implementation of the Peptiderive protocol - given a pose, it evaluates the binding energy of linear stretches, of given lengths, and indicates which of these contributes more than others to the interaction energy. It also reports on and optionally models cyclizable peptides. More...

#include <PeptideDeriverFilter.hh>

Inheritance diagram for protocols::analysis::PeptideDeriverFilter:

[legend]

Public Member Functions
	PeptideDeriverFilter ()
	default constructor More...

	PeptideDeriverFilter (PeptideDeriverFilter const &)
	copy constructor More...

PeptideDeriverFilter &	operator= (PeptideDeriverFilter const &rhs)
	assignment operator More...

virtual bool	apply (core::pose::Pose const &pose) const
	Returns true if the given pose passes the filter, false otherwise. More...

virtual void	report (std::ostream &out, core::pose::Pose const &pose) const

virtual protocols::filters::FilterOP	clone () const

virtual protocols::filters::FilterOP	fresh_instance () const

virtual std::string	name () const

utility::vector1< core::Size >	get_pep_lengths () const

void	set_pep_lengths (utility::vector1< core::Size > const &values)

utility::vector1< char >	get_restrict_receptors_to_chains () const

void	set_restrict_receptors_to_chains (utility::vector1< char > const &values)

utility::vector1< char >	get_restrict_partners_to_chains () const

void	set_restrict_partners_to_chains (utility::vector1< char > const &values)

PeptideDeriverReportFormat	get_report_format () const

void	set_report_format (PeptideDeriverReportFormat const value)

bool	get_is_skip_zero_isc () const

void	set_is_skip_zero_isc (bool const value)

bool	get_is_dump_peptide_pose () const

void	set_is_dump_peptide_pose (bool const value)

bool	get_is_dump_cyclic_poses () const

void	set_is_dump_cyclic_poses (bool const value)

bool	get_is_dump_prepared_pose () const

void	set_is_dump_prepared_pose (bool const value)

bool	get_is_dump_report_file () const

void	set_is_dump_report_file (bool const value)

bool	get_is_report_gzip () const

void	set_is_report_gzip (bool const value)

bool	get_is_do_minimize () const

void	set_is_do_minimize (bool const value)

core::Real	get_optimize_cyclic_threshold () const

void	set_optimize_cyclic_threshold (core::Real const value)

core::scoring::ScoreFunctionOP	get_scorefxn_deriver () const

void	set_scorefxn_deriver (core::scoring::ScoreFunctionOP value)

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

void	prepare_pose (PeptideDeriverOutputter &output, core::pose::Pose &pose) const
	Prepare pose before derivation, by minimizing it and finding disulfides. More...

core::Real	calculate_interface_score (core::pose::Pose const &pose, core::Size const jump_id) const
	Calculate the interface score, i.e. addition to energy resulting from the complex coming together. More...

void	calculate_per_residue_interface_score (core::pose::Pose &chain_pair_pose, std::set< core::Size > interface_residues, std::ostream &report_out, core::Size const jump_id) const

core::pose::PoseOP	build_receptor_peptide_pose (core::pose::Pose const &receptor_pose, core::pose::Pose const &partner_pose, core::Size peptide_start, core::Size peptide_end, core::Size &jump_id) const

void	derive_peptide (PeptideDeriverOutputter &output, core::pose::Pose const &pose, core::Size const first_chain_index, core::Size const second_chain_index, bool const both_ways) const
	overload of PeptideDeriverFilter::derive_peptide() which accepts a many-chain pose and chain indices, rather than single-chain poses. More...

void	derive_peptide (PeptideDeriverOutputter &output, core::pose::Pose const &receptor_pose, core::pose::Pose const &partner_pose, core::Real const total_isc) const
	The core of the filter: calculate and output a table of the energetic contribution of each linear segment of the pep_chain_pose chain (going through it with a sliding window), together with other interesting data. More...

