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protocols::simple_moves::DisulfideInsertionMover Class Reference

#include <DisulfideInsertionMover.hh>

Inheritance diagram for protocols::simple_moves::DisulfideInsertionMover:
Inheritance graph
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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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover 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 mover_is_unpublished () const
 Does this mover 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 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

protocols::simple_moves::DisulfideInsertionMover::DisulfideInsertionMover ( )
protocols::simple_moves::DisulfideInsertionMover::DisulfideInsertionMover ( DisulfideInsertionMover const &  other)
protocols::simple_moves::DisulfideInsertionMover::~DisulfideInsertionMover ( )
overridedefault

Member Function Documentation

void protocols::simple_moves::DisulfideInsertionMover::apply ( core::pose::Pose )
overridevirtual
protocols::moves::MoverOP protocols::simple_moves::DisulfideInsertionMover::clone ( ) const
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.

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
posethe protein from which peptides are derived
n_putative_cydposition in the partner pose where a putative cysteine immediatly before a derived peptide might exist
c_putative_cydposition in the partner pose where a putative cysteine immediatly after a derived peptide might exist

References 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, max_dist_multiplier_, max_dslf_pot_, min_dist_multiplier_, core::pose::Pose::residue(), core::scoring::disulfides::DisulfideMatchingPotential::score_disulfide(), core::pose::Pose::total_residue(), and protocols::simple_moves::TR().

Referenced by apply().

core::Size protocols::simple_moves::DisulfideInsertionMover::get_c_cyd_seqpos ( ) const
inline

References c_cyd_seqpos_.

Referenced by apply(), and DisulfideInsertionMover().

core::Real protocols::simple_moves::DisulfideInsertionMover::get_constraint_weight ( ) const
inline

References constraint_weight_.

Referenced by DisulfideInsertionMover().

core::Real protocols::simple_moves::DisulfideInsertionMover::get_max_dslf_energy ( )
inline

References max_dslf_energy_.

core::Real protocols::simple_moves::DisulfideInsertionMover::get_max_dslf_pot ( )
inline

References max_dslf_pot_.

core::select::movemap::MoveMapFactoryCOP protocols::simple_moves::DisulfideInsertionMover::get_movemap_factory ( ) const
inline

References movemap_factory_.

Referenced by DisulfideInsertionMover().

core::Size protocols::simple_moves::DisulfideInsertionMover::get_n_cyd_seqpos ( ) const
inline

References n_cyd_seqpos_.

Referenced by apply(), and DisulfideInsertionMover().

std::string protocols::simple_moves::DisulfideInsertionMover::get_name ( ) const
overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References mover_name().

core::Size protocols::simple_moves::DisulfideInsertionMover::get_peptide_chain ( ) const
inline

References peptide_chain_num_.

Referenced by DisulfideInsertionMover().

core::scoring::ScoreFunctionOP protocols::simple_moves::DisulfideInsertionMover::get_scorefxn ( ) const
inline

References scorefxn_.

Referenced by DisulfideInsertionMover().

std::string protocols::simple_moves::DisulfideInsertionMover::mover_name ( )
static
void protocols::simple_moves::DisulfideInsertionMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
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().

void protocols::simple_moves::DisulfideInsertionMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::simple_moves::DisulfideInsertionMover::set_c_cyd_seqpos ( core::Size const  c_cyd_seqpos)
inline

References c_cyd_seqpos_.

Referenced by DisulfideInsertionMover(), and parse_my_tag().

void protocols::simple_moves::DisulfideInsertionMover::set_constraint_weight ( core::Real const  value)
inline
void protocols::simple_moves::DisulfideInsertionMover::set_max_dslf_energy ( core::Real const  value)
inline

References max_dslf_energy_.

void protocols::simple_moves::DisulfideInsertionMover::set_max_dslf_pot ( core::Real const  value)
inline

References max_dslf_pot_.

Referenced by parse_my_tag().

void protocols::simple_moves::DisulfideInsertionMover::set_movemap_factory ( core::select::movemap::MoveMapFactoryCOP const  mm)
inline
void protocols::simple_moves::DisulfideInsertionMover::set_n_cyd_seqpos ( core::Size const  n_cyd_seqpos)
inline

References n_cyd_seqpos_.

Referenced by DisulfideInsertionMover(), and parse_my_tag().

void protocols::simple_moves::DisulfideInsertionMover::set_peptide_chain ( core::Size const  value)
inline
void protocols::simple_moves::DisulfideInsertionMover::set_scorefxn ( core::scoring::ScoreFunctionOP const  score_function)
inline

References scorefxn_.

Referenced by DisulfideInsertionMover(), and parse_my_tag().

void protocols::simple_moves::DisulfideInsertionMover::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 
)
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

core::Size protocols::simple_moves::DisulfideInsertionMover::c_cyd_seqpos_
private
core::Real protocols::simple_moves::DisulfideInsertionMover::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().

core::Real protocols::simple_moves::DisulfideInsertionMover::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().

core::Real protocols::simple_moves::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().

core::Real protocols::simple_moves::DisulfideInsertionMover::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().

core::Real protocols::simple_moves::DisulfideInsertionMover::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().

core::select::movemap::MoveMapFactoryCOP protocols::simple_moves::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().

core::Size protocols::simple_moves::DisulfideInsertionMover::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().

core::Size protocols::simple_moves::DisulfideInsertionMover::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().

core::scoring::ScoreFunctionOP protocols::simple_moves::DisulfideInsertionMover::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(), DisulfideInsertionMover(), get_scorefxn(), and set_scorefxn().


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