PeakAssignmentParameters.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 FragmentSampler.cc
/// @brief ab-initio fragment assembly protocol for proteins
/// @detailed
///   Contains currently: Classic Abinitio
///
///
/// @author Oliver Lange

// Unit Headers
#define DEFINE_OPTIONS_NOW
#include <protocols/noesy_assign/PeakAssignmentOptionKeys.hh>
#undef DEFINE_OPTIONS_NOW

#include <protocols/noesy_assign/PeakAssignmentParameters.hh>

// Package Headers
//#include <devel/noesy_assign/Exceptions.hh>

// Project Headers

// Utility headers
#include <basic/Tracer.hh>

// Utility headers
#include <basic/options/option_macros.hh>


//// C++ headers
#include <cstdlib>
#include <string>

#include <utility/vector1.hh>


bool protocols::noesy_assign::PeakAssignmentParameters::options_registered_( false );

protocols::noesy_assign::PeakAssignmentParameters* protocols::noesy_assign::PeakAssignmentParameters::instance_( NULL );

protocols::noesy_assign::PeakAssignmentParameters const*
protocols::noesy_assign::PeakAssignmentParameters::get_instance() {
  if ( instance_ ) return instance_;
  instance_ = new PeakAssignmentParameters;
  instance_->set_options_from_cmdline();
  return instance_;
}

void
protocols::noesy_assign::PeakAssignmentParameters::reset() {
  if ( instance_ ) delete instance_;
  instance_ = NULL;
}

protocols::noesy_assign::PeakAssignmentParameters*
protocols::noesy_assign::PeakAssignmentParameters::get_nonconst_instance() {
  if ( instance_ ) return instance_;
  instance_ = new PeakAssignmentParameters;
  instance_->set_options_from_cmdline();
  return instance_;
}

void protocols::noesy_assign::PeakAssignmentParameters::set_cycle( core::Size cycle ) {
  if ( instance_ ) delete instance_;
  instance_ = new PeakAssignmentParameters;
  instance_->set_options_from_cmdline( cycle );
}

void protocols::noesy_assign::PeakAssignmentParameters::register_options() {
  using namespace basic::options;
  using namespace OptionKeys;
  if ( options_registered_ ) return;

  //cycle independent
  NEW_OPT( noesy_weights::chemshift, "contribution of chem. shift overlap to peak volume", 0.5 );
  //  NEW_OPT( noesy_weights::network_high, "contribution of network anchoring to peak volume", 10.0 );
  NEW_OPT( noesy::ignore_resonancefile_tolerances, "ignore the tolerances in the resonance file", false );
  NEW_OPT( noesy::ignore_resonancefile_intensities, "ignore the tolerances in the resonance file", false );

//cycle dependent -- cycle defaults
  NEW_OPT7( noesy_weights::defaults::Vmin, "acceptable minimial volume contribution per assignment", 0.01, 0.001, 0.005, 0.01, 0.025, 0.05, 0.501 );
  NEW_OPT7( noesy_weights::defaults::symmetry, "contribution of symmetry compliance to peak volume", 10.0, 10.0, 10.0, 10.0, 1.0, 1.0, 1.0 );
  NEW_OPT7( noesy_weights::defaults::covalent, "contribution of local covalent compliance to peak volume", 10.0, 10.0, 10.0, 1.0, 1.0, 1.0, 1.0 );
  //  NEW_OPT7( noesy_weights::defaults::decoys, "exponent controlling contribution of decoy compliance to peak volume", 3, 3, 6, 6, 6, 6, 6 );
  NEW_OPT7( noesy_weights::defaults::Smax,"maximum cumulative contribution of symmetry, covalent and network to peak volume", 20, 20, 20, 20, 10, 10, 10 );
  NEW_OPT7( noesy_weights::defaults::dcut, "upper limit on acceptable distance violation for elimination of spurious NOESY cross peaks (A)", -1, 1.5, 0.9, 0.6, 0.3, 0.1, 0.1 );
  //  NEW_OPT7( noesy_weights::defaults::reswise_min, "Threshold for acceptable lower limit of network-anchoring per residue", 1.0, 0.75, 0.5, 0.5, 0.5, 0.5, 0.5 );
  //  NEW_OPT7( noesy_weights::defaults::atomwise_min, "contribution of network anchoring to peak volume", 0.25, 0.25, 0.4, 0.4, 0.4, 0.4, 0.4 );
  NEW_OPT7( noesy_weights::defaults::dcalibrate, "upper limit on acceptable distance violation for structure dependent calibration (A)", -1, 1.5, 0.9, 0.6, 0.3, 0.1, 0.1 );
  NEW_OPT7( noesy_weights::defaults::calibration_target, "target for NOE calibration > 1 -- (A) (structure independent ) <1 (%) of models violated", 3.8, 0.15, 0.15, 0.1, 0.1, 0.1, 0.1 );

