HBondOptions.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   core/scoring/hbonds/HBondOptions.cc
/// @brief  HBondOptions class, holds the options for the hbond energy function
/// @author Matthew O'Meara

/// @detail
/// To add an additional option for hydrogen bonds do the following:
///
/// In HBondOptions.hh:
/// 1) add it to the default constructor
/// 2) add it to the copy constructor
/// 3) add a getter and a setter
/// 4) add it to operator==
/// 5) add it to the private data
/// 6) add it to HBondOptions::show

// Unit Headers
#include <core/scoring/hbonds/HBondOptions.hh>

// Package Headers
#include <basic/options/option.hh>
#include <basic/options/keys/corrections.OptionKeys.gen.hh> //pba
#include <basic/options/keys/dna.OptionKeys.gen.hh> //sthyme
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/membrane.OptionKeys.gen.hh> //pba

// C++ Headers
#include <string>
#include <iostream>

#include <utility/vector1.hh>



namespace core {
namespace scoring {
namespace hbonds {

HBondOptions::HBondOptions( std::string params_db_tag ):
  exclude_DNA_DNA_( true ),
  include_intra_res_RNA_( false ),
  exclude_self_hbonds_( true ),
  use_hb_env_dep_ ( true ),
  use_hb_env_dep_DNA_( true ),
  smooth_hb_env_dep_( true ),
  bb_donor_acceptor_check_( true ),
  decompose_bb_hb_into_pair_energies_( false ),
  params_database_tag_(params_db_tag),
  use_incorrect_deriv_( true ),
  use_sp2_chi_penalty_( false ),
  sp2_BAH180_rise_( 0.75 ),
  measure_sp3acc_BAH_from_hvy_( false ),
  Mbhbond_( false ) //pba
{
  using namespace basic::options;
  if (option.has(OptionKeys::membrane::Mhbond_depth) &&
    option[OptionKeys::membrane::Mhbond_depth].user()){
    Mbhbond_ = option[OptionKeys::membrane::Mhbond_depth];//pba
  }
  exclude_DNA_DNA_ = option[OptionKeys::dna::specificity::exclude_dna_dna]; // adding because this parameter should absolutely be false for any structure with DNA in it and it doesn't seem to be read in via the weights file method, so now it's an option - sthyme
  use_incorrect_deriv_ = option[OptionKeys::corrections::score::use_incorrect_hbond_deriv];
  use_sp2_chi_penalty_ = option[OptionKeys::corrections::score::hb_sp2_chipen ];
  bb_donor_acceptor_check_ = ! option[ OptionKeys::score::hbond_disable_bbsc_exclusion_rule ];
  sp2_BAH180_rise_ = option[ OptionKeys::corrections::score::hb_sp2_BAH180_rise ];
  measure_sp3acc_BAH_from_hvy_ = option[ OptionKeys::corrections::score::hbond_measure_sp3acc_BAH_from_hvy ];
}



HBondOptions::HBondOptions():
  exclude_DNA_DNA_( true ),
  include_intra_res_RNA_( false ),
  exclude_self_hbonds_( true ),
  use_hb_env_dep_ ( true ),
  use_hb_env_dep_DNA_( true ),
  smooth_hb_env_dep_( true ),
  bb_donor_acceptor_check_( true ),
  decompose_bb_hb_into_pair_energies_( false ),
  params_database_tag_("standard_params"),
  use_incorrect_deriv_( false ),
  use_sp2_chi_penalty_( false ),
  sp2_BAH180_rise_( 0.75 ),
  measure_sp3acc_BAH_from_hvy_( false ),
  Mbhbond_( false ) //pba
{
  using namespace basic::options;
  if (option.has(OptionKeys::score::hbond_params) &&
    option[OptionKeys::score::hbond_params].user()){
    params_database_tag_ = option[OptionKeys::score::hbond_params];
  }
  if (option.has(OptionKeys::membrane::Mhbond_depth) &&
    option[OptionKeys::membrane::Mhbond_depth].user()){
    Mbhbond_ = option[OptionKeys::membrane::Mhbond_depth];//pba
  }
  exclude_DNA_DNA_ = option[OptionKeys::dna::specificity::exclude_dna_dna]; // adding because this parameter should absolutely be false for any structure with DNA in it and it doesn't seem to be read in via the weights file method, so now it's an option - sthyme
  use_incorrect_deriv_ = option[OptionKeys::corrections::score::use_incorrect_hbond_deriv];
  use_sp2_chi_penalty_ = option[OptionKeys::corrections::score::hb_sp2_chipen ];
  bb_donor_acceptor_check_ = ! option[ OptionKeys::score::hbond_disable_bbsc_exclusion_rule ];
  sp2_BAH180_rise_ = option[ OptionKeys::corrections::score::hb_sp2_BAH180_rise ];
  measure_sp3acc_BAH_from_hvy_ = option[ OptionKeys::corrections::score::hbond_measure_sp3acc_BAH_from_hvy ];
}

