove.at \
+        $(srcdir)/Molecules/RotateAroundBond/testsuite-molecules-rotate-around-bond.at \
         $(srcdir)/Molecules/RotateAroundOrigin/testsuite-molecules-rotate-around-origin.at \
         $(srcdir)/Molecules/RotateAroundSelf/testsuite-molecules-rotate-around-self.at \

tests/regression/Molecules/RotateToPrincipalAxisSystem/testsuite-molecules-rotate-to-principal-axis-system.at

@@ -49 +49 @@
 
 AT_SETUP([Molecules - Rotate to PAS with Undo])
-AT_XFAIL_IF([/bin/true])
 AT_KEYWORDS([molecules rotate-to-principal-axis-system undo])
 
@@ -80 +79 @@
 
 AT_SETUP([Molecules - Rotate to PAS with Redo])
-AT_XFAIL_IF([/bin/true])
 AT_KEYWORDS([molecules rotate-to-principal-axis-system redo])
 

tests/regression/Molecules/testsuite-molecules.at

@@ -60 +60 @@
 m4_include([Molecules/RotateToPrincipalAxisSystem/testsuite-molecules-rotate-to-principal-axis-system.at])
 
+# rotate around one of its bond
+m4_include([Molecules/RotateAroundBond/testsuite-molecules-rotate-around-bond.at])
+
 # Rotate around origin
 m4_include([Molecules/RotateAroundOrigin/testsuite-molecules-rotate-around-origin.at])

tests/regression/WorldTime/StepWorldTime/testsuite-worldtime-step-world-time.at

@@ -21 +21 @@
 AT_KEYWORDS([worldtime step-world-time set-world-time])
 
-AT_CHECK([../../molecuilder --step-world-time --steps-forward 1], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder --step-world-time 1], 0, [stdout], [stderr])
 AT_CHECK([fgrep "Current time step is now: 1" stdout], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder --set-world-time 4 --step-world-time --steps-backward 2], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder --set-world-time 4 --step-world-time -2], 0, [stdout], [stderr])
 AT_CHECK([fgrep "Current time step is now: 2" stdout], 0, [ignore], [ignore])
 # stepping back too far fails
-AT_CHECK([../../molecuilder --set-world-time 1 --step-world-time --steps-backward 2], 5, [stdout], [stderr])
+AT_CHECK([../../molecuilder --set-world-time 1 --step-world-time -2], 5, [stdout], [stderr])
 
 AT_CLEANUP
@@ -34 +34 @@
 AT_KEYWORDS([worldtime step-world-time set-world-time undo])
 
-AT_CHECK([../../molecuilder --set-world-time 2 --step-world-time --steps-backward  1 --undo], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder --set-world-time 2 --step-world-time -1 --undo], 0, [stdout], [stderr])
 AT_CHECK([fgrep "Current time step is now again: 2" stdout], 0, [ignore], [ignore])
 
@@ -42 +42 @@
 AT_KEYWORDS([worldtime step-world-time set-world-time undo redo])
 
-AT_CHECK([../../molecuilder --set-world-time 2 --step-world-time --steps-backward 1 --undo --redo], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder --set-world-time 2 --step-world-time -1 --undo --redo], 0, [stdout], [stderr])
 AT_CHECK([fgrep "Current time step is now: 1" stdout], 0, [ignore], [ignore])