#include <MotifGraftMover.hh>

Public Member Functions
	MotifGraftMover ()
	MotifGraftMover Creator. More...

void	init_parameters (std::string const &s_contextStructure, std::string const &s_motif, core::Real const &r_RMSD_tolerance, core::Real const &r_NC_points_RMSD_tolerance, core::Size const &i_clash_score_cutoff, std::string const &s_combinatory_fragment_size_delta, std::string const &s_max_fragment_replacement_size_delta, std::string const &s_clash_test_residue, std::string const &s_hotspots, bool &b_full_motif_bb_alignment, bool const &b_allow_independent_alignment_per_fragment, bool const &b_graft_only_hotspots_by_sidechain_replacement, bool const &b_only_allow_if_N_point_match_aa_identity, bool const &b_only_allow_if_C_point_match_aa_identity, bool const &b_revert_graft_to_native_sequence, bool const &b_allow_repeat_same_graft_output)
	MotifGraftMover parameters and options initializer. More...

	~MotifGraftMover ()
	MotifGraftMover Destructor. More...

virtual void	apply (Pose &)
	Apply mover function. More...

virtual core::pose::PoseOP	get_additional_output ()
	Iterate over the results to get additional matches in the queue. More...

protocols::moves::MoverOP	clone () const
	Function used by roseta to create clones of movers. More...

virtual std::string	get_name () const
	Header only mover get_name. More...

void	permutate_n_vv_of_pairs (utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > const &vv_of_pairs, utility::vector1< std::pair< core::Size, core::Size > > &buff_combVec, core::Size start_index, utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > &vv_resulting_permutations)
	As the name suggests in generates all the permutations of a vector of vectors of pairs (Alex: we should templatize this! Maybe alrready there?) More...

void	generate_combinations_of_motif_fragments_by_delta_variation (core::pose::PoseOP const &p_motif_, utility::vector1< std::pair< long int, long int > > const &combinatory_fragment_size_delta, utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > &vv_resulting_permutations)
	Generate all the combination of different legths of the motif fragment as requested in combinatory_fragment_size_delta Uses permutate_n_vv_of_pairs to generate the permutations. More...

virtual void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
	Fuction to parse RosettaScripts XML options. More...

std::priority_queue< MotifMatch >	generate_scaffold_matches (core::pose::Pose &target_scaffold, core::pose::PoseOP &target_motif_, core::pose::PoseOP &target_contextStructure_)
	Identify all potential matches for the given target scaffold (this is where the motif grafting code is called) More...

void	generate_match_pose (core::pose::Pose &target_pose, core::pose::Pose const &contextStructure, bool b_revert_graft_to_native_sequence, MotifMatch motif_match)
	Generate pose corresponding to the given match. More...

void	get_matching_fragments (core::pose::Pose const &target_scaffold, core::pose::PoseOP const &target_motif_, core::pose::PoseOP const &target_contextStructure_, core::Real const &RMSD_tol, core::Real const &NC_points_RMSD_tol, core::Size const &clash_cutoff, std::string const &clash_test_residue, utility::vector1< std::pair< long int, long int > > const &max_fragment_replacement_size_delta_, utility::vector1< std::pair< core::Size, core::Size > > const &combinatory_fragment_size_delta, utility::vector1< utility::vector1< core::Size > > const &vvr_hotspots, bool const &b_full_motif_bb_alignment, bool const &b_allow_independent_alignment_per_fragment, bool const &b_graft_only_hotspots_by_sidechain_replacement, bool const &b_only_allow_if_N_point_match_aa_identity, bool const &b_only_allow_if_C_point_match_aa_identity, std::priority_queue< MotifMatch > &pq)
	Return a priority queue with the sucessful epigrafts. More...

void	test_epigraft_and_contextStructure_clashes (core::pose::Pose const &p_scaffold, core::pose::Pose const &p_motif_, core::pose::Pose const &p_contextStructure_, core::Size const &clash_cutoff, utility::vector1< motif2scaffold_data > &v_m2s_data)
	Functions that takes the scaffold, motif, contextStructure and superposition transform data. Deletes from the supperposition data those transformations that can't pass the clash score. More...

core::Size	count_clashes_between_two_poses (core::pose::Pose const &p_A, core::pose::Pose const &p_B, core::Size clash_cutoff)
	Count the Number of Clashes between two poses. More...

core::pose::Pose	get_rotated_and_translated_pose (core::pose::Pose const &p_scaffold, numeric::xyzMatrix< core::Real > const &RotM, numeric::xyzVector< core::Real > const &TvecA, numeric::xyzVector< core::Real > const &TvecB)
	Function that returns by reference a rotated copy of the pose. More...

core::pose::Pose	join_two_poses_by_jump (core::pose::Pose const &p_A, core::pose::Pose const &p_B)
	returns a pose with two input poses merged (with a jump in-between) and with the PDB info corrected More...