/// copy constructor
HBondOptions::HBondOptions( HBondOptions const & src ):
  ReferenceCount( src )
{
  *this = src;
}

HBondOptions::~HBondOptions(){}

/// copy operator
HBondOptions const &
HBondOptions::operator=( HBondOptions const & src )
{
  exclude_DNA_DNA_ = src.exclude_DNA_DNA_;
  include_intra_res_RNA_=src.include_intra_res_RNA_;
  exclude_self_hbonds_ = src.exclude_self_hbonds_;
  use_hb_env_dep_ = src.use_hb_env_dep_;
  use_hb_env_dep_DNA_ = src.use_hb_env_dep_DNA_;
  smooth_hb_env_dep_ = src.smooth_hb_env_dep_;
  bb_donor_acceptor_check_ = src.bb_donor_acceptor_check_;
  decompose_bb_hb_into_pair_energies_ = src.decompose_bb_hb_into_pair_energies_;
  params_database_tag_ = src.params_database_tag_;
  use_incorrect_deriv_ = src.use_incorrect_deriv_;
  use_sp2_chi_penalty_ = src.use_sp2_chi_penalty_;
  sp2_BAH180_rise_ = src.sp2_BAH180_rise_;
  measure_sp3acc_BAH_from_hvy_ = src.measure_sp3acc_BAH_from_hvy_;
  Mbhbond_ = src.Mbhbond_; //pba
  return *this;
}

///
bool
HBondOptions::exclude_DNA_DNA() const
{
  return exclude_DNA_DNA_;
}

///
void
HBondOptions::exclude_DNA_DNA( bool const setting )
{
  exclude_DNA_DNA_ = setting;
}

///
bool
HBondOptions::include_intra_res_RNA() const
{
  return include_intra_res_RNA_;
}

///
void
HBondOptions::include_intra_res_RNA( bool const setting )
{
  include_intra_res_RNA_ = setting;
}

///
bool
HBondOptions::exclude_self_hbonds() const
{
  return exclude_self_hbonds_;
}

///
void
HBondOptions::exclude_self_hbonds( bool const setting )
{
  exclude_self_hbonds_ = setting;
}




///
bool
HBondOptions::use_hb_env_dep_DNA() const
{
  return use_hb_env_dep_DNA_;
}

///
void
HBondOptions::use_hb_env_dep_DNA( bool const setting )
{
  use_hb_env_dep_DNA_ = setting;
}

///
bool
HBondOptions::use_hb_env_dep() const
{
  return use_hb_env_dep_;
}

///
void
HBondOptions::use_hb_env_dep( bool const setting )
{
  use_hb_env_dep_ = setting;
}

///
bool
HBondOptions::smooth_hb_env_dep() const
{
  return smooth_hb_env_dep_;
}

///
void
HBondOptions::smooth_hb_env_dep( bool const setting )
{
  smooth_hb_env_dep_ = setting;
}

///
bool
HBondOptions::decompose_bb_hb_into_pair_energies() const
{
  return decompose_bb_hb_into_pair_energies_;
}

///
void
HBondOptions::decompose_bb_hb_into_pair_energies( bool const setting )
{
  decompose_bb_hb_into_pair_energies_ = setting;
}

///
bool
HBondOptions::bb_donor_acceptor_check() const
{
  return bb_donor_acceptor_check_;
}

///
void
HBondOptions::bb_donor_acceptor_check( bool const setting )
{
  bb_donor_acceptor_check_ = setting;
}

///
std::string const &
HBondOptions::params_database_tag() const
{
  return params_database_tag_;
}

///
void
HBondOptions::params_database_tag( std::string const & setting )
{
  params_database_tag_ = setting;
}

///pba
bool
HBondOptions::Mbhbond() const
{
  return Mbhbond_;
}

///
void
HBondOptions::Mbhbond( bool const setting )
{
  Mbhbond_ = setting;
}

///
bool
HBondOptions::use_incorrect_deriv() const
{
  return use_incorrect_deriv_;
}

///
void
HBondOptions::use_incorrect_deriv( bool const setting )
{
  use_incorrect_deriv_ = setting;
}

bool HBondOptions::use_sp2_chi_penalty() const
{
  return use_sp2_chi_penalty_;
}

void HBondOptions::use_sp2_chi_penalty( bool setting )
{
  use_sp2_chi_penalty_ = setting;
}

