DockMinMover.cc

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;
// rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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//    Rosetta Commons.
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/// @file docking_min_protocol
/// @brief
/// @author Robin A Thottungal (raugust1@jhu.edu)

// Unit Headers
#include <protocols/docking/DockMinMover.hh>

// Project headers
#include <core/kinematics/MoveMap.hh>
#include <core/scoring/ScoreFunction.hh>

#include <protocols/simple_moves/MinMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/moves/TrialMover.hh>

#include <utility/vector1.hh>

#include <basic/options/option.hh>
#include <basic/options/keys/docking.OptionKeys.gen.hh>


using namespace protocols::moves;
using namespace core;

namespace protocols{
namespace docking{

//@TODO create default values in empty constructor
DockMinMover::DockMinMover() : DockingHighRes()
{
  //need to set this up with default values;
  set_default();
  mc_= new MonteCarlo( *scorefxn(), 0.8 );
  protocols::simple_moves::MinMoverOP min_mover =new protocols::simple_moves::MinMover
        ( movemap_, scorefxn(), min_type_, min_tolerance_, nb_list_ );
  minimize_trial_ = new TrialMover( min_mover, mc_ );
}

DockMinMover::DockMinMover(
  DockJumps const movable_jumps,
  core::scoring::ScoreFunctionOP scorefxn
) : DockingHighRes(movable_jumps, scorefxn, scorefxn) {
  //need to set this up with default values;
  set_default();
  mc_= new MonteCarlo( *scorefxn(), 0.8 );
  protocols::simple_moves::MinMoverOP min_mover =new protocols::simple_moves::MinMover
        ( movemap_, scorefxn(), min_type_, min_tolerance_, nb_list_ );
  minimize_trial_ = new TrialMover( min_mover, mc_ );
}



//JQX: made a new constructor, which can take the mc_ object
DockMinMover::DockMinMover(
  DockJumps const movable_jumps,
  core::scoring::ScoreFunctionOP scorefxn,
  moves::MonteCarloOP mc
) : DockingHighRes(movable_jumps, scorefxn, scorefxn) {
  //need to set this up with default values;
  set_default();
  mc_=mc;
  protocols::simple_moves::MinMoverOP min_mover =new protocols::simple_moves::MinMover
          ( movemap_, scorefxn(), min_type_, min_tolerance_, nb_list_ );
  minimize_trial_ = new TrialMover( min_mover, mc_ );
}





DockMinMover::DockMinMover(
  DockJumps const movable_jumps,
  core::kinematics::MoveMapOP movemap,
  core::scoring::ScoreFunctionOP scorefxn,
  std::string min_type,
  core::Real min_tolerance,
  bool nb_list,
  moves::MonteCarloOP mc
): DockingHighRes(movable_jumps, scorefxn, scorefxn) {
  movemap_=movemap;
  min_type_=min_type;
  min_tolerance_=min_tolerance;
  nb_list_=nb_list;
  mc_=mc;
  protocols::simple_moves::MinMoverOP min_mover =new protocols::simple_moves::MinMover
        ( movemap_, scorefxn(), min_type_, min_tolerance_, nb_list_ );
  minimize_trial_ = new TrialMover( min_mover, mc_ );
}

DockMinMover::~DockMinMover(){}

void DockMinMover::set_default() {

  using namespace basic::options; //quick hack by rhiju
  using namespace basic::options::OptionKeys::docking; // quick hack by rhiju -- later feed this in through dockingprotocol

  //sets up default movemap
  movemap_ = new kinematics::MoveMap();
  movemap_->set_chi( false );
  movemap_->set_bb( false );
  for( DockJumps::const_iterator it = movable_jumps().begin(); it != movable_jumps().end(); ++it ) {
    movemap_->set_jump( *it, true );
  }


  // perhaps call this dock_minimize_bb_res or something.
  if ( option[ bb_min_res ].user() ){
    utility::vector1< Size > const & min_res = option[ bb_min_res ]();
    for ( Size n = 1; n <= min_res.size(); n++ ) movemap_->set_bb( min_res[n], true );
  }
  if ( option[ sc_min_res ].user() ){
    utility::vector1< Size > const & min_res = option[ sc_min_res ]();
    for ( Size n = 1; n <= min_res.size(); n++ ) movemap_->set_chi( min_res[n], true );
  }


  //sets up minimization parameters
//  min_tolerance_ = 1.0; /////was 0.01, in r++ docking, it is actually 1.0!! with 0.02 as the "tight" tolerance
//  JQX commented the line right above, the Legacy code use 0.01. Just want to match it
  min_tolerance_ = 0.01; //JQX added this line
  min_type_ = std::string( "dfpmin_armijo_nonmonotone" );
  nb_list_ = true;
}

void DockMinMover::apply(core::pose::Pose & pose){
  // since mc_ object is created without a pose, this reset is required!
  ( *scorefxn() )( pose );
//  mc_->reset(pose);   // JQX: I think it is not necessary
  minimize_trial_->apply(pose);
}

std::string DockMinMover::get_name() const {
  return "DockMinMover";
}

}
}