core::Real	get_clash_score_from_pose (core::pose::Pose &p_input, core::scoring::ScoreFunctionOP const &scorefxn_)
	Helper function to stich (epigraft) two poses given a set of indices in pose A and B stored in a motif2scaffold_data structure. More...

core::pose::Pose	stich_motif_in_scaffold_by_indexes_rotation_and_translation (core::pose::Pose const &p_scaffold, core::pose::Pose const &p_motif_, motif2scaffold_data &m2s_dat, bool const &skip_motif_extremes)
	Helper function to stich (epigraft) two poses given a set of indices in pose A and B stored in a motif2scaffold_data structure. More...

core::Real	get_bb_alignment_and_transformation (core::pose::Pose const &poseA, utility::vector1< core::Size > const &positions_to_alignA, core::pose::Pose const &poseB, utility::vector1< core::Size > const &positions_to_alignB, numeric::xyzMatrix< core::Real > &RotM, numeric::xyzVector< core::Real > &TvecA, numeric::xyzVector< core::Real > &TvecB)
	Performs alignment of the protein BB on the selected aminoacids. Returns the RMSD, Returns by reference the rotation Matrix and Translation Vector, Will fail if both poses are not protein <-This can be fixed by adding a list of the atoms to align to the function, but I am not doing it now. Will fail if the number of residues to align is not the same in the two poses. More...

core::Real	get_bb_alignment_and_transformation_wTipsExtraInfo (utility::vector1< bool > const &v_isNorC, core::pose::Pose const &poseA, utility::vector1< core::Size > const &positions_to_alignA, core::pose::Pose const &poseB, utility::vector1< core::Size > const &positions_to_alignB, numeric::xyzMatrix< core::Real > &RotM, numeric::xyzVector< core::Real > &TvecA, numeric::xyzVector< core::Real > &TvecB, utility::vector1< core::Real > &RMSD_tip_elements)
	Performs alignment of the protein BB on the selected aminoacids. Returns the RMSD, Returns by reference the rotation Matrix and Translation Vector, Will fail if both poses are not protein <-This can be fixed by adding a list of the atoms to align to the function, but I am not doing it now. Will fail if the number of residues to align is not the same in the two poses. More...

core::Real	get_bb_distance (core::pose::Pose const &poseA, utility::vector1< core::Size > const &positions_to_alignA, core::pose::Pose const &poseB, utility::vector1< core::Size > const &positions_to_alignB)
	Returns the BB distance of two poses respect to indexes. More...

void	superposition_transform (core::Size natoms, ObjexxFCL::FArray1_double const &weights, ObjexxFCL::FArray2_double &ref_coords, ObjexxFCL::FArray2_double &coords, numeric::xyzMatrix< core::Real > &RotM, numeric::xyzVector< core::Real > &TvecA, numeric::xyzVector< core::Real > &TvecB)
	Helper Fortran wrapper to get the aligment of two matrixes as well as the corresponding transform. More...

void	get_motif_scaffold_superposition_and_RMSD (core::pose::Pose const &p_scaffold, core::pose::PoseOP const &p_motif_, core::Real const &RMSD_tol, core::Real const &tip_RMSD_tol, utility::vector1< utility::vector1< core::Size > > const &vvr_hotspots, bool const &b_full_motif_bb_alignment, bool const &b_allow_independent_alignment_per_fragment, bool const &b_graft_only_hotspots_by_sidechain_replacement, utility::vector1< motif2scaffold_data > &v_m2s_data)
	performs soperposition based on the motif and returns fragments within the RMSD_tol and also returns the Rotation and translation superposition information in the first [1] vector of each fragment More...

core::pose::Pose	get_mono_aa_pose_copy (core::pose::Pose const &p_input, std::string const &aminoacid_code)
	returns a copy of the pose that replaces all the aminoacids for a single selected aminoacid More...

bool	get_fragments_by_CA_distances_and_NCpoints_restrains (core::pose::Pose const &p_scaffold, core::pose::PoseOP const &p_motif_, utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > &vv_scaffold_fragments_indexes, utility::vector1< std::pair< core::Size, core::Size > > &v_motif_fragments_indexes, core::Real const &RMSD_tol, utility::vector1< std::pair< long int, long int > > const &max_fragment_replacement_size_delta, utility::vector1< std::pair< core::Size, core::Size > > const &v_motif_fragments_permutation, bool const &b_only_allow_if_N_point_match_aa_identity, bool const &b_only_allow_if_C_point_match_aa_identity, bool const &b_N_point_can_replace_proline, bool const &b_C_point_can_replace_proline)
	returns by reference two vectors of indexes (vv_scaffold_fragments_indexes, v_motif_fragments_indexes) that hold the lower and upper bounds of the fragments. Indeed the corresponding to the scaffold one is a vector of vectors, since each pose_scaffold can have many matches More...

