#include <DisulfideInsertionMover.hh>
Public Member Functions | |
| DisulfideInsertionMover () | |
| empty constructor - member variables initialized from the options system More... | |
| DisulfideInsertionMover (DisulfideInsertionMover const &) | |
| ~DisulfideInsertionMover () override=default | |
| protocols::moves::MoverOP | clone () const override |
| Return a clone of the Mover object. More... | |
| void | apply (core::pose::Pose &pose) override |
| Main Method. More... | |
| DisulfideCyclizationViability | determine_cyclization_viability (core::pose::Pose const &partner_pose, core::Size const n_cyd_position, core::Size c_cyd_position) |
| checks if two residues in a pose are near enough in space and geometrically similar enough to existing disulfide forming cys More... | |
| void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
| void | set_scorefxn (core::scoring::ScoreFunctionOP const score_function) |
| core::scoring::ScoreFunctionOP | get_scorefxn () const |
| void | set_movemap_factory (core::select::movemap::MoveMapFactoryCOP const mm) |
| core::select::movemap::MoveMapFactoryCOP | get_movemap_factory () const |
| void | set_peptide_chain (core::Size const value) |
| core::Size | get_peptide_chain () const |
| void | set_n_cyd_seqpos (core::Size const n_cyd_seqpos) |
| void | set_c_cyd_seqpos (core::Size const c_cyd_seqpos) |
| core::Size | get_n_cyd_seqpos () const |
| core::Size | get_c_cyd_seqpos () const |
| void | set_constraint_weight (core::Real const value) |
| core::Real | get_constraint_weight () const |
| void | set_max_dslf_pot (core::Real const value) |
| core::Real | get_max_dslf_pot () |
| void | set_max_dslf_energy (core::Real const value) |
| core::Real | get_max_dslf_energy () |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
 Public Member Functions inherited from protocols::moves::Mover | |
| Mover () | |
| virtual MoverOP | create () |
| MoverCOP | get_self_ptr () const |
| MoverOP | get_self_ptr () |
| MoverCAP | get_self_weak_ptr () const |
| MoverAP | get_self_weak_ptr () |
| Mover (std::string const &type_name) | |
| sets the type for a mover; name_ has been removed (2010/05/14) More... | |
| virtual void | test_move (Pose &pose) |
| : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More... | |
| virtual bool | reinitialize_for_each_job () const |
| Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More... | |
| virtual bool | reinitialize_for_new_input () const |
| Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More... | |
| virtual MoverOP | fresh_instance () const |
| Generates a new Mover object freshly created with the default ctor. More... | |
| MoverStatus | get_last_move_status () const |
| end parser interface, start Job Distributor interface///////////// More... | |
| void | reset_status () |
| resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More... | |
| virtual core::pose::PoseOP | get_additional_output () |
| Mechanism by which a mover may return multiple output poses from a single input pose. More... | |
| void | set_type (std::string const &setting) |
| Set the 'type' string. More... | |
| std::string | get_type () const |
| void | type (const std::string &type_in) |
| Set the 'type' string. More... | |
| std::string const & | type () const |
| Get the set 'type' string. More... | |
| virtual void | set_input_pose (PoseCOP pose) |
| setter for poses contained for rms More... | |
| virtual void | set_native_pose (PoseCOP pose) |
| setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More... | |
| PoseCOP | get_input_pose () const |
| PoseCOP | get_native_pose () const |
| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
| jobdist::BasicJobCOP | get_current_job () const |
| virtual void | set_current_tag (std::string const &new_tag) |
| std::string | get_current_tag () const |
| A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More... | |
| virtual void | show (std::ostream &output=std::cout) const |
| Outputs details about the Mover, including current settings. More... | |
| virtual core::Real | last_proposal_density_ratio () |
| virtual void | clear_info () |
| Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More... | |
| virtual Strings & | info () |
| non-const accessor More... | |
| virtual Strings const & | info () const |
| const accessor More... | |
| virtual 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 std::string | mover_name () |
| static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
| Static Public Member Functions inherited from protocols::moves::Mover | |