Public Member Functions inherited from protocols::filters::Filter
	Filter ()

	Filter (std::string const &)

	Filter (Filter const &)

virtual	~Filter ()

virtual core::Real	report_sm (core::pose::Pose const &) const
	used to report filter internals through a score or silent file More...

virtual std::string	get_type () const

std::string	get_user_defined_name () const

void	set_user_defined_name (std::string const &name)

virtual void	clear ()
	used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual More...

virtual core::Real	score (core::pose::Pose &pose)

Static Public Member Functions
static PeptideDeriverReportFormat	parse_report_format_string (std::string const value)

Private Member Functions
void	minimize (core::pose::Pose &) const
	Minimization step, run on an input once before derivation. More...

void	parse_options ()
	read options from option system More...

Static Private Member Functions
static void	assign (PeptideDeriverFilter &, PeptideDeriverFilter const &)
	common implementation of cctor and operator= More...

static void	push_chain_residue_indices (core::pose::Pose const &many_chain_pose, core::Size const chain_index, utility::vector1< core::Size > &residue_indices)
	helper function, creates a vector containing the range of residues indices that span the given chain More...

static utility::vector1 < core::Size >	get_chain_indices (core::pose::Pose const &pose, utility::vector1< char > const &restrict_to_chains)
	helper function, returns a list of chain indices. If restrict_to_chains is specified, only indices of chains with these letters are retuned. Otherwise, indices of all chains (i.e., 1..num_chains) are returned. More...

static std::set< core::Size >	find_interface_residues (core::pose::Pose const &chain_pair_pose)

static core::Real	normalize_isc (core::Real const isc)
	return zero when isc is close enough to zero; used to prevent outputs such as alternating -0 and 0. More...

Private Attributes
utility::vector1< core::Size >	pep_lengths_
	the window size(s) of peptides to derive More...

bool	is_skip_zero_isc_
	whether to optimize by jumping over the windows in which the total Isc = 0 More...

bool	is_dump_peptide_pose_
	whether to output the pose of the each (best) derived peptide. Only affects the way report() does output. More...

bool	is_dump_cyclic_poses_
	whether to output each of the modelled cyclic poses (only cyclizable poses with enough contribution, i.e. beyond optimize_cyclic_threshold_, are modelled). Only affects the way report() does output. More...

bool	is_dump_prepared_pose_
	whether to output the pose of the model after minimization. Only affects the way report() does output. More...

PeptideDeriverReportFormat	report_format_
	the format in which PeptideDeriver outputs. See PeptideDeriverReportFormat for options. Only affects the way report() does output. More...

bool	is_dump_report_file_
	whether to output the peptide information report to a separate file (rather than the log). Only affects the way report() does output. More...

bool	is_report_gzip_
	whether to gzip report file; only relevant when is_dump_report_file is true. Only affects the way report() does output. More...

bool	is_do_minimize_
	whether to minimize the structure before starting the algorithm More...

core::Real	optimize_cyclic_threshold_
	set a threshold from which a peptide contributing such percent of total binding energy will be optimized More...

utility::vector1< char >	restrict_receptors_to_chains_
	list of chains to use as receptors. When empty, all chains are included. Peptides won't be derived from these chains (unless they are also specified as partners). More...

utility::vector1< char >	restrict_partners_to_chains_
	list of chain to use as partners. When empty, all chains are included. We only go over the chains listed as partners to derive the peptides. More...

core::scoring::ScoreFunctionOP	scorefxn_deriver_
	The score function used to score derived peptides. More...

core::scoring::ScoreFunctionOP	scorefxn_minimizer_
	The score function used to minimize the initial pose. More...

Additional Inherited Members
Protected Attributes inherited from protocols::filters::Filter
std::string	scorename_

Detailed Description

implementation of the Peptiderive protocol - given a pose, it evaluates the binding energy of linear stretches, of given lengths, and indicates which of these contributes more than others to the interaction energy. It also reports on and optionally models cyclizable peptides.

Data is either output to a log (using report()) or passed to the given PeptideDeriverOutputter (using derive_peptide()).