void	fragments_permutation_test_by_CA_distances (core::pose::Pose const &p_scaffold, core::pose::PoseOP const &p_motif_, utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > const &vv_scaffold_fragments_indexes, utility::vector1< std::pair< core::Size, core::Size > > const &v_motif_fragments_indexes, core::Real const &RMSD_tol, core::Size const &start_motif_num, utility::vector1< std::pair< core::Size, core::Size > > &buff_combVec, utility::vector1< motif2scaffold_data > &v_m2s_data)
	Generates all the discontinuous fragments combinations that are within the tol restriction. Reduce the combinations by matching intra chains distances by pairs. The method is/can be exahustive but fast (i.e. iteratively it test the restrains (tree unfolding) and skips to the next combination once one fails (branch removal) ). CAUTION, Uses self recursion, so use it wisely. More...

void	parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables (std::string const &s_contextStructure, std::string const &s_motif, core::Real const &r_RMSD_tolerance, core::Real const &r_NC_points_RMSD_tolerance, core::Size const &i_clash_score_cutoff, std::string const &s_combinatory_fragment_size_delta, std::string const &s_max_fragment_replacement_size_delta, std::string const &s_clash_test_residue, std::string const &s_hotspots, bool &b_full_motif_bb_alignment, bool const &b_allow_independent_alignment_per_fragment, bool const &b_graft_only_hotspots_by_sidechain_replacement, bool const &b_only_allow_if_N_point_match_aa_identity, bool const &b_only_allow_if_C_point_match_aa_identity, bool const &b_revert_graft_to_native_sequence, bool const &b_allow_repeat_same_graft_output)
	Fuction to parse the class options and populate their corresponding variables to the global private space. More...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

void	set_type (std::string const &setting)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

void	set_current_tag (std::string const &new_tag)

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

void	type (const std::string &type_in)

std::string	get_type () const

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

Protected Attributes
core::pose::PoseOP	gp_p_contextStructure_

core::pose::PoseOP	gp_p_motif_

core::Real	gp_r_RMSD_tolerance_

core::Real	gp_r_NC_points_RMSD_tolerance_

core::Size	gp_i_clash_score_cutoff_

utility::vector1< std::pair < core::Size, core::Size > >	gp_vp_combinatory_fragment_size_delta_

utility::vector1< std::pair < long int, long int > >	gp_vp_max_fragment_replacement_size_delta_

std::string	gp_s_clash_test_residue_

utility::vector1 < utility::vector1< core::Size > >	gp_vvr_hotspots_

bool	gp_b_full_motif_bb_alignment_

bool	gp_b_allow_independent_alignment_per_fragment_

bool	gp_b_allow_repeat_same_graft_output_

bool	gp_b_is_first_run_

bool	gp_b_graft_only_hotspots_by_sidechain_replacement_

bool	gp_b_only_allow_if_N_point_match_aa_identity_

bool	gp_b_only_allow_if_C_point_match_aa_identity_

bool	gp_b_revert_graft_to_native_sequence_

core::pose::PoseOP	gp_p_target_pose_

std::priority_queue< MotifMatch >	motif_match_results_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

typedef std::list< std::string >	Strings

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Constructor & Destructor Documentation

protocols::motif_grafting::movers::MotifGraftMover::MotifGraftMover ( )

MotifGraftMover Creator.

References gp_b_is_first_run_.

Referenced by clone().

protocols::motif_grafting::movers::MotifGraftMover::~MotifGraftMover ( )

MotifGraftMover Destructor.

Member Function Documentation

void protocols::motif_grafting::movers::MotifGraftMover::apply ( Pose & pose )

virtual

Apply mover function.

Implements protocols::moves::Mover.

References protocols::moves::FAIL_DO_NOT_RETRY, generate_match_pose(), generate_scaffold_matches(), gp_b_allow_repeat_same_graft_output_, gp_b_is_first_run_, gp_b_revert_graft_to_native_sequence_, gp_p_contextStructure_, gp_p_motif_, gp_p_target_pose_, motif_match_results_, protocols::moves::Mover::set_last_move_status(), and protocols::motif_grafting::movers::TR.

protocols::moves::MoverOP protocols::motif_grafting::movers::MotifGraftMover::clone ( ) const

virtual

Function used by roseta to create clones of movers.

Reimplemented from protocols::moves::Mover.

References MotifGraftMover().

core::Size protocols::motif_grafting::movers::MotifGraftMover::count_clashes_between_two_poses	(	core::pose::Pose const &	p_A,
		core::pose::Pose const &	p_B,
		core::Size	clash_cutoff
	)

Count the Number of Clashes between two poses.

References core::conformation::Residue::atom(), core::chemical::ResidueType::atom_type(), core::chemical::AtomType::element(), core::chemical::ResidueType::natoms(), norm(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and core::conformation::Atom::xyz().

