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Rosetta
2016.11
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Rosetta
2016.11
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"Dummy" connection used when we wnat to track connection information but not build anything More...
#include <Connection.hh>
Public Member Functions | |
| GenericConnection () | |
| "Dummy" connection used when we wnat to track connection information but not build anything More... | |
| virtual | ~GenericConnection () |
| virtual std::string | get_name () const |
| Each derived class must specify its name. The class name. More... | |
| virtual protocols::moves::MoverOP | fresh_instance () const |
| Generates a new Mover object freshly created with the default ctor. More... | |
| virtual protocols::moves::MoverOP | clone () const |
| Return a clone of the Mover object. More... | |
| virtual void | apply_connection (components::StructureData &perm) const |
| applies the loop building, in this case does nothing More... | |
| virtual bool | polymer_connection () const |
| derived classes should return true if the Connection forms a polymer bond (e.g. peptide) and false if it forms another type of chemical linkage (e.g. disulfide) More... | |
| virtual bool | are_connectable (components::StructureData const &sd, std::string const &segment1, std::string const &segment2, Motif const &motif) const |
| check whether the given segments are connectable More... | |
 Public Member Functions inherited from protocols::denovo_design::connection::Connection | |
| Connection () | |
| default constructor More... | |
| virtual | ~Connection () |
| destructor - this class has no dynamic allocation, so / nothing needs to be cleaned. C++ will take care of that for us. More... | |
| virtual void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, core::pose::Pose const &pose) |
| setup the parameters via an xml tag More... | |
| virtual void | apply (core::pose::Pose &pose) |
| performs setup and applies loop building More... | |
| void | apply_permutation (components::StructureData &perm) const |
| uses the permutation to set up, builds, and updates permutation More... | |
| virtual void | setup_permutation (components::StructureData &perm) const |
| set up the connection mover based on the information in the permutation More... | |
| virtual void | setup_from_random (components::StructureData &perm, core::Real random) const |
| sets up the connection mover based on the information in the permutation More... | |
| virtual void | check_permutation (components::StructureData const &perm) const |
| checks the generated StructureData object to ensure it fits with what the user wants before building More... | |
| virtual bool | check (components::StructureData const &perm) const |
| checks the inserted region vs. the desired ss/abego. True if it matches, false otherwise More... | |
| virtual core::pose::PoseOP | build_pose (components::StructureData const &perm) const |
| Creates a pose based on the information saved to the provided StructureData object. More... | |
| virtual void | process_permutation (components::StructureData &perm) const |
| virtual void | set_id (std::string const &newid) |
| sets an identifier for this mover More... | |
| core::Size | build_left (components::StructureData const &perm) const |
| Methods for setting/getting data in StructureData Object. More... | |
| core::Size | build_right (components::StructureData const &perm) const |
| get "right" residue of loop region taking overlap into account More... | |
| core::Size | build_len (components::StructureData const &perm) const |
| length of the connection to be built More... | |
| void | set_build_len (components::StructureData &perm, core::Size const len_val) const |
| stores build length in the permutation More... | |
| std::string | build_ss (components::StructureData const &perm) const |
| secondary structure of the connection to be built More... | |
| void | set_build_ss (components::StructureData &perm, std::string const &ss_val) const |
| stores build secondary structure in the permutation More... | |
| std::string | build_abego (components::StructureData const &perm) const |
| abego of the connection to be built More... | |
| void | set_build_abego (components::StructureData &perm, std::string const &abego_val) const |
| stores build abego in the permutation More... | |
| core::Size | cut_resi (components::StructureData const &perm) const |
| location of the cut to be placed (within the loop) More... | |
| void | set_cut_resi (components::StructureData &perm, core::Size const cut_val) const |
| stores cut point within the loop into the permutation More... | |
| std::string const & | lower_segment_id (components::StructureData const &perm) const |
| get id of the segment immediately lower to the loop More... | |
| std::string const & | upper_segment_id (components::StructureData const &perm) const |
| get id of the segment immediately upper to the loop More... | |
| std::string const & | loop_lower (components::StructureData const &perm) const |
| get id of the segment at the lower terminus of the first chain being connected More... | |
| void | set_loop_lower (components::StructureData &perm, std::string const &comp) const |
| set id of the lower component actually being connected More... | |
| std::string const & | loop_upper (components::StructureData const &perm) const |
| get id of the upper component actually being connected More... | |
| void | set_loop_upper (components::StructureData &perm, std::string const &comp) const |
| set id of the upper component actually being connected More... | |
| bool | performs_orientation () const |
| Class Member Variable Accessors/Mutators. More... | |
| void | set_performs_orientation (bool const or_val) |
| core::Size | lower_overlap () const |
| the number of residues adjacent to the loop to also include in remodeling More... | |
| core::Size | upper_overlap () const |
