source: src/Actions/MoleculeAction/RotateAroundBondAction.cpp@ 1ca493a

/*
 * Project: MoleCuilder
 * Description: creates and alters molecular systems
 * Copyright (C)  2017 Frederik Heber. All rights reserved.
 * 
 *
 *   This file is part of MoleCuilder.
 *
 *    MoleCuilder is free software: you can redistribute it and/or modify
 *    it under the terms of the GNU General Public License as published by
 *    the Free Software Foundation, either version 2 of the License, or
 *    (at your option) any later version.
 *
 *    MoleCuilder is distributed in the hope that it will be useful,
 *    but WITHOUT ANY WARRANTY; without even the implied warranty of
 *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *    GNU General Public License for more details.
 *
 *    You should have received a copy of the GNU General Public License
 *    along with MoleCuilder.  If not, see <http://www.gnu.org/licenses/>.
 */

/*
 * RotateAroundBondAction.cpp
 *
 *  Created on: Mar 22, 2017
 *      Author: heber
 */

// include config.h
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

//#include "CodePatterns/MemDebug.hpp"

#include "Actions/MoleculeAction/RotateAroundBondAction.hpp"

#include "CodePatterns/Assert.hpp"
#include "CodePatterns/Log.hpp"

#include "LinearAlgebra/Line.hpp"
#include "LinearAlgebra/Plane.hpp"

#include "Actions/UndoRedoHelpers.hpp"
#include "Graph/CyclicStructureAnalysis.hpp"
#include "Graph/DepthFirstSearchAnalysis.hpp"
#include "Graph/BoostGraphCreator.hpp"
#include "Graph/BoostGraphHelpers.hpp"
#include "Graph/BreadthFirstSearchGatherer.hpp"

#include "Atom/atom.hpp"
#include "Atom/AtomicInfo.hpp"
#include "Bond/bond.hpp"
#include "molecule.hpp"
#include "World.hpp"
#include "WorldTime.hpp"

using namespace MoleCuilder;

// and construct the stuff
#include "RotateAroundBondAction.def"
#include "Action_impl_pre.hpp"

/** =========== define the function ====================== */
static bool IsBondContainedInCycle(const bond::ptr &_bond)
{
  // get the BackEdgeStack from somewhere
  DepthFirstSearchAnalysis DFS;
  DFS();
  DFS.CyclicBondAnalysis();
//  std::deque<bond::ptr> BackEdgeStack = DFS.getBackEdgeStack();
//  // then we analyse the cycles and get them
//  CyclicStructureAnalysis CycleAnalysis(ExcludeHydrogen); // hydrogens never contained in cycles
//  CycleAnalysis(&BackEdgeStack);
  return _bond->Cyclic;
}

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()
{
  // check preconditions
  const std::vector< atom *> atoms = World::getInstance().getSelectedAtoms();
  if (atoms.size() != 2) {
    STATUS("Exactly two atoms must be selected to specify a bond.");
    return Action::failure;
  }
  if (!atoms[0]->IsBondedTo(WorldTime::getTime(), atoms[1])) {
    STATUS("Two given atoms are not bonded.");
    return Action::failure;
  }
  molecule *mol = World::getInstance().
      getMolecule(MoleculeById(atoms[0]->getMolecule()->getId()));
  if (mol != atoms[1]->getMolecule()) {
    STATUS("The two selected atoms must belong to the same molecule.");
    return Action::failure;
  }
  if (IsBondContainedInCycle(atoms[0]->getBond(atoms[1]))) {
    STATUS("The given bond is contained in a cycle, cannot rotate!");
    return Action::failure;
  }

  // gather undo information: store position of all atoms of molecule
  std::vector<AtomicInfo> UndoInfo;
  UndoInfo.reserve(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));
    }
  }

  // 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.;

  // create the bond plane and mid-distance
  Vector NormalVector = (atoms[0]->getPosition() - atoms[1]->getPosition());
  NormalVector.Normalize();
  const Vector OffsetVector = 0.5*(atoms[0]->getPosition() + atoms[1]->getPosition());
  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 (std::binary_search(bondside_sets.begin(), bondside_sets.end(), atomid)) {
      LOG(4, "DEBUG: Rotating atom " << **iter << " by " << angle_radian
          << " rad around " << RotationAxis);
      (*iter)->setPosition(RotationAxis.rotateVector((*iter)->getPosition(), angle_radian));
      LOG(4, "DEBUG: New position of atom " << **iter);
      ASSERT( fabs(signed_distance - bondplane.SignedDistance(position)) < MYEPSILON,
          "MoleculeRotateAroundBondAction::performCall() - signed distance was "
          +toString(signed_distance)+" and is now "+toString(bondplane.SignedDistance(position)));
    }
  }

  MoleculeRotateAroundBondState *UndoState =
      new MoleculeRotateAroundBondState(UndoInfo, OffsetVector, NormalVector, mol, params);
  return ActionState::ptr(UndoState);
}

ActionState::ptr MoleculeRotateAroundBondAction::performUndo(ActionState::ptr _state) {
  MoleculeRotateAroundBondState *state = assert_cast<MoleculeRotateAroundBondState*>(_state.get());

  // set stored old state
  SetAtomsFromAtomicInfo(state->UndoInfo);

  return ActionState::ptr(_state);
}

ActionState::ptr MoleculeRotateAroundBondAction::performRedo(ActionState::ptr _state){
  MoleculeRotateAroundBondState *state = assert_cast<MoleculeRotateAroundBondState*>(_state.get());

  // create the bond plane and mid-distance
  Plane bondplane(state->NormalVector, state->OffsetVector);
  Line RotationAxis(state->OffsetVector, state->NormalVector);
  const double angle_radian = params.angle.get() * M_PI/180.;
  // go through the molecule and rotate each atom relative two plane
  for (molecule::iterator iter = state->mol->begin(); iter != state->mol->end(); ++iter) {
    const Vector &position = (*iter)->getPosition();
    if ((params.bondside.get() && (bondplane.SignedDistance(position) > 0)) ||
        (!params.bondside.get() && (bondplane.SignedDistance(position) < 0))) {
      (*iter)->setPosition(RotationAxis.rotateVector((*iter)->getPosition(), angle_radian));
    }
  }

  return ActionState::ptr(_state);
}

bool MoleculeRotateAroundBondAction::canUndo() {
  return true;
}

bool MoleculeRotateAroundBondAction::shouldUndo() {
  return true;
}
/** =========== end of function ====================== */