Referenced by test_epigraft_and_contextStructure_clashes().

void protocols::motif_grafting::movers::MotifGraftMover::fragments_permutation_test_by_CA_distances	(	core::pose::Pose const &	p_scaffold,
		core::pose::PoseOP const &	p_motif_,
		utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > const &	vv_scaffold_fragments_indexes,
		utility::vector1< std::pair< core::Size, core::Size > > const &	v_motif_fragments_indexes,
		core::Real const &	RMSD_tol,
		core::Size const &	start_motif_num,
		utility::vector1< std::pair< core::Size, core::Size > > &	buff_combVec,
		utility::vector1< motif2scaffold_data > &	v_m2s_data
	)

Generates all the discontinuous fragments combinations that are within the tol restriction. Reduce the combinations by matching intra chains distances by pairs. The method is/can be exahustive but fast (i.e. iteratively it test the restrains (tree unfolding) and skips to the next combination once one fails (branch removal) ). CAUTION, Uses self recursion, so use it wisely.

Generates all the discontinuous fragments combinations that are within the RMSD_tol restriction. Reduce the combinations by matching intra chains distances by pairs. The method is/can be exahustive but fast (i.e. iteratively it test the restrains (tree unfolding) and skips to the next combination once one fails (branch removal) ). CAUTION, Uses self recursion, so use it wisely.

References protocols::motif_grafting::movers::motif2scaffold_indexes::motifHigh, protocols::motif_grafting::movers::motif2scaffold_indexes::motifLow, norm(), core::pose::Pose::residue(), protocols::motif_grafting::movers::motif2scaffold_indexes::scaffoldHigh, protocols::motif_grafting::movers::motif2scaffold_indexes::scaffoldLow, protocols::motif_grafting::movers::TR, protocols::motif_grafting::movers::motif2scaffold_data::v_indexes, and core::conformation::Residue::xyz().

Referenced by get_matching_fragments().

void protocols::motif_grafting::movers::MotifGraftMover::generate_combinations_of_motif_fragments_by_delta_variation	(	core::pose::PoseOP const &	p_motif_,
		utility::vector1< std::pair< long int, long int > > const &	combinatory_fragment_size_delta,
		utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > &	vv_resulting_permutations
	)

Generate all the combination of different legths of the motif fragment as requested in combinatory_fragment_size_delta Uses permutate_n_vv_of_pairs to generate the permutations.

Generate all the combination of different legths of the motif fragment as requested in combinatory_fragment_size_delta.

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::conformation::Conformation::num_chains(), permutate_n_vv_of_pairs(), and protocols::motif_grafting::movers::TR.

Referenced by get_matching_fragments().

void protocols::motif_grafting::movers::MotifGraftMover::generate_match_pose	(	core::pose::Pose &	target_pose,
		core::pose::Pose const &	contextStructure,
		bool	b_revert_graft_to_native_sequence,
		MotifMatch	motif_match
	)

Generate pose corresponding to the given match.

Function used generate a match_pose epigraft using the results stored in the MotifMatch database.

Referenced by apply(), and get_additional_output().

std::priority_queue< MotifMatch > protocols::motif_grafting::movers::MotifGraftMover::generate_scaffold_matches	(	core::pose::Pose &	target_scaffold,
		core::pose::PoseOP &	target_motif_,
		core::pose::PoseOP &	target_contextStructure_
	)

Identify all potential matches for the given target scaffold (this is where the motif grafting code is called)

References core::conformation::Conformation::chain_begin(), core::pose::Pose::conformation(), protocols::moves::FAIL_DO_NOT_RETRY, get_matching_fragments(), gp_b_allow_independent_alignment_per_fragment_, gp_b_full_motif_bb_alignment_, gp_b_graft_only_hotspots_by_sidechain_replacement_, gp_b_only_allow_if_C_point_match_aa_identity_, gp_b_only_allow_if_N_point_match_aa_identity_, gp_i_clash_score_cutoff_, gp_r_NC_points_RMSD_tolerance_, gp_r_RMSD_tolerance_, gp_s_clash_test_residue_, gp_vp_combinatory_fragment_size_delta_, gp_vp_max_fragment_replacement_size_delta_, gp_vvr_hotspots_, core::conformation::Residue::has_variant_type(), core::chemical::LOWER_TERMINUS_VARIANT, core::conformation::Conformation::num_chains(), core::pose::Pose::pdb_info(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), protocols::moves::Mover::set_last_move_status(), core::pose::Pose::total_residue(), protocols::motif_grafting::movers::TR, and core::chemical::UPPER_TERMINUS_VARIANT.

Referenced by apply().

core::pose::PoseOP protocols::motif_grafting::movers::MotifGraftMover::get_additional_output ( )

virtual

Iterate over the results to get additional matches in the queue.

Reimplemented from protocols::moves::Mover.