| void | set_overlap (core::Size const overlap_val) |
| sets overlap for both lower and upper segments More... | |
| void | set_lower_overlap (core::Size const overlap_val) |
| sets overlap for the lower segment only More... | |
| void | set_upper_overlap (core::Size const overlap_val) |
| sets overlap for the upper segment only More... | |
| bool | allow_cyclic () const |
| sets whether to allow components to connect to themselves to create cyclic peptides More... | |
| bool | do_remodel () const |
| void | set_do_remodel (bool const val) |
| core::Real | connecting_bond_dist () const |
| MotifList const & | motifs () const |
| Returns list of possible lengths/SS/Abegos. More... | |
| void | set_motifs (std::string const &motif_str) |
| set possible motifs of the connection with a comma-separated string More... | |
| void | set_motifs (utility::vector1< std::string > const &motif_strs) |
| set possible motifs of the connection with a vector of strings More... | |
| void | set_motifs (Connection::MotifList const &mlist) |
| utility::vector1< std::string > const & | comp1_ids () const |
| name of component1 More... | |
| void | set_comp1_ids (std::string const &id_str) |
| sets comp1 ids from a string More... | |
| void | set_comp1_ids (utility::vector1< std::string > const &id_list) |
| sets the list of options for component 1 More... | |
| utility::vector1< std::string > const & | comp2_ids () const |
| name of component2 More... | |
| void | set_comp2_ids (std::string const &id_str) |
| sets comp2 ids from a string More... | |
| void | set_comp2_ids (utility::vector1< std::string > const &id_list) |
| sets the list of options for component 1 More... | |
| bool | idealized_abego () const |
| Tells whether or not to construct motifs based on Nobu/Rie/YuRu abego rules. More... | |
| void | set_idealized_abego (bool const val) |
| core::Size | user_chain1 () const |
| returns user-set chain1 More... | |
| void | set_user_chain1 (core::Size const chain1) |
| core::Size | user_chain2 () const |
| returns user-set chain2 More... | |
| void | set_user_chain2 (core::Size const chain2) |
| void | set_check_abego (bool const val) |
| if set to true, abego of the build insert will be checked More... | |
| void | set_trials (core::Size const tr) |
| sets number of trials More... | |
| void | set_lengths (std::string const &length_str) |
| sets the list of acceptable lengths by parsing a string More... | |
| void | set_lengths (utility::vector1< core::Size > const &lengths_val) |
| set possible lengths of the connection with a vector More... | |
| void | set_cut_resis (std::string const &cut_str) |
| set possible cut residues (relative to the start of the loop) More... | |
| void | set_cut_resis (utility::vector1< core::Size > const &cuts_val) |
| set possible lengths of the connection with a vector More... | |
| void | disallow_pair (std::string const &c1, std::string const &c2) |
| sets the given pair of segments as not allowed More... | |
| bool | pair_allowed (std::string const &c1, std::string const &c2) const |
| returns true if this specific pairing of components hasn't been explicitly disallowed by the user More... | |
| void | clear_disallowed_pairs () |
| erases all information on disallowed pairs of segments More... | |
| void | set_allow_cyclic (bool const cyc_val) |
| sets whether to allow components to connect to themselves to create cyclic peptides More... | |
| void | set_extend_ss (bool const extend_ss) |
| sets whether or not to extend SS elements to try to connect them, or to use loop residues only. Default = true More... | |
| void | set_connecting_bond_dist (core::Real const val) |
| void | add_constraint_generator (protocols::moves::ConstraintGeneratorOP) |
| void | clear_constraint_generators () |
| void | setup (components::StructureData &perm) const |
| Performs pre-build setup and makes loop residues. More... | |
| bool | check_insert (core::pose::Pose const &pose, std::string const &build_ss, utility::vector1< std::string > const &build_abego, core::Size const left) const |
| checks the inserted region vs. the desired ss/abego. True if it matches, false otherwise More... | |
| Motif | parse_motif (std::string const &motif_str) const |
| parse a motif string, return a list of paired lengths and ss+abegos More... | |
| MotifList | parse_motifs (utility::vector1< std::string > const &motif_strs) const |
| utility::vector1< std::string > | find_available_upper_termini (components::StructureData const &perm) const |
| finds usable/available upper termini (i.e. those for comp1) More... | |
| utility::vector1< std::string > | find_available_lower_termini (components::StructureData const &perm) const |
| finds usable/available upper termini (i.e. those for comp1) More... | |
| MotifList | calc_idealized_motifs (std::string const &abego1, std::string const &abego2, std::set< core::Size > const &len_set) const |
| Given desired lengths, compute a set of idealized loop motifs via Nobu/Rie/YuRu rules. More... | |
| Public Member Functions inherited from protocols::denovo_design::components::NamedMover | |
| NamedMover () | |
| NamedMover (std::string const &id, std::string const &parent_id) | |
| virtual | ~NamedMover () |
| std::string const & | id () const |
| returns an identifier for this mover More... | |
| std::string const & | parent_id () const |
| returns the name of the parent mover More... | |
| void | set_parent_id (std::string const &parent) |
| sets an identifier for the parent of this mover, for nested moves More... | |
| StringList const & | segment_names () const |
| names of segment pieces built by this mover More... | |
| Public Member Functions inherited from protocols::moves::Mover | |
| Mover () | |
| virtual | ~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... | |
| Mover (Mover const &other) | |
| Mover & | operator= (Mover const &other) |
| assignment operator More... | |
| virtual core::Real | last_proposal_density_ratio () |