When calling report(), the output format is determined by a list of flags:

is_dump_peptide_pose
is_dump_cyclic_poses
is_dump_prepared_pose
is_dump_report_file
is_report_gzip See each flag's documentation for their effect. These flags are settable via command-line or RosettaScripts options, and may also be set programmatically. These only affect the output coming from report(), since report() uses these to determine which PeptideDeriverOutputter instances it passes to derive_peptide().

When calling derive_peptide(), however, it is up to the consumer to provide the PeptideDeriverOutputter instance of choice. Naturally, it may use any of the subclasses provided in this file:

Note: the PeptideDeriverFilter doesn't actually filter anything, so it might have been better to suffix it with -Reporter, but wasn't so not to confuse it with the FeatureReporter class hierarchy.

Constructor & Destructor Documentation

protocols::analysis::PeptideDeriverFilter::PeptideDeriverFilter ( )

default constructor

References core::scoring::coordinate_constraint, core::scoring::get_score_function(), parse_options(), pep_lengths_, scorefxn_deriver_, and scorefxn_minimizer_.

Referenced by clone().

protocols::analysis::PeptideDeriverFilter::PeptideDeriverFilter ( PeptideDeriverFilter const & rhs )

copy constructor

References assign().

Member Function Documentation

bool protocols::analysis::PeptideDeriverFilter::apply ( core::pose::Pose const & pose ) const

virtual

Returns true if the given pose passes the filter, false otherwise.

Implements protocols::filters::Filter.

void protocols::analysis::PeptideDeriverFilter::assign	(	PeptideDeriverFilter &	lhs,
		PeptideDeriverFilter const &	rhs
	)

staticprivate

common implementation of cctor and operator=

References is_do_minimize_, is_dump_cyclic_poses_, is_dump_peptide_pose_, is_dump_prepared_pose_, is_dump_report_file_, is_report_gzip_, is_skip_zero_isc_, optimize_cyclic_threshold_, pep_lengths_, report_format_, scorefxn_deriver_, and scorefxn_minimizer_.

Referenced by operator=(), and PeptideDeriverFilter().

core::pose::PoseOP protocols::analysis::PeptideDeriverFilter::build_receptor_peptide_pose	(	core::pose::Pose const &	receptor_pose,
		core::pose::Pose const &	partner_pose,
		core::Size	peptide_start,
		core::Size	peptide_end,
		core::Size &	jump_id
	)		const

For two given full proteins poses, builds a new pose with the full receptor pose connected to the peptide found between start and end positions in the partner pose

Parameters

receptor_pose	the receptor chain to be maintained
partner_pose	the chain from which a peptide should be cut and connected to the receptor in a new pose
peptide_start	starting position in the partner pose to cut from
peptide_end	last position in the partner pose to be cut out
jump_id	the number of the jump that was used to connect the two chains

References core::pose::add_variant_type_to_pose_residue(), core::conformation::Residue::atom(), core::conformation::change_cys_state(), core::chemical::DISULFIDE, core::chemical::LOWER_TERMINUS_VARIANT, core::chemical::LOWERTERM_TRUNC_VARIANT, core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), core::pose::residue_center_of_mass(), core::pose::return_nearest_residue(), core::pose::Pose::total_residue(), core::chemical::UPPER_TERMINUS_VARIANT, core::chemical::UPPERTERM_TRUNC_VARIANT, and core::conformation::Atom::xyz().

Referenced by derive_peptide().

core::Real protocols::analysis::PeptideDeriverFilter::calculate_interface_score	(	core::pose::Pose const &	pose,
		core::Size const	jump_id
	)		const

Calculate the interface score, i.e. addition to energy resulting from the complex coming together.

Given a two-monomer pose and a score function - the interface score is the score difference between the given complex and the unbound monomers, 'unbound' meaning that they are spatially seperated.

Parameters

pose	A two-monomer pose. TODO : this might have code in common with DdgScan. Consider using that.

