FullatomRelaxMover.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.
// (c) This file is part of the Rosetta software suite and is made available
//      under license.
// (c) The Rosetta software is developed by the contributing members of the
//      Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org.
//      Questions about this can be
// (c) addressed to University of Washington UW TechTransfer,
//                                             email: license@u.washington.edu.

/// @file FullatomRelaxMover.cc
/// @author Robin A Thottungal  (rathottungal@gmail.com)

//Unit header
#include <protocols/surface_docking/FullatomRelaxMover.hh>

// Package header
#include <protocols/surface_docking/SlideIntoSurface.hh>
#include <protocols/surface_docking/SurfaceOrientMover.hh>

// Project headers

#include <protocols/docking/DockingInitialPerturbation.hh>
#include <protocols/docking/DockingHighRes.hh>
#include <protocols/docking/DockMCMProtocol.hh>
#include <protocols/docking/DockFilters.hh> // get error if you did not include
#include <protocols/docking/DockingHighRes.hh>
#include <protocols/rigid/RigidBodyMover.hh>

#include <protocols/moves/Mover.fwd.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/MonteCarlo.fwd.hh>
#include <protocols/simple_moves/BackboneMover.hh>
#include <protocols/simple_moves/MinMover.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/moves/PyMolMover.hh>

#include <core/scoring/dssp/Dssp.hh>

#include <protocols/jd2/JobDistributor.hh>
#include <protocols/jd2/JobOutputter.hh>
#include <protocols/jd2/Job.hh>

#include <core/conformation/Residue.hh>
#include <core/chemical/ResidueType.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreType.hh>

#include <core/pose/Pose.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <core/pose/PDBInfo.hh>
#include <basic/Tracer.hh>
#include <core/kinematics/FoldTree.hh>

// Numeric Headers
#include <numeric/random/random.hh>

// C++ Headers
#include <utility/exit.hh>
#include <basic/prof.hh>
#include <basic/Tracer.hh>

#include <ctime>

using basic::T;
using basic::Error;
using basic::Warning;

static basic::Tracer TR("protocols.SurfaceDocking.FullatomRelaxMover");
static numeric::random::RandomGenerator RG(27510);

namespace protocols {
namespace surface_docking {

using namespace core;
using protocols::jd2::JobDistributor;

//constructor
FullatomRelaxMover::FullatomRelaxMover() : Mover(){
  // initilized here to avoid warning!
  nmoves_=6;
  temperature_=0.5;
  kT_=0.5;
  Mover::type("FullatomRelaxMover");
  TR << "FullatomRelaxMover Constructor Called" << std::endl;
  setup_defaults();
}

//destructor
FullatomRelaxMover::~FullatomRelaxMover() {}


void FullatomRelaxMover::setup_defaults(){
  TR << "Setting Defaults" << std::endl;
  // setting MoveMaps
  //Setting up default scorefunction --> rosetta++ modified score12
  score_high_res_ = scoring::ScoreFunctionFactory::create_score_function
                                                    ( "standard","score12" );
  // setting weighs for score12
  TR << "Setting Weighs for score12" << std::endl;
  score_high_res_->set_weight( core::scoring::hack_elec, 0.25 );
  //score_high_res_->set_weight(core::scoring::fa_atr,0.95);
  //score_high_res_->set_weight(core::scoring::fa_sol,0.90);
  //score_high_res_->set_weight(core::scoring::fa_rep,0.70);
  // added by Robin on Jun 17
  //score_high_res_->set_weight( core::scoring::hack_elec, 0.5 );
  smallmin_type_="linmin";
  shearmin_type_="dfpmin";
  benchmark_=false;
  encounter_cycle_= RG.random_range(1,5); //2; // need to get replaced by a random number
  TR << "Random Number Generated:" <<encounter_cycle_<< std::endl;
  setupMovers();
  }

void FullatomRelaxMover::init_from_options() {
  using namespace basic::options;
  using namespace basic::options::OptionKeys;
  benchmark_ = option[ OptionKeys::run::benchmark ]();

}

void FullatomRelaxMover::setupMovers(){
  // Setting Common Parameters for movers
  moveMapOP_=new core::kinematics::MoveMap;
  //moveMapOP_->set_bb( true );
  Real tolerance=0.001;// for minimizer
  //Setting up smallTrialMover
  //Creating smallMove; temperature_ : explanation;
  //          nnmoves_ : number of residues to move(Robin thinks its a
  //          good idea to change this based on length of peptide !!!!
  smallmover_=new simple_moves::SmallMover(moveMapOP_,temperature_,nmoves_);
  // temp commented out
  //smallmover_->angle_max(30); // max angle deviation.