  //cycle dependent
  NEW_OPT( noesy_weights::Vmin, "acceptable minimial volume contribution per assignment", 0.01 );
  NEW_OPT( noesy_weights::symmetry, "contribution of symmetry compliance to peak volume", 10.0 );
  NEW_OPT( noesy_weights::covalent, "contribution of local covalent compliance to peak volume", 10.0 );
  //  NEW_OPT( noesy_weights::decoys, "exponent controlling contribution of decoy compliance to peak volume", 3 );
  NEW_OPT( noesy_weights::Smax,"maximum cumulative contribution of symmetry, covalent and network to peak volume", 20 );
  NEW_OPT( noesy_weights::dcut, "upper limit on acceptable distance violation for elimination of spurious NOESY cross peaks (A)", -1 );

  //  NEW_OPT( noesy_weights::network_min, "Threshold for acceptable lower limit of network-anchoring per residue", 1.0 );
  //NEW_OPT( noesy_weights::network_atom_min, "contribution of network anchoring to peak volume", 0.25 );
  NEW_OPT( noesy_weights::dcalibrate, "upper limit on acceptable distance violation for structure dependent calibration (A)", -1 );
  NEW_OPT( noesy_weights::calibration_target, "target for NOE calibration > 1 -- (A) (structure independent ) <1 (%) of models violated", 5 );
  NEW_OPT( noesy::atom_dependent_calibration, "individual calibration constants per atom-group: backbone, side-chain, methyl", false );

  NEW_OPT( noesy::map_to_cen_atom,"map the centroid restraints to CEN atom", false );

  NEW_OPT( noesy_weights::elim_dist_viol, "percentage of decoys that can be violated by distance constraints before it is eliminated ->set to 1 to switch this feature off", 0.5 );

  NEW_OPT( noesy_weights::cst_strength, "curvature of the constraint potential after upper distance is violated", 4 );
  NEW_OPT( noesy_weights::cycle, "set to cycle 1-7 to select a set of cycle-dependent options", 1 );
  NEW_OPT( noesy_weights::centroid_padding, "if sidechain NOESY are mapped to CB add some padding", 0.5 );
  NEW_OPT( noesy_weights::min_symmetry_reinforcement, "minimum contribution to symmetry score from a symmetric peak", 0.0 );
  NEW_OPT( noesy::no_network, "skip network analysis", false );
  NEW_OPT( noesy::network::reswise_min, "Threshold for acceptable lower limit of network-anchoring per residue",  1.0 );
  NEW_OPT( noesy::network::reswise_high, "Threshold for always accepted (disregard atomwise_min) network anchoring per residue", 4.0 );
  NEW_OPT( noesy::network::atomwise_min, "Threshold for acceptable network-anchoring per assignment", 0.25 );
  NEW_OPT( noesy::network::include_reverse_dir, "scan a->y->b and also b->y->a noesy connections to validate a->b", true );
  NEW_OPT( noesy::network::allow_same_residue_connect, "scan also a->y->b', a'->y->b and a'->y-b' with a' and b' in same residues as a and b, respectively", true);
  NEW_OPT( noesy::network::use_all_covalent_atoms, "resonance list contains atoms (e.g., CA, CB) that are never part of an assignment (e.g., H, QD1, etc.) should CA, CB be included in network analysis? ", false );
  NEW_OPT( noesy::network::mode, "choose implementation of network anchoring to be used [orig,clean]", "clean" );
  NEW_OPT( noesy::network::vmin, "minimum contribution to peak-volume to be considered for network anchoring", 0.1 );
  NEW_OPT( noesy::network::vmax, "minimum contribution to peak-volume to be considered for network anchoring", 1.0 );
  NEW_OPT( noesy::use_local_distviol, "don't use global distance-violation parameter dcut, but make-up local one using the distribution of distances", false );
  NEW_OPT( noesy::local_distviol::range, "get distance-difference between lowest X% and hightest X% of decoys", 0.99 );
  NEW_OPT( noesy::local_distviol::global_buffer, "add an extra grace-buffer (A) to the local range before you evaluate dist-cutoff", 0.5 );
  NEW_OPT( noesy::local_distviol::global_factor, "allow violation of X*interval beofre eliminated", 1.0 );
  NEW_OPT( noesy::local_distviol::cutoff, "peaks with a low-quartil distance of more than X are always removed", 8.0 );
  NEW_OPT( noesy::local_distviol::cutoff_buffer, "peaks with a low-quartil distance of more than X+distance_bound are always removed", 2.0 );

  NEW_OPT( noesy::calibration::convergence, "use only distance with stddev (over ensemble) of less than X Angstrom for calibration (0=all)", 0 );
  NEW_OPT( noesy::calibration::max_noe_dist, "use max_noe_dist to cap upper distance bounds, this value is overwritten by content in file", 0 );
  NEW_OPT( noesy::calibration::max_nudging, "individual restraint can be extended by maximum of X% of original calibrated distance", 1.0 );
  NEW_OPT( noesy::calibration::start_nudging,"start nudging if X% or more conformers violate original calibrated distance", 0.1 );
  NEW_OPT( noesy::calibration::stop_nudging,"stop nudging if only X% of conformers violated original calibrated distance", 0.1 );
  NEW_OPT( noesy::calibration::eliminate, "enable elimination by distance violation and nudging even when dcalibrate -1", false );
  NEW_OPT( noesy::calibration::use_median, "use median and not average for calibration", false );
  NEW_OPT( noesy::calibration::cycles, "how many cycles of calibration and elimination by distance-violation", 1 );
  NEW_OPT( noesy::calibration::ignore_eliminated_peaks, "ignore peaks that are already eliminated", false );

  NEW_OPT5( noesy::prob::sigmoid::tau, "tau and m parameter for sigmoids in crosspeak-probability score", 0.3, 1, .2,  0.2, 2);
  NEW_OPT5( noesy::prob::sigmoid::m, "tau and m parameter for sigmoids in crosspeak-probability score", 0.5, 2, .4, 0.5, 4);
  NEW_OPT2( noesy::prob::level, "selection levels for HI, MED, LOW probability cross-peaks", 0.7, 0.45 );
  NEW_OPT5( noesy::prob::sigmoid::w, "sigmoid contribution", 0.2000, 0.6000, 0.2000, 0.4000, 0.2000 );
  options_registered_ = true;
}


static basic::Tracer tr("protocols.noesy_assign.parameters");


void protocols::noesy_assign::PeakAssignmentParameters::set_options_from_cmdline( core::Size cycle_selector ) {
  using namespace basic::options::OptionKeys;
  using namespace basic::options;

  runtime_assert( options_registered_ );

  //set cycle from cmdline if not specified
  //if ( cycle_selector_ == 0 )
  if ( !cycle_selector ) {
    cycle_selector_ = option[ noesy_weights::cycle ]();
  } else {
    cycle_selector_ = cycle_selector;
  }

  //cycle independent
  chemshift_overlap_weight_ = option[ noesy_weights::chemshift ](); //Gamma, eq. (4)
  ignore_resonancefile_tolerances_ = option[ noesy::ignore_resonancefile_tolerances ]();
  ignore_resonancefile_intensities_ = option[ noesy::ignore_resonancefile_intensities ]();
  //  dmax_ = 5.5;
  vmin_ = option[ noesy::network::vmin ](); //previously 0.1 minimum peak-volume contribution to network anchoring
  vmax_ = option[ noesy::network::vmax ](); //previously 1.0; //maximum peak-volume contribution to network anchoring
  nmax_ = 20; //maximum number of assignments
  nr_conformers_violatable_ = option[ noesy_weights::elim_dist_viol ](); // M/2
  network_reswise_min_ = option[ noesy::network::reswise_min ]();
  network_atom_min_ = option[ noesy::network::atomwise_min ]();
  //  opt_read_out_macro( network_reswise_min_, network_min );
  //  opt_read_out_macro( network_atom_min_, network_atom_min );
  network_reswise_high_ = option[ noesy::network::reswise_high ]();// 4.0; //used in network-based elimination
  centroid_mapping_distance_padding_ = option[ noesy_weights::centroid_padding ]();

  //cycle dependent
#define opt_read_out_macro( VAR, OPT )                              \
{ VAR = option[ noesy_weights::defaults::OPT ]()[ cycle_selector_ ]; \
  if ( option [ noesy_weights::OPT ].user() ) {  \
    VAR = option[ noesy_weights::OPT ](); \
  }\
}\


  //read cycle-dependent default value -- overwrite if option is selected
  opt_read_out_macro( min_volume_, Vmin );
  opt_read_out_macro( symmetry_compliance_weight_, symmetry );
  opt_read_out_macro( covalent_compliance_weight_, covalent );
  //  opt_read_out_macro( decoy_compatibility_exponent_, decoys );
  opt_read_out_macro( smax_, Smax );
  opt_read_out_macro( dcut_, dcut );
  opt_read_out_macro( dcalibrate_, dcalibrate );

  opt_read_out_macro( calibration_target_, calibration_target );

  atom_dependent_calibration_ = option[ noesy::atom_dependent_calibration ];
  map_to_cen_atom_ = option[ noesy::map_to_cen_atom ];

  no_network_ = option[ noesy::no_network ]();
  network_include_reverse_dir_= option[ noesy::network::include_reverse_dir ];
  network_allow_same_residue_connect_ = option[ noesy::network::allow_same_residue_connect ];
  network_use_all_covalent_atoms_ = option[ noesy::network::use_all_covalent_atoms ];
  network_mode_ = option[ noesy::network::mode ]();
  cst_strength_ = option[ noesy_weights::cst_strength ]();
  min_contribution_symmetric_peaks_ = option[ noesy_weights::min_symmetry_reinforcement ];
  use_local_distviol_ = option[ noesy::use_local_distviol ]();
  local_distviol_range_ = option[ noesy::local_distviol::range ]();
  local_distviol_global_buffer_ = option[ noesy::local_distviol::global_buffer ]();
  local_distviol_global_factor_ = option[ noesy::local_distviol::global_factor ]();
  local_distviol_cutoff_ = option[ noesy::local_distviol::cutoff ]();
  local_distviol_cutoff_buffer_ = option[ noesy::local_distviol::cutoff_buffer ]();

  calibration_convergence_ = option[ noesy::calibration::convergence ]();
  calibration_max_noe_dist_ = option[ noesy::calibration::max_noe_dist ]();
  calibration_stop_nudging_ = option[ noesy::calibration::stop_nudging ]();
  calibration_start_nudging_ = option[ noesy::calibration::start_nudging ]();
  calibration_max_nudging_ = option[ noesy::calibration::max_nudging ]();
  calibration_eliminate_ = option[ noesy::calibration::eliminate ]();
  calibration_use_median_ = option[ noesy::calibration::use_median ]();
  calibration_ignore_eliminated_peaks_ = option[ noesy::calibration::ignore_eliminated_peaks ]();
  calibration_cycles_ = option[ noesy::calibration::cycles ]();

  if ( local_distviol_range_ <= 0.5 ) {
    utility_exit_with_message( "local_distviol::range must be in the range 0.5...1.0" );
  }

  prob_level_ = option[ noesy::prob::level ]();
  prob_sigmoid_tau_ = option[ noesy::prob::sigmoid::tau ]();
  prob_sigmoid_m_ = option[ noesy::prob::sigmoid::m ]();
  prob_sigmoid_w_ = option[ noesy::prob::sigmoid::w ]();
  show_on_tracer();
}

void protocols::noesy_assign::PeakAssignmentParameters::show( std::ostream& os ) const {
  os << " ============== cycle-dependent parameter selection for Noesy peak assignment =============== " << std::endl;
  os << "   cycle: " << cycle_selector_ << std::endl;
  os << "----------------------------------------------------------------------------------------------" << std::endl;
  os << "        Vmin: " << min_volume_ << std::endl;
  os << "        T:    " << symmetry_compliance_weight_ << std::endl;
  os << "        V:    " << covalent_compliance_weight_ << std::endl;
  //  os << "        eta:  " << decoy_compatibility_exponent_ << std::endl;
  os << "        Smax: " << smax_ << std::endl;
  os << "        dcut: " << dcut_ << std::endl;
  os << "   Nmin(res): " << network_reswise_min_ << std::endl;
  os << "  Nmin(atom): " << network_atom_min_ << std::endl;
  os << " Calibration Target: " << calibration_target_ << ( calibration_target_ >= 1 ? " (A) average distance " : " fract. of constraints violate input structures " ) << std::endl;
  os << " Calibration distance: " << dcalibrate_ << " A above upper bound is a violation" << std::endl;
  os << "==============================================================================================" << std::endl;

  os << " ============== cycle-independent parameter for Noesy peak assignment =============== " << std::endl;
  os << "      chemical shift agreement-weight: " << chemshift_overlap_weight_ << std::endl;
  os << "      elimination of peak if distance-bound violates more than: " << nr_conformers_violatable_ << std::endl;
  os << "      elimination MAXASSIGN if assignments count is above: " << nmax_ << std::endl;
  //  os << "      contribution of network anchoring to peak volume XXX" << std::endl;
  os << "      strength (curvature) of the constraint potential after upper distance is violated " << cst_strength_ << std::endl;
  os << "      padding for CB-mapped protons in centroid mode: " << centroid_mapping_distance_padding_ << std::endl;
  os << "      atom_dependent_calibration: " << (atom_dependent_calibration_ ? "yes" : "no" ) << std::endl;
  os << "----------------------------------------------------------------------------------------------" << std::endl;
  if ( !no_network_ ) {
    os << "      network-anchoring options: " << std::endl;
    os << "                minimum contribution to peak-volume " << vmin_ << std::endl;
    os << "                maximum contribution to peak-volume " << vmax_ << std::endl;
    os << "                do not eliminate if network score per residue is above " << network_reswise_high_ << std::endl;
    os << "                network_include_reverse_dir:           " << (network_include_reverse_dir_ ? "yes ": "no " ) << std::endl;
    os << "                network_allow_same_residue_connection: " << (network_allow_same_residue_connect_ ? "yes ": "no " ) << std::endl;
    os << "                network_use_all_covalent_atoms:        " << (network_use_all_covalent_atoms_ ? "yes" : "no" ) << std::endl;
  } else {
    os << "      no network-anchoring applied! " << std::endl;
  }
  if ( use_local_distviol_ ) {
    os << "     use local distance violation " << std::endl;
    os << "                local distance violation range " << local_distviol_range_*100 << "%" << std::endl;
    os << "                add the following constant distance " << local_distviol_global_buffer_ << std::endl;
    os << "                multiply max-extension by " << local_distviol_global_factor_ << std::endl;
  }
  os << "==============================================================================================" << std::endl;
}

void protocols::noesy_assign::PeakAssignmentParameters::show_on_tracer() const {
  show( tr.Info );
}


namespace protocols {
namespace noesy_assign {
using namespace core;

}
}