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>
Public Member Functions | |
| PeptideDeriverFilter () | |
| default constructor More... | |
| PeptideDeriverFilter (PeptideDeriverFilter const &) | |
| copy constructor More... | |
| PeptideDeriverFilter & | operator= (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::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) 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 () 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 void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
| Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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::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:
- PeptideDeriverOutputterContainer
- PeptideDeriverBasicStreamOutputter
- PeptideDeriverMarkdownStreamOutputter
- PeptideDeriverPoseOutputter
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
◆ PeptideDeriverFilter() [1/2]
| protocols::peptide_deriver::PeptideDeriverFilter::PeptideDeriverFilter | ( | ) |
default constructor
References core::scoring::coordinate_constraint, core::scoring::get_score_function(), parse_options(), pep_lengths_, scorefxn_deriver_, and scorefxn_minimizer_.
◆ PeptideDeriverFilter() [2/2]
| protocols::peptide_deriver::PeptideDeriverFilter::PeptideDeriverFilter | ( | PeptideDeriverFilter const & | rhs | ) |
copy constructor
References assign().
Member Function Documentation
◆ apply()
|
overridevirtual |
Returns true if the given pose passes the filter, false otherwise.
Implements protocols::filters::Filter.
◆ assign()
|
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().
◆ build_receptor_peptide_pose()
| 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_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::size(), core::chemical::UPPER_TERMINUS_VARIANT, core::chemical::UPPERTERM_TRUNC_VARIANT, and core::conformation::Atom::xyz().
Referenced by derive_peptide().
◆ calculate_interface_score()
| 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
-
pose A two-monomer pose. TODO : this might have code in common with DdgScan. Consider using that.
Referenced by derive_peptide().
◆ calculate_per_residue_interface_score()
| 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
-
pose a 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_.
◆ class_name()
|
static |
Referenced by protocols::peptide_deriver::PeptideDeriverFilterCreator::keyname(), name(), and provide_xml_schema().
◆ clone()
|
inlineoverridevirtual |
Implements protocols::filters::Filter.
◆ derive_peptide() [1/2]
| 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
-
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::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().
◆ derive_peptide() [2/2]
| 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.
◆ find_interface_residues()
|
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().
◆ fresh_instance()
|
inlineoverridevirtual |
Implements protocols::filters::Filter.
◆ generate_N2C_cyclic_peptide_protein_complex()
| 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_pose linear peptide-protein complex pep_nter_idx index of peptide start position in the given complex pep_cter_idx index of peptide end position in the given complex scorefxn_N2C_minimize scorefunction with constraints turned on to be used in complex minimization
References protocols::minimization_packing::MinMover::apply().
Referenced by derive_peptide().
◆ get_chain_indices()
|
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().
◆ get_is_do_minimize()
|
inline |
References is_do_minimize_.
◆ get_is_dump_cyclic_poses()
|
inline |
References is_dump_cyclic_poses_.
◆ get_is_dump_peptide_pose()
|
inline |
References is_dump_peptide_pose_.
◆ get_is_dump_prepared_pose()
|
inline |
References is_dump_prepared_pose_.
◆ get_is_dump_report_file()
|
inline |
References is_dump_report_file_.
◆ get_is_report_gzip()
|
inline |
References is_report_gzip_.
◆ get_is_skip_zero_isc()
|
inline |
References is_skip_zero_isc_.
◆ get_optimize_cyclic_threshold()
|
inline |
References optimize_cyclic_threshold_.
◆ get_pep_lengths()
|
inline |
References pep_lengths_.
◆ get_report_format()
|
inline |
References report_format_.
◆ get_restrict_partners_to_chains()
|
inline |
References restrict_partners_to_chains_.
◆ get_restrict_receptors_to_chains()
|
inline |
References restrict_receptors_to_chains_.
◆ get_scorefxn_deriver()
|
inline |
References scorefxn_deriver_.
◆ minimize()
|
private |
Minimization step, run on an input once before derivation.
Minimize the pose, while using native constraints.
References protocols::minimization_packing::MinMover::apply(), core::conformation::Residue::atom_index(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::conformation::Residue::is_protein(), core::pose::Pose::remove_constraints(), core::pose::Pose::residue(), scorefxn_minimizer_, core::pose::Pose::size(), and core::conformation::Conformation::xyz().
Referenced by prepare_pose().
◆ name()
|
overridevirtual |
Reimplemented from protocols::filters::Filter.
References class_name().
◆ normalize_isc()
|
staticprivate |
return zero when isc is close enough to zero; used to prevent outputs such as alternating -0 and 0.
◆ operator=()
| PeptideDeriverFilter & protocols::peptide_deriver::PeptideDeriverFilter::operator= | ( | PeptideDeriverFilter const & | rhs | ) |
assignment operator
References assign().