| static std::string | name () |
| static void | register_options () |
| Overload this static method if you access options within the mover. More... | |
Static Private Member Functions | |
| static void | setup_constraints (core::pose::Pose &peptide_receptor_pose, core::conformation::Residue lower_cys, core::conformation::Residue upper_cys, core::Size n_cyd_two_chain_position, core::Size c_cyd_two_chain_position) |
| adds angle, dihedral angle and atom-pair constraints to the pose Based on code by Nir London More... | |
Private Attributes | |
| core::Size | peptide_chain_num_ |
| the chain number for the chain to introduce the Cys mutations to More... | |
| core::scoring::ScoreFunctionOP | scorefxn_ |
| the score function to use in all operations; if constraint_weight > 0 this function may be modified to include constraints. More... | |
| core::select::movemap::MoveMapFactoryCOP | movemap_factory_ |
| the movemap for minimization upon call to rebuild_disulfide() (after mutation) More... | |
| core::Size | n_cyd_seqpos_ |
| together with c_cyd_seqpos_, the residue numbers to be mutated into Cys and modeled as having a disulfide bond. More... | |
| core::Size | c_cyd_seqpos_ |
| core::Real | constraint_weight_ |
| when > 0, applies angle, dihedral angle and atom-pair constraints using this weight in the score function, to the newly formed disulfide bond before repacking and minimization. More... | |
| core::Real | max_dslf_pot_ |
| the maximal allowed value of rot-trans deviation from database dslf bond geometry when comparing two residues to potentially be mutated to cys to form a disulfide More... | |
| core::Real | max_dslf_energy_ |
| the maximal allowed value of change in disulfide energy for the generated disulfide bonded peptide More... | |
| core::Real | min_dist_multiplier_ |
| A multiplier for the miniumum distance cutoff when detecting whether two positinos could possibly form a disulfide. Default 1.0. More... | |
| core::Real | max_dist_multiplier_ |
| A multiplier for the muximum distance cutoff when detecting whether two positinos could possibly form a disulfide. Default 1.0. More... | |
Additional Inherited Members | |
| Public Types inherited from protocols::moves::Mover | |
| typedef utility::tag::TagCOP | TagCOP |
| typedef core::pose::Pose | Pose |
| typedef core::pose::PoseCOP | PoseCOP |
| typedef std::list< std::string > | Strings |
| Protected Member Functions inherited from protocols::moves::Mover | |
| void | set_last_move_status (MoverStatus status) |
| nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More... | |
Detailed Description
a mover that given a receptor peptide pose mutates the peptides edge residues to cysteins, if needed, and enforces disulfide bonding by constrained minimization of the bond and the interaction
Constructor & Destructor Documentation
◆ DisulfideInsertionMover() [1/2]
| protocols::simple_moves::DisulfideInsertionMover::DisulfideInsertionMover | ( | ) |
empty constructor - member variables initialized from the options system
References c_cyd_seqpos_, constraint_weight_, max_dist_multiplier_, max_dslf_energy_, max_dslf_pot_, min_dist_multiplier_, n_cyd_seqpos_, and peptide_chain_num_.
◆ DisulfideInsertionMover() [2/2]
| protocols::simple_moves::DisulfideInsertionMover::DisulfideInsertionMover | ( | DisulfideInsertionMover const & | other | ) |
◆ ~DisulfideInsertionMover()
|
overridedefault |
Member Function Documentation
◆ apply()
|
overridevirtual |
Main Method.
Implements protocols::moves::Mover.
References core::scoring::angle_constraint, protocols::minimization_packing::MinMover::apply(), core::scoring::atom_pair_constraint, c_cyd_seqpos_, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), constraint_weight_, protocols::simple_moves::DCV_CYCLIZABLE, protocols::simple_moves::DCV_NOT_CYCLIZABLE, core::conformation::Conformation::detect_disulfides(), determine_cyclization_viability(), core::scoring::dihedral_constraint, core::pose::Pose::energies(), protocols::moves::FAIL_RETRY, core::conformation::form_disulfide(), core::scoring::EMapVector::get(), get_c_cyd_seqpos(), get_n_cyd_seqpos(), core::scoring::get_score_function(), max_dslf_energy_, movemap_factory_, protocols::moves::MS_SUCCESS, n_cyd_seqpos_, peptide_chain_num_, core::util::rebuild_disulfide(), core::pose::Pose::residue(), core::scoring::score_type_from_name(), scorefxn_, protocols::moves::Mover::set_last_move_status(), setup_constraints(), core::scoring::Energies::total_energies(), and protocols::simple_moves::TR().