| std::string const & | type () const |
| void | set_type (std::string const &setting) |
| 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 | set_current_tag (std::string const &new_tag) |
| 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 |
| 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... | |
| void | type (const std::string &type_in) |
| std::string | get_type () const |
| 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... | |
| 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 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... | |
| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
| jobdist::BasicJobCOP | get_current_job () const |
| virtual void | show (std::ostream &output=std::cout) const |
| Outputs details about the Mover, including current settings. More... | |
Additional Inherited Members | |
| Public Types inherited from protocols::denovo_design::connection::Connection | |
| typedef utility::vector1< Motif > | MotifList |
| Public Types inherited from protocols::moves::Mover | |
| typedef utility::tag::TagCOP | TagCOP |
| typedef core::pose::Pose | Pose |
| typedef core::pose::PoseCOP | PoseCOP |
| typedef protocols::filters::Filters_map | Filters_map |
| typedef std::list< std::string > | Strings |
| 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... | |
| Protected Member Functions inherited from protocols::denovo_design::connection::Connection | |
| std::pair< utility::vector1 < std::string > , utility::vector1 < std::string > > | clear_segments_and_compute_valid_segment_values (components::StructureData &perm) const |
| Connection::ConnectionInfo | select_connection_info (components::StructureData const &perm, utility::vector1< std::string > const &valid_segment1_ids, utility::vector1< std::string > const &valid_segment2_ids, core::Real &random) const |
| void | setup_from_connection_info (components::StructureData &perm, core::Real &random, ConnectionInfo const &c_info) const |
| components::StructureDataOP | create_loop_sd (std::pair< std::string, std::string > const &c1, std::pair< std::string, std::string > const &c2, Motif const &motif, core::Real &random) const |
| void | move_segments (components::StructureData &perm, StringList const &desired_order) const |
| void | move_segments_cyclic (components::StructureData &perm) const |
| void | connect_lower_loop (components::StructureData &perm) const |
| void | connect_upper_loop (components::StructureData &perm) const |
| void | post_process_permutation (components::StructureData &perm) const |
| performs post-connection-building tasks More... | |
| virtual void | setup_structuredata (components::StructureData &perm, core::Size const len, std::string const &ss, std::string const &abego, std::string const &seg1, std::string const &seg2, std::string const &seg1_lower, std::string const &seg2_upper, core::Size const cut_resi_val) const |
| void | parse_subtag (utility::tag::TagCOP tag, protocols::moves::Movers_map const &movers) |
| parses subtag More... | |
| void | apply_constraints (components::StructureData &sd) const |
| void | remove_constraints (components::StructureData &sd) const |
| Protected Member Functions inherited from protocols::denovo_design::components::NamedMover | |
| std::string | add_parent_prefix (std::string const &s) const |
| adds prefix if necessary, returns result More... | |
| void | add_segment_name (std::string const &sname) |
| adds a segment name More... | |
| void | set_segment_names (StringList const &snames) |
| sets segment names More... | |
| void | clear_segment_names () |
| clears segment names More... | |
| 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... | |
"Dummy" connection used when we wnat to track connection information but not build anything
| protocols::denovo_design::connection::GenericConnection::GenericConnection | ( | ) |
"Dummy" connection used when we wnat to track connection information but not build anything
References protocols::denovo_design::connection::Connection::set_performs_orientation().
Referenced by clone(), and fresh_instance().
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applies the loop building, in this case does nothing
| EXCN_ConnectionFailed | on failure to connect |
Implements protocols::denovo_design::connection::Connection.
References protocols::denovo_design::connection::Connection::loop_lower(), protocols::denovo_design::connection::Connection::loop_upper(), polymer_connection(), and protocols::denovo_design::connection::staple_work_function().
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check whether the given segments are connectable
Reimplemented from protocols::denovo_design::connection::Connection.
References protocols::denovo_design::connection::Connection::allow_cyclic(), protocols::denovo_design::components::StructureData::are_connectable(), protocols::denovo_design::connection::Connection::connecting_bond_dist(), and protocols::denovo_design::connection::Connection::Motif::len.
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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.
References GenericConnection().
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Generates a new Mover object freshly created with the default ctor.
fresh_instance is meant to return a new object of this class, created with the default constructor. 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. This is used by the August 08 job distributor.
Reimplemented from protocols::moves::Mover.
References GenericConnection().
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Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
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inlinevirtual |
derived classes should return true if the Connection forms a polymer bond (e.g. peptide) and false if it forms another type of chemical linkage (e.g. disulfide)
Implements protocols::denovo_design::connection::Connection.
Referenced by apply_connection().
1.8.7