source: src/Actions/MoleculeAction/ChangeBondAngleAction.cpp@ d93d2c

/*
 * Project: MoleCuilder
 * Description: creates and alters molecular systems
 * Copyright (C)  2012 University of Bonn. 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/>.
 */

/*
 * ChangeBondAngleAction.cpp
 *
 *  Created on: Nov 14, 2012
 *      Author: heber
 */

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

#include "CodePatterns/MemDebug.hpp"

#include "Actions/MoleculeAction/ChangeBondAngleAction.hpp"

#include <boost/assign.hpp>

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

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

#include "Atom/atom.hpp"
#include "Bond/bond.hpp"
#include "CodePatterns/Log.hpp"
#include "CodePatterns/Verbose.hpp"
#include "Descriptors/AtomIdDescriptor.hpp"
#include "molecule.hpp"
#include "World.hpp"
#include "WorldTime.hpp"

using namespace boost::assign;
using namespace MoleCuilder;

// and construct the stuff
#include "ChangeBondAngleAction.def"
#include "Action_impl_pre.hpp"
/** =========== define the function ====================== */

const std::vector<size_t> sortIndicesFromCentralAtom(const std::vector< atom *> &atoms)
{
  std::vector<size_t> indices;
  {
    std::vector<size_t> matches;
    size_t index = 0;
    for (; index < 3; ++index)
      if ((atoms[index]->IsBondedTo(WorldTime::getTime(), atoms[(index+1)%3]))
          && (atoms[index]->IsBondedTo(WorldTime::getTime(), atoms[(index+2)%3])))
        matches.push_back(index);
    if (matches.size() != 1) {
      ELOG(1, "The three atoms are not linearly bonded.");
    } else {
      LOG(1, "INFO: Picking " << *atoms[ matches[0] ] << " as the central atom.");
      indices += matches[0], (matches[0]+1)%3, (matches[0]+2)%3;
    }
  }
  return indices;
}

void ChangeBondAngleSymmetrically(
    const std::vector<size_t> &indices,
    const double newangle,
    const std::vector<atom*> &atoms)
{
  const Vector firstPosition = atoms[ indices[1] ]->getPosition();
  const Vector secondPosition = atoms[ indices[2] ]->getPosition();

  // create the bond plane and mid-distance
  const double normaldistance = firstPosition.distance(secondPosition);
  const Vector NormalVector = (1. / normaldistance) * (firstPosition - secondPosition);
  const Vector OffsetVector = atoms[indices[0]]->getPosition();
  Plane midplane(NormalVector, OffsetVector);
  // go through the molecule and stretch each atom relative two plane
  for (size_t index = 1; index < 3; ++index) {
    const Vector &position = atoms[indices[index]]->getPosition();
    const Vector planespot = midplane.getClosestPoint(position);
    const double opposite_side = position.distance(planespot);
    const double adjacent_side = OffsetVector.distance(planespot);
    const double hypotenuse = position.distance(OffsetVector);
    if (fabs(hypotenuse) > MYEPSILON) {
      const double angle = acos(adjacent_side / hypotenuse);
      LOG(1, "INFO: Old angle is " << (180. / M_PI) * (2. * angle) << ".");
      const double new_opposite_side = hypotenuse * sin(newangle);
      const double new_adjacent_side = hypotenuse * cos(newangle);
      Vector newposition = (new_opposite_side / opposite_side) * (position - planespot);
      newposition += (new_adjacent_side / adjacent_side) * (planespot - OffsetVector);
      newposition += OffsetVector;
      atoms[indices[index]]->setPosition(newposition);
    }
  }
}

ActionState::ptr MoleculeChangeBondAngleAction::performCall()
{
  // check precondition: three atoms
  const std::vector< atom *> atoms = World::getInstance().getSelectedAtoms();
  if (atoms.size() != 3) {
    STATUS("Exactly three atoms must be selected.");
    return Action::failure;
  }
  // check precondition: linearly bonded atoms
  const std::vector<size_t> indices = sortIndicesFromCentralAtom(atoms);
  if (indices.size() != 3) {
    STATUS("Selected atoms must be linearly bonded/form a chain");
    return Action::failure;
  }
  const molecule *mol = atoms[0]->getMolecule();
  if ((mol != atoms[1]->getMolecule()) || (mol != atoms[2]->getMolecule())) {
    STATUS("The two selected atoms must belong to the same molecule.");
    return Action::failure;
  }

  // gather undo info
  const Vector firstPosition = atoms[ indices[1] ]->getPosition();
  const Vector secondPosition = atoms[ indices[2] ]->getPosition();

  // change the bond angle
  const double newangle = .5* (M_PI / 180.) * params.bondangle.get();
  LOG(1, "INFO: New angle is " << (180. / M_PI) * (2. * newangle) << ".");
  ChangeBondAngleSymmetrically(indices, newangle, atoms);

  // create undo information
  MoleculeChangeBondAngleState *UndoState =  new MoleculeChangeBondAngleState(
      indices[1], indices[2],
      firstPosition, secondPosition,
      atoms[ indices[1] ]->getPosition(), atoms[ indices[2] ]->getPosition(),
      params);
  return ActionState::ptr(UndoState);
}

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

  // undo both position changes
  atom * const first = World::getInstance().getAtom(AtomById(state->firstId));
  atom * const second = World::getInstance().getAtom(AtomById(state->secondId));
  first->setPosition(state->firstOldPosition);
  second->setPosition(state->secondOldPosition);

  return ActionState::ptr(_state);
}

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

  // redo both position changes
  atom * const first = World::getInstance().getAtom(AtomById(state->firstId));
  atom * const second = World::getInstance().getAtom(AtomById(state->secondId));
  first->setPosition(state->firstNewPosition);
  second->setPosition(state->secondNewPosition);

  return ActionState::ptr(_state);
}

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

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