◆ clone()
|
overridevirtual |
Return a clone of the Mover object.
clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.
Reimplemented from protocols::moves::Mover.
◆ determine_cyclization_viability()
| DisulfideCyclizationViability protocols::simple_moves::DisulfideInsertionMover::determine_cyclization_viability | ( | core::pose::Pose const & | pose, |
| core::Size const | n_putative_cyd_idx, | ||
| core::Size | c_cyd_position | ||
| ) |
checks if two residues in a pose are near enough in space and geometrically similar enough to existing disulfide forming cys
Finds out if the residues next to the peptide chain (assumed second in pose) are in a specified distance range (3-5 Ang, unless one of the residues is Gly, in which case 4.5-6.5 Ang) so that the peptide they wrap can be stabilized by cyclization.
- Parameters
-
pose the protein from which peptides are derived n_putative_cyd position in the partner pose where a putative cysteine immediatly before a derived peptide might exist c_putative_cyd position in the partner pose where a putative cysteine immediatly after a derived peptide might exist
References core::conformation::Residue::atom_index(), core::conformation::Residue::chain(), core::conformation::Conformation::chain_begin(), core::pose::Pose::conformation(), protocols::simple_moves::DCV_ALREADY_CYCLIZED, protocols::simple_moves::DCV_CYCLIZABLE, protocols::simple_moves::DCV_NOT_CYCLIZABLE, core::kinematics::distance(), core::chemical::DISULFIDE, core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_protein(), max_dist_multiplier_, max_dslf_pot_, min_dist_multiplier_, core::conformation::Residue::name1(), core::pose::Pose::residue(), core::chemical::ResidueType::residue_connection_id_for_atom(), core::conformation::Residue::residue_connection_partner(), core::scoring::disulfides::DisulfideMatchingPotential::score_disulfide(), core::pose::Pose::total_residue(), protocols::simple_moves::TR(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().
Referenced by apply().
◆ get_c_cyd_seqpos()
|
inline |
References c_cyd_seqpos_.
Referenced by apply(), and DisulfideInsertionMover().
◆ get_constraint_weight()
|
inline |
References constraint_weight_.
Referenced by DisulfideInsertionMover().
◆ get_max_dslf_energy()
|
inline |
References max_dslf_energy_.
◆ get_max_dslf_pot()
|
inline |
References max_dslf_pot_.
◆ get_movemap_factory()
|
inline |
References movemap_factory_.
Referenced by DisulfideInsertionMover().
◆ get_n_cyd_seqpos()
|
inline |
References n_cyd_seqpos_.
Referenced by apply(), and DisulfideInsertionMover().
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
References mover_name().
◆ get_peptide_chain()
|
inline |
References peptide_chain_num_.
Referenced by DisulfideInsertionMover().
◆ get_scorefxn()
|
inline |
References scorefxn_.
Referenced by DisulfideInsertionMover().
◆ mover_name()
|
static |
◆ parse_my_tag()
|
overridevirtual |
Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.
Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()
Reimplemented from protocols::moves::Mover.
References protocols::rosetta_scripts::parse_movemap_factory_legacy(), core::scoring::parse_score_function(), set_c_cyd_seqpos(), set_constraint_weight(), set_max_dslf_pot(), set_movemap_factory(), set_n_cyd_seqpos(), set_peptide_chain(), and set_scorefxn().
◆ provide_xml_schema()
|
static |
References protocols::rosetta_scripts::append_subelement_for_parse_movemap_factory_legacy(), core::scoring::attributes_for_parse_score_function(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().
Referenced by protocols::simple_moves::DisulfideInsertionMoverCreator::provide_xml_schema().