References generate_match_pose(), gp_b_revert_graft_to_native_sequence_, gp_p_contextStructure_, gp_p_target_pose_, motif_match_results_, protocols::moves::MS_SUCCESS, protocols::moves::Mover::set_last_move_status(), and protocols::motif_grafting::movers::TR.

core::Real protocols::motif_grafting::movers::MotifGraftMover::get_bb_alignment_and_transformation	(	core::pose::Pose const &	poseA,
		utility::vector1< core::Size > const &	positions_to_alignA,
		core::pose::Pose const &	poseB,
		utility::vector1< core::Size > const &	positions_to_alignB,
		numeric::xyzMatrix< core::Real > &	RotM,
		numeric::xyzVector< core::Real > &	TvecA,
		numeric::xyzVector< core::Real > &	TvecB
	)

Performs alignment of the protein BB on the selected aminoacids. Returns the RMSD, Returns by reference the rotation Matrix and Translation Vector, Will fail if both poses are not protein <-This can be fixed by adding a list of the atoms to align to the function, but I am not doing it now. Will fail if the number of residues to align is not the same in the two poses.

Function that performs alignment of the protein BB on the selected aminoacids. Returns the RMSD, Returns by reference the rotation Matrix and Translation Vector, Will fail if both poses are not protein <-This can be fixed by adding a list of the atoms to align to the function, but I am not doing it now. Will fail if the number of residues to align is not the same in the two poses.

References core::pose::Pose::residue(), superposition_transform(), and core::conformation::Residue::xyz().

Referenced by stich_motif_in_scaffold_by_indexes_rotation_and_translation().

core::Real protocols::motif_grafting::movers::MotifGraftMover::get_bb_alignment_and_transformation_wTipsExtraInfo	(	utility::vector1< bool > const &	v_isNorC,
		core::pose::Pose const &	poseA,
		utility::vector1< core::Size > const &	positions_to_alignA,
		core::pose::Pose const &	poseB,
		utility::vector1< core::Size > const &	positions_to_alignB,
		numeric::xyzMatrix< core::Real > &	RotM,
		numeric::xyzVector< core::Real > &	TvecA,
		numeric::xyzVector< core::Real > &	TvecB,
		utility::vector1< core::Real > &	RMSD_tip_elements
	)

Performs alignment of the protein BB on the selected aminoacids. Returns the RMSD, Returns by reference the rotation Matrix and Translation Vector, Will fail if both poses are not protein <-This can be fixed by adding a list of the atoms to align to the function, but I am not doing it now. Will fail if the number of residues to align is not the same in the two poses.

Function that performs alignment of the protein BB on the selected aminoacids. Returns the RMSD, Returns by reference the rotation Matrix and Translation Vector, Will fail if both poses are not protein <-This can be fixed by adding a list of the atoms to align to the function, but I am not doing it now. Will fail if the number of residues to align is not the same in the two poses.

References core::pose::Pose::residue(), superposition_transform(), and core::conformation::Residue::xyz().

Referenced by get_motif_scaffold_superposition_and_RMSD().

core::Real protocols::motif_grafting::movers::MotifGraftMover::get_bb_distance	(	core::pose::Pose const &	poseA,
		utility::vector1< core::Size > const &	positions_to_alignA,
		core::pose::Pose const &	poseB,
		utility::vector1< core::Size > const &	positions_to_alignB
	)

Returns the BB distance of two poses respect to indexes.

References core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by stich_motif_in_scaffold_by_indexes_rotation_and_translation().

core::Real protocols::motif_grafting::movers::MotifGraftMover::get_clash_score_from_pose	(	core::pose::Pose &	p_input,
		core::scoring::ScoreFunctionOP const &	scorefxn_
	)

Helper function to stich (epigraft) two poses given a set of indices in pose A and B stored in a motif2scaffold_data structure.

score fa_rep and fa_atr in the pose

References core::pose::Pose::energies(), fa_atr, core::scoring::fa_atr, core::scoring::fa_rep, fa_rep, and core::scoring::Energies::total_energies().

bool protocols::motif_grafting::movers::MotifGraftMover::get_fragments_by_CA_distances_and_NCpoints_restrains	(	core::pose::Pose const &	p_scaffold,
		core::pose::PoseOP const &	p_motif_,
		utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > &	vv_scaffold_fragments_indexes,
		utility::vector1< std::pair< core::Size, core::Size > > &	v_motif_fragments_indexes,
		core::Real const &	RMSD_tol,
		utility::vector1< std::pair< long int, long int > > const &	max_fragment_replacement_size_delta,
		utility::vector1< std::pair< core::Size, core::Size > > const &	v_motif_fragments_permutation,
		bool const &	b_only_allow_if_N_point_match_aa_identity,
		bool const &	b_only_allow_if_C_point_match_aa_identity,
		bool const &	b_N_point_can_replace_proline,
		bool const &	b_C_point_can_replace_proline
	)

returns by reference two vectors of indexes (vv_scaffold_fragments_indexes, v_motif_fragments_indexes) that hold the lower and upper bounds of the fragments. Indeed the corresponding to the scaffold one is a vector of vectors, since each pose_scaffold can have many matches

Generates the combinations of fragments that match the motif(s). Returns by reference: A) For each motif fragment a vector element with the indices of the motif fragments B) For each motif fragment a vector element with the indices of the fragments in the Scaffold that are within the CA distance restraint.