Real HBondOptions::sp2_BAH180_rise() const { return sp2_BAH180_rise_; }
void HBondOptions::sp2_BAH180_rise( Real setting ) { sp2_BAH180_rise_ = setting; }

bool HBondOptions::measure_sp3acc_BAH_from_hvy() const { return measure_sp3acc_BAH_from_hvy_; }
void HBondOptions::measure_sp3acc_BAH_from_hvy( bool setting ) { measure_sp3acc_BAH_from_hvy_ = setting; }


bool
operator==( HBondOptions const & a, HBondOptions const & b )
{
  return ( ( a.exclude_DNA_DNA_ == b.exclude_DNA_DNA_ ) &&
    ( a.include_intra_res_RNA_ == b.include_intra_res_RNA_   ) &&
    ( a.exclude_self_hbonds_ == b.exclude_self_hbonds_ ) &&
    ( a.use_hb_env_dep_ == b.use_hb_env_dep_ ) &&
    ( a.use_hb_env_dep_DNA_ == b.use_hb_env_dep_DNA_ ) &&
    ( a.smooth_hb_env_dep_ == b.smooth_hb_env_dep_ ) &&
    ( a.bb_donor_acceptor_check_ == b.bb_donor_acceptor_check_ ) &&
    ( a.decompose_bb_hb_into_pair_energies_ == b.decompose_bb_hb_into_pair_energies_ ) &&
    ( a.params_database_tag_ == b.params_database_tag_ ) &&
    ( a.use_incorrect_deriv_ == b.use_incorrect_deriv_ ) &&
    ( a.use_sp2_chi_penalty_ == b.use_sp2_chi_penalty_ ) &&
    ( a.sp2_BAH180_rise_ == b.sp2_BAH180_rise_ ) &&
    ( a.measure_sp3acc_BAH_from_hvy_ == b.measure_sp3acc_BAH_from_hvy_ ) &&
    ( a.Mbhbond_ == b.Mbhbond_ ) ); //pba
}

bool
operator!=( HBondOptions const & a, HBondOptions const & b )
{
  return !( a == b );
}

std::ostream &
operator<< ( std::ostream & out, const HBondOptions & options ){
  options.show( out );
  return out;
}

///
void
HBondOptions::show( std::ostream & out ) const
{
  out <<"HBondOptions::show: exclude_DNA_DNA: "
    <<( exclude_DNA_DNA_ ? "true" : "false" ) << std::endl;
   out <<"HBondOptions::show: include_intra_res_RNA_: "
    <<( include_intra_res_RNA_ ? "true" : "false" ) << std::endl;
  out <<"HBondOptions::show: exclude_self_hbonds: "
    <<( exclude_self_hbonds_ ? "true" : "false" ) << std::endl;
  out <<"HBondOptions::show: use_hb_env_dep: "
    <<( use_hb_env_dep_ ? "true" : "false" ) << std::endl;
  out <<"HBondOptions::show: use_hb_env_dep_DNA: "
    <<( use_hb_env_dep_DNA_ ? "true" : "false" ) << std::endl;
  out <<"HBondOptions::show: smooth_hb_env_dep: "
    <<( smooth_hb_env_dep_ ? "true" : "false " ) << std::endl;
  out <<"HBondOptions::show: bb_donor_acceptor_check: "
    <<( bb_donor_acceptor_check_ ? "true" : "false " ) << std::endl;
  out <<"HBondOptions::show: decompose_bb_hb_into_pair_energies: "
    <<( decompose_bb_hb_into_pair_energies_ ? "true" : "false" ) << std::endl;
  out <<"HBondOptions::show: params_database_tag_: "
    << params_database_tag_ << std::endl;
  out <<"HBondOptions::show: use_incorrect_deriv_: "
    <<( use_incorrect_deriv_ ? "true" : "false" ) << std::endl;
  out <<"HBondOptions::show: use_sp2_chi_penalty_: "
    <<( use_sp2_chi_penalty_ ? "true" : "false" ) << std::endl;
  out <<"HBondOptions::show: sp2_BAH180_rise_: "
    << sp2_BAH180_rise_ << std::endl;
  out <<"HBondOptions::show: measure_sp3acc_BAH_from_hvy_: "
    <<( measure_sp3acc_BAH_from_hvy_ ? "true" : "false" ) << std::endl;
  out <<"HBondOptions::show: Mbhbond: "
    <<( Mbhbond_ ? "true" : "false " ) << std::endl; //pba
}

}
}
}