util.hh

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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 util.hh
/// @brief
/// @author ashworth

#ifndef INCLUDED_protocols_dna_util_hh
#define INCLUDED_protocols_dna_util_hh

#include <protocols/dna/DnaChains.fwd.hh>
#include <protocols/dna/typedefs.hh>
#include <protocols/dna/DnaDesignDef.fwd.hh>

#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ResidueType.hh>
#include <core/conformation/Atom.fwd.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/pack/rotamer_set/RotamerSets.fwd.hh>
#include <core/pack/task/PackerTask.fwd.hh>
#include <core/pose/Pose.fwd.hh>

// Utility headers
#include <utility/vector0.fwd.hh>
#include <utility/vector1.hh> // there is no forward declaration possible for const_iterator(?)

// C++ headers
#include <list>
#include <iosfwd>


namespace protocols {
namespace dna {

///@brief basic struct for remembering position/type information before/during/after design
class PositionType {
public:
  PositionType(
    core::Size pos = 0,
    core::chemical::ResidueTypeCOP rt = 0,
    bool design = false
  ) : position( pos ), type( rt ), designable( design ) {}

  core::Size position;
  core::chemical::ResidueTypeCOP type;
  bool designable;
};

typedef utility::vector1< PositionType > PositionTypes;

bool
close_to_dna(
  core::conformation::Residue const & pres,
  core::conformation::Residue const & dres,
  core::Real cut2,
  bool base_only = false
);

core::Real
argrot_dna_dis2(
  core::pose::Pose const & pose,
  core::Size presid,
  core::conformation::Residue const & pres,
  core::conformation::Residue const & dres,
  core::Real threshold,
  bool base_only = false
);

core::Real
contact_distance2(
  core::conformation::Atoms::const_iterator a_begin,
  core::conformation::Atoms::const_iterator a_end,
  core::conformation::Atoms::const_iterator b_begin,
  core::conformation::Atoms::const_iterator b_end,
  core::Real threshold = 0.0
);

core::Real
z_axis_dist(
  core::conformation::Residue const & pres,
  core::conformation::Residue const & dres
);

std::string dna_comp_name_str( std::string const & dna );

std::string dna_full_name3( std::string const & name3 );

core::chemical::AA
dna_base_partner( core::chemical::AA const & na );

void
find_basepairs(
  core::pose::Pose const & pose,
  DnaChains & dna_chains,
  bool include_unpaired = true
);

/* void
make_sequence_combinations(
  ResTypeSequences & sequences,
  utility::vector1< core::Size > const & seq_indices,
  core::pack::task::PackerTaskCOP ptask
); */

void
make_single_mutants(
  ResTypeSequence const & sequence,
  core::pack::task::PackerTaskCOP ptask,
  ResTypeSequences & sequences
);

void
design_residues_list(
  std::list< PositionType > & design_residues,
  core::pose::Pose const & pose,
  core::pack::task::PackerTask const & ptask
);

void
make_sequence_combinations(
  utility::vector1< core::Size >::const_iterator seqset_iter,
  utility::vector1< core::Size > const & seq_indices,
  core::pack::task::PackerTaskCOP ptask,
  ResTypeSequence & sequence,
  ResTypeSequences & sequences
);

std::ostream & operator << ( std::ostream & os, ResTypeSequence const & seq );

std::string seq_to_str( ResTypeSequence const & seq );

std::ostream & operator << ( std::ostream & os, ResTypeSequences const & seqs );

std::string seq_pdb_str(
  ResTypeSequence const &,
  core::pose::Pose const &
);

void print_sequence_pdb_nums(
  ResTypeSequence const &,
  core::pose::Pose const &,
  std::ostream &
);

void print_sequences_pdb_nums(
  ResTypeSequences const &,
  core::pose::Pose const &,
  std::ostream &
);

void
restrict_dna_rotamers(
  core::pack::rotamer_set::RotamerSetsCOP rotsets,
  ResTypeSequence const & seq,
  utility::vector0<int> & rot_to_pack
);

void
restrict_to_single_sequence(
  core::pack::rotamer_set::RotamerSetsCOP rotamer_sets,
  utility::vector1< core::chemical::ResidueTypeCOP > const & single_sequence,
  utility::vector0< int > & rot_to_pack
);

void
substitute_residue(
  core::pose::Pose & pose,
  core::Size index,
  core::chemical::ResidueType const & new_type
);

void write_checkpoint( core::pose::Pose & pose, core::Size iter );
void load_checkpoint( core::pose::Pose & pose, core::Size & iter );
void checkpoint_cleanup();

void
load_dna_design_defs_from_strings(
  DnaDesignDefOPs & defs,
  utility::vector1< std::string > const & str_defs
);

void
load_dna_design_defs_from_file(
  DnaDesignDefOPs & defs,
  std::string const & filename,
  std::string const & pdb_prefix
);

void
load_dna_design_defs_from_options(
  DnaDesignDefOPs & defs,
  std::string pdb_prefix = std::string()
);

void
add_constraints_from_file(
  core::pose::Pose & pose
);

core::kinematics::FoldTree
make_base_pair_aware_fold_tree(
  core::pose::Pose const & pose
);

bool
not_already_connected(
  core::pose::Pose const & pose,
  core::Size const num_jumps,
  char const this_chain,
  char const other_chain,
  ObjexxFCL::FArray2D_int & jump_pairs
);


void
set_base_segment_chainbreak_constraints(
  core::pose::Pose & pose,
  core::Size const this_base,
  core::Size const end_base
);


} // namespace dna
} // namespace protocols

#endif