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protocols::peptide_deriver::PeptideDeriverFilter Class Reference

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::peptide_deriver::PeptideDeriverFilter:
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Public Member Functions

 PeptideDeriverFilter ()
 default constructor More...
 
 PeptideDeriverFilter (PeptideDeriverFilter const &)
 copy constructor More...
 
PeptideDeriverFilteroperator= (PeptideDeriverFilter const &rhs)
 assignment operator More...
 
bool apply (core::pose::Pose const &pose) const override
 Returns true if the given pose passes the filter, false otherwise. More...
 
void report (std::ostream &out, core::pose::Pose const &pose) const override
 
protocols::filters::FilterOP clone () const override
 
protocols::filters::FilterOP fresh_instance () const override
 
utility::vector1< core::Sizeget_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) override
 Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing. More...
 
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...
 
core::pose::PoseOP generate_N2C_cyclic_peptide_protein_complex (core::pose::PoseOP const receptor_peptide_pose, core::Size const pep_nter_idx, core::Size const pep_cter_idx, core::scoring::ScoreFunctionOP const scorefxn_N2C_minimize) const
 Take a given linear peptide-protein complex and return a head-to-tail (N-ter to C-ter) cyclic peptide - receptor complex. 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...
 
std::string name () const override
 
- Public Member Functions inherited from protocols::filters::Filter
 Filter ()
 
 Filter (std::string const &)
 
 Filter (Filter const &)
 
 ~Filter () override
 
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)
 
virtual bool filter_provides_citation_info () const
 Does this filter provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool filter_is_unpublished () const
 Does this filter indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static PeptideDeriverReportFormat parse_report_format_string (std::string const &value)
 
static std::string class_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 

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::Sizefind_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::Sizepep_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:

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

copy constructor

References assign().

Member Function Documentation

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

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

Implements protocols::filters::Filter.

void protocols::peptide_deriver::PeptideDeriverFilter::assign ( PeptideDeriverFilter lhs,
PeptideDeriverFilter const &  rhs 
)
staticprivate
core::pose::PoseOP protocols::peptide_deriver::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_posethe receptor chain to be maintained
partner_posethe chain from which a peptide should be cut and connected to the receptor in a new pose
peptide_startstarting position in the partner pose to cut from
peptide_endlast position in the partner pose to be cut out
jump_idthe 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::size(), core::chemical::UPPER_TERMINUS_VARIANT, core::chemical::UPPERTERM_TRUNC_VARIANT, and core::conformation::Atom::xyz().

Referenced by derive_peptide().

core::Real protocols::peptide_deriver::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
poseA two-monomer pose. TODO : this might have code in common with DdgScan. Consider using that.

Referenced by derive_peptide().

void protocols::peptide_deriver::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
posea two-monomer pose.

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

std::string protocols::peptide_deriver::PeptideDeriverFilter::class_name ( )
static
protocols::filters::FilterOP protocols::peptide_deriver::PeptideDeriverFilter::clone ( ) const
inlineoverridevirtual
void protocols::peptide_deriver::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
posea many-chain pose
first_chain_indexchain index of the receptor (and also partner, if both_ways is true)
second_chain_indexchain index of the partner (and also receptor, if both_ways is true)
both_wayswhether 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::peptide_deriver::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::peptide_deriver::tracer().

Referenced by report().

void protocols::peptide_deriver::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.