References core::pose::Pose::aa(), core::chemical::aa_from_oneletter_code(), core::pose::Pose::conformation(), norm(), core::conformation::Conformation::num_chains(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), protocols::motif_grafting::movers::TR, and core::conformation::Residue::xyz().

Referenced by get_matching_fragments().

void protocols::motif_grafting::movers::MotifGraftMover::get_matching_fragments	(	core::pose::Pose const &	target_scaffold,
		core::pose::PoseOP const &	target_motif_,
		core::pose::PoseOP const &	target_contextStructure_,
		core::Real const &	RMSD_tol,
		core::Real const &	NC_points_RMSD_tol,
		core::Size const &	clash_cutoff,
		std::string const &	clash_test_residue,
		utility::vector1< std::pair< long int, long int > > const &	max_fragment_replacement_size_delta_,
		utility::vector1< std::pair< core::Size, core::Size > > const &	combinatory_fragment_size_delta,
		utility::vector1< utility::vector1< core::Size > > const &	vvr_hotspots,
		bool const &	b_full_motif_bb_alignment,
		bool const &	b_allow_independent_alignment_per_fragment,
		bool const &	b_graft_only_hotspots_by_sidechain_replacement,
		bool const &	b_only_allow_if_N_point_match_aa_identity,
		bool const &	b_only_allow_if_C_point_match_aa_identity,
		std::priority_queue< MotifMatch > &	pq
	)

Return a priority queue with the sucessful epigrafts.

Return a priority queue with the successful epigrafts.

References fragments_permutation_test_by_CA_distances(), generate_combinations_of_motif_fragments_by_delta_variation(), get_fragments_by_CA_distances_and_NCpoints_restrains(), get_mono_aa_pose_copy(), get_motif_scaffold_superposition_and_RMSD(), test_epigraft_and_contextStructure_clashes(), and protocols::motif_grafting::movers::TR.

Referenced by generate_scaffold_matches().

core::pose::Pose protocols::motif_grafting::movers::MotifGraftMover::get_mono_aa_pose_copy	(	core::pose::Pose const &	p_input,
		std::string const &	aminoacid_code
	)

returns a copy of the pose that replaces all the aminoacids for a single selected aminoacid

Generates a copy of the pose with the same aminoacid type in all the positions, but keeping the bb Note: may crash or give unexpected results if you put a big residue (e.g. VAL or TRP)

References protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(), core::chemical::FA_STANDARD, core::chemical::ChemicalManager::get_instance(), core::pose::Pose::pdb_info(), residue_type_set, and core::pose::Pose::total_residue().

Referenced by get_matching_fragments().

void protocols::motif_grafting::movers::MotifGraftMover::get_motif_scaffold_superposition_and_RMSD	(	core::pose::Pose const &	p_scaffold,
		core::pose::PoseOP const &	p_motif_,
		core::Real const &	RMSD_tol,
		core::Real const &	tip_RMSD_tol,
		utility::vector1< utility::vector1< core::Size > > const &	vvr_hotspots,
		bool const &	b_full_motif_bb_alignment,
		bool const &	b_allow_independent_alignment_per_fragment,
		bool const &	b_graft_only_hotspots_by_sidechain_replacement,
		utility::vector1< motif2scaffold_data > &	v_m2s_data
	)

performs soperposition based on the motif and returns fragments within the RMSD_tol and also returns the Rotation and translation superposition information in the first [1] vector of each fragment

References get_bb_alignment_and_transformation_wTipsExtraInfo(), and protocols::motif_grafting::movers::TR.

Referenced by get_matching_fragments().

virtual std::string protocols::motif_grafting::movers::MotifGraftMover::get_name ( ) const

inlinevirtual

Header only mover get_name.

Implements protocols::moves::Mover.

core::pose::Pose protocols::motif_grafting::movers::MotifGraftMover::get_rotated_and_translated_pose	(	core::pose::Pose const &	p_scaffold,
		numeric::xyzMatrix< core::Real > const &	RotM,
		numeric::xyzVector< core::Real > const &	TvecA,
		numeric::xyzVector< core::Real > const &	TvecB
	)

Function that returns by reference a rotated copy of the pose.

References core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), core::pose::Pose::total_residue(), and core::pose::Pose::xyz().

Referenced by stich_motif_in_scaffold_by_indexes_rotation_and_translation().

void protocols::motif_grafting::movers::MotifGraftMover::init_parameters	(	std::string const &	s_contextStructure,
		std::string const &	s_motif,
		core::Real const &	r_RMSD_tolerance,
		core::Real const &	r_NC_points_RMSD_tolerance,
		core::Size const &	i_clash_score_cutoff,
		std::string const &	s_combinatory_fragment_size_delta,
		std::string const &	s_max_fragment_replacement_size_delta,
		std::string const &	s_clash_test_residue,
		std::string const &	s_hotspots,
		bool &	b_full_motif_bb_alignment,
		bool const &	b_allow_independent_alignment_per_fragment,
		bool const &	b_graft_only_hotspots_by_sidechain_replacement,
		bool const &	b_only_allow_if_N_point_match_aa_identity,
		bool const &	b_only_allow_if_C_point_match_aa_identity,
		bool const &	b_revert_graft_to_native_sequence,
		bool const &	b_allow_repeat_same_graft_output
	)

MotifGraftMover parameters and options initializer.

References parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables().

core::pose::Pose protocols::motif_grafting::movers::MotifGraftMover::join_two_poses_by_jump	(	core::pose::Pose const &	p_A,
		core::pose::Pose const &	p_B
	)

returns a pose with two input poses merged (with a jump in-between) and with the PDB info corrected

References core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), core::conformation::Conformation::insert_conformation_by_jump(), core::kinematics::FoldTree::num_jump(), core::pose::Pose::pdb_info(), and core::pose::Pose::total_residue().

Referenced by generate_match_pose().

void protocols::motif_grafting::movers::MotifGraftMover::parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables	(	std::string const &	s_contextStructure,
		std::string const &	s_motif,
		core::Real const &	r_RMSD_tolerance,
		core::Real const &	r_NC_points_RMSD_tolerance,
		core::Size const &	i_clash_score_cutoff,
		std::string const &	s_combinatory_fragment_size_delta,
		std::string const &	s_max_fragment_replacement_size_delta,
		std::string const &	s_clash_test_residue,
		std::string const &	s_hotspots,
		bool &	b_full_motif_bb_alignment,
		bool const &	b_allow_independent_alignment_per_fragment,
		bool const &	b_graft_only_hotspots_by_sidechain_replacement,
		bool const &	b_only_allow_if_N_point_match_aa_identity,
		bool const &	b_only_allow_if_C_point_match_aa_identity,
		bool const &	b_revert_graft_to_native_sequence,
		bool const &	b_allow_repeat_same_graft_output
	)

Fuction to parse the class options and populate their corresponding variables to the global private space.

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), gp_b_allow_independent_alignment_per_fragment_, gp_b_allow_repeat_same_graft_output_, gp_b_full_motif_bb_alignment_, gp_b_graft_only_hotspots_by_sidechain_replacement_, gp_b_only_allow_if_C_point_match_aa_identity_, gp_b_only_allow_if_N_point_match_aa_identity_, gp_b_revert_graft_to_native_sequence_, gp_i_clash_score_cutoff_, gp_p_contextStructure_, gp_p_motif_, gp_r_NC_points_RMSD_tolerance_, gp_r_RMSD_tolerance_, gp_s_clash_test_residue_, gp_vp_combinatory_fragment_size_delta_, gp_vp_max_fragment_replacement_size_delta_, gp_vvr_hotspots_, core::conformation::Conformation::num_chains(), core::import_pose::pose_from_pdb(), size(), utility::string_split(), and protocols::motif_grafting::movers::TR.

Referenced by init_parameters(), and parse_my_tag().

void protocols::motif_grafting::movers::MotifGraftMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	,
		protocols::filters::Filters_map const &	,
		protocols::moves::Movers_map const &	,
		core::pose::Pose const &
	)

virtual

Fuction to parse RosettaScripts XML options.

Reimplemented from protocols::moves::Mover.

References parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables(), and protocols::motif_grafting::movers::TR.

void protocols::motif_grafting::movers::MotifGraftMover::permutate_n_vv_of_pairs	(	utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > const &	vv_of_pairs,
		utility::vector1< std::pair< core::Size, core::Size > > &	buff_combVec,
		core::Size	start_index,
		utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > &	vv_resulting_permutations
	)

As the name suggests in generates all the permutations of a vector of vectors of pairs (Alex: we should templatize this! Maybe alrready there?)

As the name suggests in generates all the permutations of a vector of vectors of pairs (Alex: we should templatize this)

Referenced by generate_combinations_of_motif_fragments_by_delta_variation().

core::pose::Pose protocols::motif_grafting::movers::MotifGraftMover::stich_motif_in_scaffold_by_indexes_rotation_and_translation	(	core::pose::Pose const &	p_scaffold,
		core::pose::Pose const &	p_motif_,
		motif2scaffold_data &	m2s_dat,
		bool const &	skip_motif_extremes
	)

Helper function to stich (epigraft) two poses given a set of indices in pose A and B stored in a motif2scaffold_data structure.

Referenced by generate_match_pose(), and test_epigraft_and_contextStructure_clashes().

void protocols::motif_grafting::movers::MotifGraftMover::superposition_transform	(	core::Size	natoms,
		ObjexxFCL::FArray1_double const &	weights,
		ObjexxFCL::FArray2_double &	ref_coords,
		ObjexxFCL::FArray2_double &	coords,
		numeric::xyzMatrix< core::Real > &	RotM,
		numeric::xyzVector< core::Real > &	TvecA,
		numeric::xyzVector< core::Real > &	TvecB
	)

Helper Fortran wrapper to get the aligment of two matrixes as well as the corresponding transform.