  //Default Values copied from  MinMover.cc
  smallminmover_= new simple_moves::MinMover(moveMapOP_,
    score_high_res_,smallmin_type_,tolerance,true,false,false);
  //smallsequenceMover_ =
  ///     new moves::SequenceMover(smallmover_,smallminmover_);
  smallsequenceMover_= new moves::SequenceMover;
  smallsequenceMover_->add_mover(smallmover_);
  smallsequenceMover_->add_mover(smallminmover_);

  //Setting up shearTrialMover
  //Creating smallMove; temperature_ : explanation;
  //                  nnmoves_ : number of residues to move
  shearmover_=new simple_moves::ShearMover(moveMapOP_,temperature_,nmoves_/2);
  // Jeff thinks its a large perturbation
  //shearmover_->angle_max(30);

  //Default Values copied from  MinMover.cc
  shearminmover_= new simple_moves::MinMover(moveMapOP_,score_high_res_,
    shearmin_type_,tolerance,true,false,false);
  //shearsequenceMover_ =
  //     new moves::SequenceMover(shearmover_,shearminmover_);
  shearsequenceMover_= new moves::SequenceMover;
  shearsequenceMover_->add_mover(shearmover_);
  shearsequenceMover_->add_mover(shearminmover_);

}


void FullatomRelaxMover::FinalizeMovers(pose::Pose & pose)
{
  TR << "Finalizing Movers" << std::endl;
  // Setting the move map for the peptide
  // For setting movemap in fullatom
  Size protein_startseqnum;
  for (Size i=1; i<=pose.total_residue(); ++i){
    if (pose.residue_type(i).is_protein()){
      protein_startseqnum=i;
      break;
    }

  }
  TR<<"Protein Start Location:"<<protein_startseqnum<<std::endl;
  moveMapOP_->set_bb_true_range(protein_startseqnum,pose.total_residue());
  // Add flexibility to the sidechains in move_map
  moveMapOP_->set_chi( protein_startseqnum,pose.total_residue() );
  // Setting the jump between the protein and the surface movable
  moveMapOP_->set_jump(pose.num_jump(),true);

  // To init the final part of the min_trial_small & mini_trial_shear mover
  // Creating a global mc object that can be used by both
  // small_min_trial_mover() and shear_min_trial_mover()
  monteCarlo_ = new moves::MonteCarlo(pose,*score_high_res_,kT_);
  //smallTrialMover
  smallmonteCarlo_ = new moves::MonteCarlo(pose,*score_high_res_,kT_);
  small_trial_min_mover_ =
    new moves::TrialMover(smallsequenceMover_,monteCarlo_);
  //shearTrialMover
  shearmonteCarlo_ = new moves::MonteCarlo(pose,*score_high_res_,kT_);
  shear_trial_min_mover_ =
    new moves::TrialMover(shearsequenceMover_,monteCarlo_);
}

void FullatomRelaxMover::set_smallmovesize(Size scale){
  smallmover_->angle_max('H',scale/3);
  smallmover_->angle_max('E',scale/2);
  smallmover_->angle_max('L',scale);
}

void FullatomRelaxMover::set_ljrepulsion_weight(Real weight_scale){
  score_high_res_->set_weight(core::scoring::fa_rep,weight_scale);
}

void FullatomRelaxMover::set_ecounter(Size ecount){
  encounter_=ecount;
}


void FullatomRelaxMover::apply(pose::Pose & pose)
{
  using namespace docking;
  using namespace moves;
  FinalizeMovers(pose);
  