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, protocols::peptide_deriver::PeptideDeriverOutputter::begin_receptor_partner_pair(), build_receptor_peptide_pose(), calculate_interface_score(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::kinematics::FoldTree::cutpoints(), protocols::peptide_deriver::CYCLIZATION_METHOD_DISULFIDE, protocols::peptide_deriver::CYCLIZATION_METHOD_END_TO_END, protocols::simple_moves::DCV_ALREADY_CYCLIZED, protocols::simple_moves::DCV_CYCLIZABLE, core::scoring::dihedral_constraint, protocols::peptide_deriver::PeptideDeriverOutputter::end_receptor_partner_pair(), protocols::peptide_deriver::ET_BEST_CYCLIC, protocols::peptide_deriver::ET_BEST_LINEAR, protocols::peptide_deriver::ET_GENERAL, core::pose::Pose::fold_tree(), generate_N2C_cyclic_peptide_protein_complex(), core::scoring::EMapVector::get(), core::scoring::get_score_function(), is_do_minimize_, is_skip_zero_isc_, protocols::moves::MS_SUCCESS, protocols::peptide_deriver::NUM_CYCLIZATION_METHODS, optimize_cyclic_threshold_, core::pose::Pose::pdb_info(), pep_lengths_, protocols::peptide_deriver::PeptideDeriverOutputter::peptide_entry(), protocols::peptide_deriver::PeptideDeriverOutputter::peptide_length(), core::scoring::score_type_from_name(), protocols::peptide_deriver::tracer(), and protocols::peptide_deriver::UNLIKELY_ISC_VALUE.

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

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

Parameters
posea two-monomer pose.

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

protocols::filters::FilterOP protocols::peptide_deriver::PeptideDeriverFilter::fresh_instance ( ) const
inlineoverridevirtual
core::pose::PoseOP protocols::peptide_deriver::PeptideDeriverFilter::generate_N2C_cyclic_peptide_protein_complex ( core::pose::PoseOP const  receptor_peptide_pose,
core::Size const  pep_nter_idx,
core::Size const  pep_cter_idx,
core::scoring::ScoreFunctionOP const  scorefxn_N2C_minimize 
) const

Take a given linear peptide-protein complex and return a head-to-tail (N-ter to C-ter) cyclic peptide - receptor complex.

Take a given linear peptide-protein complex and return a head-to-tail (N-ter to C-ter) cyclic peptide - receptor complex

Parameters
receptor_peptide_poselinear peptide-protein complex
pep_nter_idxindex of peptide start position in the given complex
pep_cter_idxindex of peptide end position in the given complex
scorefxn_N2C_minimizescorefunction with constraints turned on to be used in complex minimization

References protocols::minimization_packing::MinMover::apply().

Referenced by derive_peptide().

utility::vector1< core::Size > protocols::peptide_deriver::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::peptide_deriver::PeptideDeriverFilter::get_is_do_minimize ( ) const
inline

References is_do_minimize_.

bool protocols::peptide_deriver::PeptideDeriverFilter::get_is_dump_cyclic_poses ( ) const
inline

References is_dump_cyclic_poses_.

bool protocols::peptide_deriver::PeptideDeriverFilter::get_is_dump_peptide_pose ( ) const
inline

References is_dump_peptide_pose_.

bool protocols::peptide_deriver::PeptideDeriverFilter::get_is_dump_prepared_pose ( ) const
inline
bool protocols::peptide_deriver::PeptideDeriverFilter::get_is_dump_report_file ( ) const
inline

References is_dump_report_file_.

bool protocols::peptide_deriver::PeptideDeriverFilter::get_is_report_gzip ( ) const
inline

References is_report_gzip_.

bool protocols::peptide_deriver::PeptideDeriverFilter::get_is_skip_zero_isc ( ) const
inline

References is_skip_zero_isc_.

core::Real protocols::peptide_deriver::PeptideDeriverFilter::get_optimize_cyclic_threshold ( ) const
inline
utility::vector1<core::Size> protocols::peptide_deriver::PeptideDeriverFilter::get_pep_lengths ( ) const
inline

References pep_lengths_.