Referenced by derive_peptide().

void protocols::analysis::PeptideDeriverFilter::calculate_per_residue_interface_score	(	core::pose::Pose &	chain_pair_pose,
		std::set< core::Size >	interface_residues,
		std::ostream &	report_out,
		core::Size const	jump_id
	)		const

Given a two-monomer pose and a score function - the interface score (delta between energy of complex and of the seperated monomers) is calculated for each residue. This signifies the energetic contribution of each residue to the complex binding.

Parameters

pose	a two-monomer pose.

References core::conformation::Residue::chain(), core::sequence::end, core::pose::Pose::energies(), core::pose::Pose::residue(), core::scoring::Energies::residue_total_energy(), and scorefxn_deriver_.

virtual protocols::filters::FilterOP protocols::analysis::PeptideDeriverFilter::clone ( ) const

inlinevirtual

Implements protocols::filters::Filter.

References PeptideDeriverFilter().

void protocols::analysis::PeptideDeriverFilter::derive_peptide	(	PeptideDeriverOutputter &	output,
		core::pose::Pose const &	pose,
		core::Size const	first_chain_index,
		core::Size const	second_chain_index,
		bool const	both_ways
	)		const

overload of PeptideDeriverFilter::derive_peptide() which accepts a many-chain pose and chain indices, rather than single-chain poses.

cuts the specified chains from the original pose using core::io::pdb::pose_from_pose() and calculates the complex (receptor and partner)

Parameters

pose	a many-chain pose
first_chain_index	chain index of the receptor (and also partner, if both_ways is true)
second_chain_index	chain index of the partner (and also receptor, if both_ways is true)
both_ways	whether the two specified chains may play the role of both the partner and the receptor. When false, the first chain is considered to be the receptor, and the second one is considered to be the partner

References calculate_interface_score(), core::conformation::Conformation::chain_begin(), protocols::analysis::PeptideDeriverOutputter::chain_pair_pose_prepared(), core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_jump_that_builds_residue(), core::pose::Pose::pdb_info(), core::io::pose_from_pose(), prepare_pose(), push_chain_residue_indices(), core::pose::Pose::split_by_chain(), and protocols::analysis::tracer().

Referenced by report().

void protocols::analysis::PeptideDeriverFilter::derive_peptide	(	PeptideDeriverOutputter &	output,
		core::pose::Pose const &	receptor_pose,
		core::pose::Pose const &	partner_pose,
		core::Real const	total_isc
	)		const

The core of the filter: calculate and output a table of the energetic contribution of each linear segment of the pep_chain_pose chain (going through it with a sliding window), together with other interesting data.

Goes through the residues in partner_pose with a sliding window (the size of which is determined by PeptideDeriverFilter::pep_lengths_), and calculates the energetic contribution of each such linear segment. This is output for each position in the partner_pose, together with additional data, such as the fraction of the energetic contribution to the total interface score (

See also: PeptideDeriverFilter::calculate_interface_score()), and putative SS bridge sites).

Finally, the best position is output again, with a special mark ('best') to indicate that it is the best position.

Note: for lack of a better term, we call the chain from which the peptide will be derived, the partner.

std::set< core::Size > protocols::analysis::PeptideDeriverFilter::find_interface_residues ( core::pose::Pose const & chain_pair_pose )

staticprivate

for a two-monomer pose, returns a set of interface residues

Parameters

pose	a two-monomer pose.

References core::pose::metrics::CalculatorFactory::Instance(), core::pose::Pose::metric(), and core::pose::metrics::CalculatorFactory::register_calculator().

virtual protocols::filters::FilterOP protocols::analysis::PeptideDeriverFilter::fresh_instance ( ) const

inlinevirtual

Implements protocols::filters::Filter.

utility::vector1< core::Size > protocols::analysis::PeptideDeriverFilter::get_chain_indices	(	core::pose::Pose const &	pose,
		utility::vector1< char > const &	restrict_to_chains
	)

staticprivate

helper function, returns a list of chain indices. If restrict_to_chains is specified, only indices of chains with these letters are retuned. Otherwise, indices of all chains (i.e., 1..num_chains) are returned.