  TR << "Starting FullatomRelax" << std::endl;

  
  core::Size upper_limit=5;
  if ( basic::options::option[ basic::options::OptionKeys::run::benchmark ] ) {upper_limit = 1;}
  TR<<"SolutionState Cycle Number:"<<encounter_cycle_<<std::endl;
  // object for slide into contact
  FaSlideIntoSurface surfaceContact( pose.num_jump());
  for ( Size j = 1; j <=upper_limit; ++j ){ // Original is 5
    if ( encounter_ > encounter_cycle_ ){
      //slide into contact
      surfaceContact.apply( pose );
    }
   
    smallminmover_->min_type("dfpmin");
    shearminmover_->min_type("dfpmin");
    small_trial_min_mover_->apply(pose); // dfpmin
    shear_trial_min_mover_->apply(pose);  //dfpmin
    //crank mover is missing
    for ( Size k = 1; k <= upper_limit; ++k ){//k<=5 original value;k=2 test
      smallminmover_->min_type("linmin");
      shearminmover_->min_type("linmin");
      small_trial_min_mover_->apply(pose); //linmin
      shear_trial_min_mover_->apply(pose);  //linmin
      //crank mover is missing
    }
    if ( encounter_ == encounter_cycle_ && j%upper_limit == 0 ){//original 5
      TR<<"Solution State Structure Found"<<std::endl;
      //Write the solutionState Structure
      //getting lowest energy pose
      monteCarlo_->recover_low(pose);
      monteCarlo_->show_state();
      monteCarlo_->show_counters();
      TR<<"Calculating Secondary Structure of Solution State:"<<std::endl;
      CalcSecondayStruct(pose);
      // Creating a job compatible with JD2
      protocols::jd2::JobOP job2
        =jd2::JobDistributor::get_instance()->current_job();
      std::string job_name (JobDistributor::get_instance()->
        job_outputter()->output_name( job2 ) );
      job2->add_string_string_pair("SolState_SecondaryStructure:",SecStruct_);
      JobDistributor::get_instance()->job_outputter()->
        other_pose( job2,pose, "SolState_");

      // Random Orient the Partner (make sure this is the peptide)
      TR<<"Preparing for Docking Protein to Surface"<<std::endl;
      TR<<"RigidBodyRandomizeMover"<<std::endl;
      Size rb_jump_=pose.num_jump(); //default value
            rigid::RigidBodyRandomizeMover rmover( pose, rb_jump_, rigid::partner_upstream );
      rmover.apply( pose );
      //Axis Spin
            rigid::RigidBodySpinMover smover( rb_jump_ );
      smover.apply( pose );
      // SurfaceOrient Mover
      surface_docking::SurfaceOrientMoverOP sf=
                     new surface_docking::SurfaceOrientMover();
      sf->apply(pose);
      surfaceContact.apply( pose );
      //resetting the monteCarlo object
      monteCarlo_->reset(pose);
      TR<<"Protein adsorbed onto the Surface:"<<std::endl;
    }
    if ( encounter_ >= encounter_cycle_ && j%upper_limit== 0 ){
                                   //original 5
    TR<<"Started HighResolution Surface Docking "<<std::endl;
    moveMapOP_->set_chi(true);
    DockingHighResOP dockmcm =new DockMCMProtocol(pose.num_jump());
    dockmcm->apply(pose);

    }

  }


}

void FullatomRelaxMover::set_nmoves( core::Size const nmoves_in ){
  nmoves_ = nmoves_in;
    }

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

void FullatomRelaxMover::CalcSecondayStruct(core::pose::Pose & pose){
  SecStruct_="";
  // creating a new pose and splitting!
  //split the pose into separate chains
  pose::PoseOP pose_tmp=new pose::Pose(pose);
  utility::vector1< pose::PoseOP > singlechain_poses;
  singlechain_poses = pose_tmp->split_by_chain();
  core::scoring::dssp::Dssp dssp( *singlechain_poses[2] );
  dssp.insert_ss_into_pose( *singlechain_poses[2] );
  for ( Size ii = 1; ii <= singlechain_poses[2]->total_residue(); ++ii ) {
    SecStruct_+=singlechain_poses[2]->secstruct(ii);
  }
}

std::string FullatomRelaxMover::getSecondayStruct(){
  return SecStruct_;
}



}//surfaceDockingProtocol

} //protocol