PeptideDeriverReportFormat protocols::peptide_deriver::PeptideDeriverFilter::get_report_format ( ) const
inline

References report_format_.

utility::vector1<char> protocols::peptide_deriver::PeptideDeriverFilter::get_restrict_partners_to_chains ( ) const
inline
utility::vector1<char> protocols::peptide_deriver::PeptideDeriverFilter::get_restrict_receptors_to_chains ( ) const
inline
core::scoring::ScoreFunctionOP protocols::peptide_deriver::PeptideDeriverFilter::get_scorefxn_deriver ( ) const
inline

References scorefxn_deriver_.

void protocols::peptide_deriver::PeptideDeriverFilter::minimize ( core::pose::Pose pose) const
private
std::string protocols::peptide_deriver::PeptideDeriverFilter::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

static core::Real protocols::peptide_deriver::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::peptide_deriver::PeptideDeriverFilter::operator= ( PeptideDeriverFilter const &  rhs)

assignment operator

References assign().

void protocols::peptide_deriver::PeptideDeriverFilter::parse_my_tag ( utility::tag::TagCOP  ,
basic::datacache::DataMap &   
)
overridevirtual
void protocols::peptide_deriver::PeptideDeriverFilter::parse_options ( )
private
PeptideDeriverReportFormat protocols::peptide_deriver::PeptideDeriverFilter::parse_report_format_string ( std::string const &  value)
static
void protocols::peptide_deriver::PeptideDeriverFilter::prepare_pose ( PeptideDeriverOutputter output,
core::pose::Pose pose 
) const
void protocols::peptide_deriver::PeptideDeriverFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::peptide_deriver::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::peptide_deriver::PeptideDeriverFilter::report ( std::ostream &  out,
core::pose::Pose const &  pose 
) const
overridevirtual
void protocols::peptide_deriver::PeptideDeriverFilter::set_is_do_minimize ( bool const  value)
inline

References is_do_minimize_.

Referenced by parse_my_tag(), and parse_options().

void protocols::peptide_deriver::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::peptide_deriver::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::peptide_deriver::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::peptide_deriver::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::peptide_deriver::PeptideDeriverFilter::set_is_report_gzip ( bool const  value)
inline

References is_report_gzip_.

Referenced by parse_my_tag(), and parse_options().

void protocols::peptide_deriver::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::peptide_deriver::PeptideDeriverFilter::set_optimize_cyclic_threshold ( core::Real const  value)
inline
void protocols::peptide_deriver::PeptideDeriverFilter::set_pep_lengths ( utility::vector1< core::Size > const &  values)
inline

References pep_lengths_.

Referenced by parse_my_tag(), and parse_options().

void protocols::peptide_deriver::PeptideDeriverFilter::set_report_format ( PeptideDeriverReportFormat const  value)
inline

References report_format_.

Referenced by parse_my_tag(), and parse_options().

void protocols::peptide_deriver::PeptideDeriverFilter::set_restrict_partners_to_chains ( utility::vector1< char > const &  values)
inline
void protocols::peptide_deriver::PeptideDeriverFilter::set_restrict_receptors_to_chains ( utility::vector1< char > const &  values)
inline
void protocols::peptide_deriver::PeptideDeriverFilter::set_scorefxn_deriver ( core::scoring::ScoreFunctionOP  value)
inline

References scorefxn_deriver_.

Referenced by parse_my_tag().

Member Data Documentation

bool protocols::peptide_deriver::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::peptide_deriver::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::peptide_deriver::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::peptide_deriver::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::peptide_deriver::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::peptide_deriver::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::peptide_deriver::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::peptide_deriver::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::peptide_deriver::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::peptide_deriver::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::peptide_deriver::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::peptide_deriver::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).

See also
restrict_partners_to_chains_

Referenced by get_restrict_receptors_to_chains(), report(), and set_restrict_receptors_to_chains().

core::scoring::ScoreFunctionOP protocols::peptide_deriver::PeptideDeriverFilter::scorefxn_deriver_
private

The score function used to score derived peptides.

Referenced by assign(), calculate_per_residue_interface_score(), get_scorefxn_deriver(), PeptideDeriverFilter(), report(), and set_scorefxn_deriver().

core::scoring::ScoreFunctionOP protocols::peptide_deriver::PeptideDeriverFilter::scorefxn_minimizer_
private

The score function used to minimize the initial pose.

Referenced by assign(), minimize(), and PeptideDeriverFilter().


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