References core::pose::Pose::conformation(), core::pose::get_chain_id_from_chain(), and core::conformation::Conformation::num_chains().

Referenced by report().

bool protocols::analysis::PeptideDeriverFilter::get_is_do_minimize ( ) const

inline

References is_do_minimize_.

bool protocols::analysis::PeptideDeriverFilter::get_is_dump_cyclic_poses ( ) const

inline

References is_dump_cyclic_poses_.

bool protocols::analysis::PeptideDeriverFilter::get_is_dump_peptide_pose ( ) const

inline

References is_dump_peptide_pose_.

bool protocols::analysis::PeptideDeriverFilter::get_is_dump_prepared_pose ( ) const

inline

References is_dump_prepared_pose_.

bool protocols::analysis::PeptideDeriverFilter::get_is_dump_report_file ( ) const

inline

References is_dump_report_file_.

bool protocols::analysis::PeptideDeriverFilter::get_is_report_gzip ( ) const

inline

References is_report_gzip_.

bool protocols::analysis::PeptideDeriverFilter::get_is_skip_zero_isc ( ) const

inline

References is_skip_zero_isc_.

core::Real protocols::analysis::PeptideDeriverFilter::get_optimize_cyclic_threshold ( ) const

inline

References optimize_cyclic_threshold_.

utility::vector1<core::Size> protocols::analysis::PeptideDeriverFilter::get_pep_lengths ( ) const

inline

References pep_lengths_.

PeptideDeriverReportFormat protocols::analysis::PeptideDeriverFilter::get_report_format ( ) const

inline

References report_format_.

utility::vector1<char> protocols::analysis::PeptideDeriverFilter::get_restrict_partners_to_chains ( ) const

inline

References restrict_partners_to_chains_.

utility::vector1<char> protocols::analysis::PeptideDeriverFilter::get_restrict_receptors_to_chains ( ) const

inline

References restrict_receptors_to_chains_.

core::scoring::ScoreFunctionOP protocols::analysis::PeptideDeriverFilter::get_scorefxn_deriver ( ) const

inline

References scorefxn_deriver_.

void protocols::analysis::PeptideDeriverFilter::minimize ( core::pose::Pose & pose ) const

private

Minimization step, run on an input once before derivation.

Minimize the pose, while using native constraints.

References protocols::simple_moves::MinMover::apply(), core::conformation::Residue::atom_index(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::conformation::Residue::is_protein(), core::pose::Pose::residue(), scorefxn_minimizer_, and core::pose::Pose::total_residue().

Referenced by prepare_pose().

virtual std::string protocols::analysis::PeptideDeriverFilter::name ( ) const

inlinevirtual

Reimplemented from protocols::filters::Filter.

static core::Real protocols::analysis::PeptideDeriverFilter::normalize_isc ( core::Real const isc )

staticprivate

return zero when isc is close enough to zero; used to prevent outputs such as alternating -0 and 0.

PeptideDeriverFilter & protocols::analysis::PeptideDeriverFilter::operator= ( PeptideDeriverFilter const & rhs )

assignment operator

References assign().

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

virtual

Reimplemented from protocols::filters::Filter.

References parse_report_format_string(), protocols::rosetta_scripts::parse_score_function(), set_is_do_minimize(), set_is_dump_cyclic_poses(), set_is_dump_peptide_pose(), set_is_dump_prepared_pose(), set_is_dump_report_file(), set_is_report_gzip(), set_is_skip_zero_isc(), set_optimize_cyclic_threshold(), set_pep_lengths(), set_report_format(), set_restrict_partners_to_chains(), set_restrict_receptors_to_chains(), and set_scorefxn_deriver().

void protocols::analysis::PeptideDeriverFilter::parse_options ( )

private

read options from option system

References parse_report_format_string(), set_is_do_minimize(), set_is_dump_cyclic_poses(), set_is_dump_peptide_pose(), set_is_dump_prepared_pose(), set_is_dump_report_file(), set_is_report_gzip(), set_is_skip_zero_isc(), set_optimize_cyclic_threshold(), set_pep_lengths(), set_report_format(), set_restrict_partners_to_chains(), and set_restrict_receptors_to_chains().

Referenced by PeptideDeriverFilter().

PeptideDeriverReportFormat protocols::analysis::PeptideDeriverFilter::parse_report_format_string ( std::string const value )

static

References protocols::analysis::PRF_BASIC, and protocols::analysis::PRF_MARKDOWN.

Referenced by parse_my_tag(), and parse_options().

void protocols::analysis::PeptideDeriverFilter::prepare_pose	(	PeptideDeriverOutputter &	output,
		core::pose::Pose &	pose
	)		const

Prepare pose before derivation, by minimizing it and finding disulfides.

Verifies the pose has at least two chains. Minimizes the pose and detects disulfides.

Parameters

pose	the pose to prepare.

References core::pose::Pose::conformation(), core::conformation::Conformation::detect_disulfides(), is_do_minimize_, minimize(), core::conformation::Conformation::num_chains(), and protocols::analysis::tracer().

Referenced by derive_peptide().

void protocols::analysis::PeptideDeriverFilter::push_chain_residue_indices	(	core::pose::Pose const &	many_chain_pose,
		core::Size const	chain_index,
		utility::vector1< core::Size > &	residue_indices
	)

staticprivate

helper function, creates a vector containing the range of residues indices that span the given chain

Pushes the residue indices belonging to the specified chain index into a given vector.

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), and core::pose::Pose::conformation().

Referenced by derive_peptide().

void protocols::analysis::PeptideDeriverFilter::report	(	std::ostream &	out,
		core::pose::Pose const &	pose
	)		const

virtual

void protocols::analysis::PeptideDeriverFilter::set_is_do_minimize ( bool const value )

inline

References is_do_minimize_.

Referenced by parse_my_tag(), and parse_options().

void protocols::analysis::PeptideDeriverFilter::set_is_dump_cyclic_poses ( bool const value )

inline

References is_dump_cyclic_poses_.

Referenced by parse_my_tag(), and parse_options().

void protocols::analysis::PeptideDeriverFilter::set_is_dump_peptide_pose ( bool const value )

inline

References is_dump_peptide_pose_.

Referenced by parse_my_tag(), and parse_options().

void protocols::analysis::PeptideDeriverFilter::set_is_dump_prepared_pose ( bool const value )

inline

References is_dump_prepared_pose_.

Referenced by parse_my_tag(), and parse_options().

void protocols::analysis::PeptideDeriverFilter::set_is_dump_report_file ( bool const value )

inline

References is_dump_report_file_.

Referenced by parse_my_tag(), and parse_options().

void protocols::analysis::PeptideDeriverFilter::set_is_report_gzip ( bool const value )

inline

References is_report_gzip_.

Referenced by parse_my_tag(), and parse_options().

void protocols::analysis::PeptideDeriverFilter::set_is_skip_zero_isc ( bool const value )

inline

References is_skip_zero_isc_.

Referenced by parse_my_tag(), and parse_options().

void protocols::analysis::PeptideDeriverFilter::set_optimize_cyclic_threshold ( core::Real const value )

inline

References optimize_cyclic_threshold_.

Referenced by parse_my_tag(), and parse_options().

void protocols::analysis::PeptideDeriverFilter::set_pep_lengths ( utility::vector1< core::Size > const & values )

inline

References pep_lengths_.

Referenced by parse_my_tag(), and parse_options().

void protocols::analysis::PeptideDeriverFilter::set_report_format ( PeptideDeriverReportFormat const value )

inline

References report_format_.

Referenced by parse_my_tag(), and parse_options().

void protocols::analysis::PeptideDeriverFilter::set_restrict_partners_to_chains ( utility::vector1< char > const & values )

inline

References restrict_partners_to_chains_.

Referenced by parse_my_tag(), and parse_options().

void protocols::analysis::PeptideDeriverFilter::set_restrict_receptors_to_chains ( utility::vector1< char > const & values )

inline

References restrict_receptors_to_chains_.

Referenced by parse_my_tag(), and parse_options().

void protocols::analysis::PeptideDeriverFilter::set_scorefxn_deriver ( core::scoring::ScoreFunctionOP value )

inline

References scorefxn_deriver_.

Referenced by parse_my_tag().

Member Data Documentation

bool protocols::analysis::PeptideDeriverFilter::is_do_minimize_

private

whether to minimize the structure before starting the algorithm

Referenced by assign(), derive_peptide(), get_is_do_minimize(), prepare_pose(), and set_is_do_minimize().

bool protocols::analysis::PeptideDeriverFilter::is_dump_cyclic_poses_

private

whether to output each of the modelled cyclic poses (only cyclizable poses with enough contribution, i.e. beyond optimize_cyclic_threshold_, are modelled). Only affects the way report() does output.

Referenced by assign(), get_is_dump_cyclic_poses(), report(), and set_is_dump_cyclic_poses().

bool protocols::analysis::PeptideDeriverFilter::is_dump_peptide_pose_

private

whether to output the pose of the each (best) derived peptide. Only affects the way report() does output.

Referenced by assign(), get_is_dump_peptide_pose(), report(), and set_is_dump_peptide_pose().

bool protocols::analysis::PeptideDeriverFilter::is_dump_prepared_pose_

private

whether to output the pose of the model after minimization. Only affects the way report() does output.

Referenced by assign(), get_is_dump_prepared_pose(), report(), and set_is_dump_prepared_pose().

bool protocols::analysis::PeptideDeriverFilter::is_dump_report_file_

private

whether to output the peptide information report to a separate file (rather than the log). Only affects the way report() does output.

Referenced by assign(), get_is_dump_report_file(), report(), and set_is_dump_report_file().

bool protocols::analysis::PeptideDeriverFilter::is_report_gzip_

private

whether to gzip report file; only relevant when is_dump_report_file is true. Only affects the way report() does output.

Referenced by assign(), get_is_report_gzip(), report(), and set_is_report_gzip().

bool protocols::analysis::PeptideDeriverFilter::is_skip_zero_isc_

private

whether to optimize by jumping over the windows in which the total Isc = 0

Referenced by assign(), derive_peptide(), get_is_skip_zero_isc(), and set_is_skip_zero_isc().

core::Real protocols::analysis::PeptideDeriverFilter::optimize_cyclic_threshold_

private

set a threshold from which a peptide contributing such percent of total binding energy will be optimized

Referenced by assign(), derive_peptide(), get_optimize_cyclic_threshold(), and set_optimize_cyclic_threshold().

utility::vector1< core::Size > protocols::analysis::PeptideDeriverFilter::pep_lengths_

private

the window size(s) of peptides to derive

Referenced by assign(), derive_peptide(), get_pep_lengths(), PeptideDeriverFilter(), and set_pep_lengths().

PeptideDeriverReportFormat protocols::analysis::PeptideDeriverFilter::report_format_

private

the format in which PeptideDeriver outputs. See PeptideDeriverReportFormat for options. Only affects the way report() does output.

Referenced by assign(), get_report_format(), report(), and set_report_format().

utility::vector1<char> protocols::analysis::PeptideDeriverFilter::restrict_partners_to_chains_

private

list of chain to use as partners. When empty, all chains are included. We only go over the chains listed as partners to derive the peptides.

See also: restrict_receptors_to_chains_

Referenced by get_restrict_partners_to_chains(), report(), and set_restrict_partners_to_chains().

utility::vector1<char> protocols::analysis::PeptideDeriverFilter::restrict_receptors_to_chains_

private

list of chains to use as receptors. When empty, all chains are included. Peptides won't be derived from these chains (unless they are also specified as partners).