◆ set_c_cyd_seqpos()
|
inline |
References c_cyd_seqpos_.
Referenced by DisulfideInsertionMover(), and parse_my_tag().
◆ set_constraint_weight()
|
inline |
References constraint_weight_.
Referenced by DisulfideInsertionMover(), and parse_my_tag().
◆ set_max_dslf_energy()
|
inline |
References max_dslf_energy_.
◆ set_max_dslf_pot()
|
inline |
References max_dslf_pot_.
Referenced by parse_my_tag().
◆ set_movemap_factory()
|
inline |
References movemap_factory_.
Referenced by DisulfideInsertionMover(), and parse_my_tag().
◆ set_n_cyd_seqpos()
|
inline |
References n_cyd_seqpos_.
Referenced by DisulfideInsertionMover(), and parse_my_tag().
◆ set_peptide_chain()
|
inline |
References peptide_chain_num_.
Referenced by DisulfideInsertionMover(), and parse_my_tag().
◆ set_scorefxn()
|
inline |
References scorefxn_.
Referenced by DisulfideInsertionMover(), and parse_my_tag().
◆ setup_constraints()
|
staticprivate |
adds angle, dihedral angle and atom-pair constraints to the pose Based on code by Nir London
Setup the score function with the appropriate weights on the constraints. If user has provided a score function and set the weights to a specific value, that value is kept. If weight is not set, prints a warning. This is based on a function written by Nir London.
References core::conformation::Residue::atom_index(), and core::pose::Pose::constraint_set().
Referenced by apply().
Member Data Documentation
◆ c_cyd_seqpos_
|
private |
Referenced by apply(), DisulfideInsertionMover(), get_c_cyd_seqpos(), and set_c_cyd_seqpos().
◆ constraint_weight_
|
private |
when > 0, applies angle, dihedral angle and atom-pair constraints using this weight in the score function, to the newly formed disulfide bond before repacking and minimization.
Referenced by apply(), DisulfideInsertionMover(), get_constraint_weight(), and set_constraint_weight().
◆ max_dist_multiplier_
|
private |
A multiplier for the muximum distance cutoff when detecting whether two positinos could possibly form a disulfide. Default 1.0.
Referenced by determine_cyclization_viability(), and DisulfideInsertionMover().
◆ max_dslf_energy_
|
private |
the maximal allowed value of change in disulfide energy for the generated disulfide bonded peptide
Referenced by apply(), DisulfideInsertionMover(), get_max_dslf_energy(), and set_max_dslf_energy().
◆ max_dslf_pot_
|
private |
the maximal allowed value of rot-trans deviation from database dslf bond geometry when comparing two residues to potentially be mutated to cys to form a disulfide
Referenced by determine_cyclization_viability(), DisulfideInsertionMover(), get_max_dslf_pot(), and set_max_dslf_pot().
◆ min_dist_multiplier_
|
private |
A multiplier for the miniumum distance cutoff when detecting whether two positinos could possibly form a disulfide. Default 1.0.
Referenced by determine_cyclization_viability(), and DisulfideInsertionMover().
◆ movemap_factory_
|
private |
the movemap for minimization upon call to rebuild_disulfide() (after mutation)
Referenced by apply(), get_movemap_factory(), and set_movemap_factory().
◆ n_cyd_seqpos_
|
private |
together with c_cyd_seqpos_, the residue numbers to be mutated into Cys and modeled as having a disulfide bond.
Referenced by apply(), DisulfideInsertionMover(), get_n_cyd_seqpos(), and set_n_cyd_seqpos().
◆ peptide_chain_num_
|
private |
the chain number for the chain to introduce the Cys mutations to
Referenced by apply(), DisulfideInsertionMover(), get_peptide_chain(), and set_peptide_chain().
◆ scorefxn_
|
private |
the score function to use in all operations; if constraint_weight > 0 this function may be modified to include constraints.
Referenced by apply(), get_scorefxn(), and set_scorefxn().
The documentation for this class was generated from the following files:
- src/protocols/simple_moves/DisulfideInsertionMover.hh
- src/protocols/simple_moves/DisulfideInsertionMover.cc