Superposition_transform wrapper (as in Alex Ford code protocols/toolbox/superimpose.[cc,hh])

References protocols::toolbox::fit_centered_coords(), and protocols::toolbox::reset_x().

Referenced by get_bb_alignment_and_transformation(), and get_bb_alignment_and_transformation_wTipsExtraInfo().

void protocols::motif_grafting::movers::MotifGraftMover::test_epigraft_and_contextStructure_clashes	(	core::pose::Pose const &	p_scaffold,
		core::pose::Pose const &	p_motif_,
		core::pose::Pose const &	p_contextStructure_,
		core::Size const &	clash_cutoff,
		utility::vector1< motif2scaffold_data > &	v_m2s_data
	)

Functions that takes the scaffold, motif, contextStructure and superposition transform data. Deletes from the supperposition data those transformations that can't pass the clash score.

References core::pose::Pose::append_residue_by_bond(), count_clashes_between_two_poses(), core::pose::Pose::residue(), stich_motif_in_scaffold_by_indexes_rotation_and_translation(), and protocols::motif_grafting::movers::TR.

Referenced by get_matching_fragments().

Member Data Documentation

bool protocols::motif_grafting::movers::MotifGraftMover::gp_b_allow_independent_alignment_per_fragment_

protected

Referenced by generate_scaffold_matches(), and parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables().

bool protocols::motif_grafting::movers::MotifGraftMover::gp_b_allow_repeat_same_graft_output_

protected

Referenced by apply(), and parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables().

bool protocols::motif_grafting::movers::MotifGraftMover::gp_b_full_motif_bb_alignment_

protected

Referenced by generate_scaffold_matches(), and parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables().

bool protocols::motif_grafting::movers::MotifGraftMover::gp_b_graft_only_hotspots_by_sidechain_replacement_

protected

Referenced by generate_scaffold_matches(), and parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables().

bool protocols::motif_grafting::movers::MotifGraftMover::gp_b_is_first_run_

protected

Referenced by apply(), and MotifGraftMover().

bool protocols::motif_grafting::movers::MotifGraftMover::gp_b_only_allow_if_C_point_match_aa_identity_

protected

Referenced by generate_scaffold_matches(), and parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables().

bool protocols::motif_grafting::movers::MotifGraftMover::gp_b_only_allow_if_N_point_match_aa_identity_

protected

Referenced by generate_scaffold_matches(), and parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables().

bool protocols::motif_grafting::movers::MotifGraftMover::gp_b_revert_graft_to_native_sequence_

protected

Referenced by apply(), get_additional_output(), and parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables().

core::Size protocols::motif_grafting::movers::MotifGraftMover::gp_i_clash_score_cutoff_

protected

Referenced by generate_scaffold_matches(), and parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables().

core::pose::PoseOP protocols::motif_grafting::movers::MotifGraftMover::gp_p_contextStructure_

protected

Referenced by apply(), get_additional_output(), and parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables().

core::pose::PoseOP protocols::motif_grafting::movers::MotifGraftMover::gp_p_motif_

protected

Referenced by apply(), generate_match_pose(), and parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables().

core::pose::PoseOP protocols::motif_grafting::movers::MotifGraftMover::gp_p_target_pose_

protected

Referenced by apply(), and get_additional_output().

core::Real protocols::motif_grafting::movers::MotifGraftMover::gp_r_NC_points_RMSD_tolerance_

protected

Referenced by generate_scaffold_matches(), and parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables().

core::Real protocols::motif_grafting::movers::MotifGraftMover::gp_r_RMSD_tolerance_

protected

Referenced by generate_scaffold_matches(), and parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables().

std::string protocols::motif_grafting::movers::MotifGraftMover::gp_s_clash_test_residue_

protected

Referenced by generate_scaffold_matches(), and parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables().

utility::vector1< std::pair< core::Size, core::Size > > protocols::motif_grafting::movers::MotifGraftMover::gp_vp_combinatory_fragment_size_delta_

protected

Referenced by generate_scaffold_matches(), and parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables().

utility::vector1< std::pair< long int, long int > > protocols::motif_grafting::movers::MotifGraftMover::gp_vp_max_fragment_replacement_size_delta_

protected

Referenced by generate_scaffold_matches(), and parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables().

utility::vector1< utility::vector1< core::Size > > protocols::motif_grafting::movers::MotifGraftMover::gp_vvr_hotspots_

protected

Referenced by generate_scaffold_matches(), and parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables().

std::priority_queue<MotifMatch> protocols::motif_grafting::movers::MotifGraftMover::motif_match_results_

protected

Referenced by apply(), and get_additional_output().

The documentation for this class was generated from the following files:

src/protocols/motif_grafting/movers/MotifGraftMover.hh
src/protocols/motif_grafting/movers/MotifGraftMover.cc

Public Member Functions

Protected Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation