FastaInputter.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 protocols/inputter/FastaInputter.cc
/// @brief An inputter that takes a list of fasta
/// @author Ken Jung

// Unit Headers
#include <protocols/inputter/FastaInputter.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/Pose.hh>
#include <utility/lua/LuaIterator.hh>

#include <core/pose/annotated_sequence.hh>
#include <core/sequence/util.hh>

#include <core/pose/util.hh>
#include <utility/string_util.hh>
// tracer
#include <basic/Tracer.hh>

using core::Size;

namespace protocols {
namespace inputter {

static basic::Tracer TR("protocols.inputter.FastaInputter");

#ifdef USELUA
void lregister_FastaInputter( lua_State * lstate ) {
  lregister_Inputter( lstate );
  luabind::module(lstate, "protocols")
  [
    luabind::namespace_("inputter")
    [
      luabind::class_<FastaInputter, Inputter>("FastaInputter")
    ]
  ];
}
#endif

FastaInputter::~FastaInputter(){}

core::pose::PoseSP FastaInputter::get_nth_pose( int n ) {
  offset_ = true;
  core::chemical::ResidueTypeSetCAP residue_set = core::chemical::ChemicalManager::get_instance()->residue_type_set( residue_set_ );
  core::pose::PoseSP tmppose(new core::pose::Pose());
  if( multiply_over_all_ ) {
    // we go through all the filenames once, then more times according to multiplier
    for( int i = 1; i<n; i++){
      file_names_[curr_idx_].first++;
      if( file_names_[curr_idx_].first >= multiplier_ )  {
        // this only can happen when curr_idx_ == 0
        file_names_.pop_front();
      } else {
        curr_idx_++;
        curr_idx_ = curr_idx_ == file_names_.size() ? 0 : curr_idx_;
      }
    }
    // assume each fasta file only holds one sequence
    utility::vector1< std::string > sequences = core::sequence::read_fasta_file_str( file_names_[curr_idx_].second );
    core::pose::make_pose_from_sequence( *tmppose, sequences[1], *residue_set );
    for (core::Size i = 1; i <= tmppose->total_residue(); ++i) {
      tmppose->set_phi(i, -150);
      tmppose->set_psi(i, 150);
      tmppose->set_omega(i, 180);
    }
    file_names_[curr_idx_].first++;
    core::pose::add_comment( *tmppose, "inputfile", file_names_[curr_idx_].second );
    core::pose::add_comment( *tmppose, "filemultiplier", utility::to_string(file_names_[curr_idx_].first) );
    if( file_names_[curr_idx_].first >= multiplier_ )  {
      // this only can happen when curr_idx_ == 0
      file_names_.pop_front();
    } else {
      curr_idx_++;
      curr_idx_ = curr_idx_ == file_names_.size()  ? 0 : curr_idx_;
    }
    return tmppose;
  } else {
    // we go through each file name MULTIPLIER times, then pop it
    for( int i = 1; i<n; i++){
      file_names_.front().first++;
      if( file_names_.front().first >= multiplier_ )
        file_names_.pop_front();
    }
    // assume each fasta file only holds one sequence
    utility::vector1< std::string > sequences = core::sequence::read_fasta_file_str( file_names_[curr_idx_].second );
    core::pose::make_pose_from_sequence( *tmppose, sequences[1], *residue_set );
    for (core::Size i = 1; i <= tmppose->total_residue(); ++i) {
      tmppose->set_phi(i, -150);
      tmppose->set_psi(i, 150);
      tmppose->set_omega(i, 180);
    }
    file_names_.front().first++;
    core::pose::add_comment( *tmppose, "inputfile", file_names_.front().second );
    core::pose::add_comment( *tmppose, "file_multiplier", utility::to_string(file_names_.front().first) );
    if( file_names_.front().first >= multiplier_ )
      file_names_.pop_front();
    return tmppose;
  }
}

bool FastaInputter::has_nth_pose( int n ) {
  int sum = 0;
  for( Size i = 0; i < file_names_.size(); i++ ) {
    sum += (multiplier_ - file_names_[i].first  );
    if (sum >= n )
      return true;
  }
  return false;
}

InputterSP FastaInputter::create() {
  return InputterSP( new FastaInputter() );
}

#ifdef USELUA
void FastaInputter::parse_def( utility::lua::LuaObject const & def,
        utility::lua::LuaObject const & tasks,
        utility::lua::LuaObject & inputters ) {
  residue_set_ =  def["residue_set"] ? def["residue_set"].to<std::string>() : "centroid";
  if( def["multiplier"] ) multiplier_ = def["multiplier"].to<int>();
  if( def["multiply_over_all"] ) multiply_over_all_ = def["multiply_over_all"].to<bool>();
  for (utility::lua::LuaIterator i=def["filelist"].begin(), end; i != end; ++i) {
    file_names_.push_back( std::pair<int, std::string> ( 0, (*i).to<std::string>()) );
  }
}

void FastaInputter::lregister( lua_State * lstate ) {
  lregister_FastaInputter( lstate );
}
#endif
} // inputter
} // protocols