◆ parse_my_tag()
|
overridevirtual |
Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing.
Reimplemented from protocols::filters::Filter.
References parse_report_format_string(), core::scoring::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().
◆ 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().
◆ parse_report_format_string()
|
static |
References protocols::peptide_deriver::PRF_BASIC, and protocols::peptide_deriver::PRF_MARKDOWN.
Referenced by parse_my_tag(), and parse_options().
◆ prepare_pose()
| void protocols::peptide_deriver::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::add_variant_type_to_pose_residue(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::conformation::Conformation::detect_disulfides(), core::conformation::Residue::has_variant_type(), is_do_minimize_, core::chemical::LOWER_TERMINUS_VARIANT, core::chemical::LOWERTERM_TRUNC_VARIANT, minimize(), core::conformation::Conformation::num_chains(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), protocols::peptide_deriver::tracer(), core::chemical::UPPER_TERMINUS_VARIANT, and core::chemical::UPPERTERM_TRUNC_VARIANT.
Referenced by derive_peptide().
◆ provide_xml_schema()
|
static |
◆ push_chain_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().
◆ report()
|
overridevirtual |
Reimplemented from protocols::filters::Filter.
References protocols::peptide_deriver::PeptideDeriverOutputterContainer::begin_structure(), protocols::jd2::current_output_name(), derive_peptide(), protocols::peptide_deriver::PeptideDeriverOutputterContainer::end_structure(), get_chain_indices(), is_dump_cyclic_poses_, is_dump_peptide_pose_, is_dump_prepared_pose_, is_dump_report_file_, is_report_gzip_, protocols::jd2::jd2_used(), core::conformation::membrane::out, protocols::hybridization::path, protocols::peptide_deriver::PRF_BASIC, protocols::peptide_deriver::PRF_MARKDOWN, protocols::peptide_deriver::PeptideDeriverOutputterContainer::push_back(), report_format_, restrict_partners_to_chains_, restrict_receptors_to_chains_, scorefxn_deriver_, and protocols::peptide_deriver::tracer().
◆ set_is_do_minimize()
|
inline |
References is_do_minimize_.
Referenced by parse_my_tag(), and parse_options().
◆ set_is_dump_cyclic_poses()
|
inline |
References is_dump_cyclic_poses_.
Referenced by parse_my_tag(), and parse_options().
◆ set_is_dump_peptide_pose()
|
inline |
References is_dump_peptide_pose_.
Referenced by parse_my_tag(), and parse_options().
◆ set_is_dump_prepared_pose()
|
inline |
References is_dump_prepared_pose_.
Referenced by parse_my_tag(), and parse_options().
◆ set_is_dump_report_file()
|
inline |
References is_dump_report_file_.
Referenced by parse_my_tag(), and parse_options().
◆ set_is_report_gzip()
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inline |
References is_report_gzip_.
Referenced by parse_my_tag(), and parse_options().
◆ set_is_skip_zero_isc()
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inline |
References is_skip_zero_isc_.
Referenced by parse_my_tag(), and parse_options().
◆ set_optimize_cyclic_threshold()
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inline |
References optimize_cyclic_threshold_.
Referenced by parse_my_tag(), and parse_options().
◆ set_pep_lengths()
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inline |
References pep_lengths_.
Referenced by parse_my_tag(), and parse_options().
◆ set_report_format()
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inline |
References report_format_.
Referenced by parse_my_tag(), and parse_options().
◆ set_restrict_partners_to_chains()
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inline |
References restrict_partners_to_chains_.
Referenced by parse_my_tag(), and parse_options().
◆ set_restrict_receptors_to_chains()
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inline |
References restrict_receptors_to_chains_.
Referenced by parse_my_tag(), and parse_options().
◆ set_scorefxn_deriver()
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inline |
References scorefxn_deriver_.
Referenced by parse_my_tag().
Member Data Documentation
◆ is_do_minimize_
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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().
◆ is_dump_cyclic_poses_
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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().
◆ is_dump_peptide_pose_
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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().
◆ is_dump_prepared_pose_
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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().
◆ is_dump_report_file_
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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().
◆ is_report_gzip_
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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().
◆ is_skip_zero_isc_
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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().
◆ optimize_cyclic_threshold_
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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().
◆ pep_lengths_
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private |
the window size(s) of peptides to derive
Referenced by assign(), derive_peptide(), get_pep_lengths(), PeptideDeriverFilter(), and set_pep_lengths().
◆ report_format_
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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().
◆ restrict_partners_to_chains_
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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().
◆ restrict_receptors_to_chains_
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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().
◆ scorefxn_deriver_
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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().
◆ scorefxn_minimizer_
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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:
- src/protocols/peptide_deriver/PeptideDeriverFilter.hh
- src/protocols/peptide_deriver/PeptideDeriverFilter.cc
