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Rosetta 3.5
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All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
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Rosetta 3.5
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designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines. More...
#include <Splice.hh>
Public Types | |
| typedef core::pose::Pose | Pose |
| typedef utility::vector1 < ResidueBBDofs > ::const_iterator | dbase_const_iterator |
 Public Types inherited from protocols::moves::Mover | |
| typedef utility::tag::TagPtr | TagPtr |
| typedef core::pose::Pose | Pose |
| typedef core::pose::PoseCOP | PoseCOP |
| typedef protocols::filters::Filters_map | Filters_map |
| typedef std::list< std::string > | Strings |
Public Member Functions | |
| Splice () | |
| void | apply (Pose &pose) |
| virtual std::string | get_name () const |
| Each derived class must specify its name. The class name. More... | |
| protocols::moves::MoverOP | clone () const |
| clone has to be overridden only if clone invocation is expected. More... | |
| protocols::moves::MoverOP | fresh_instance () const |
| this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More... | |
| void | parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &) |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
| virtual | ~Splice () |
| void | from_res (core::Size const f) |
| core::Size | from_res () const |
| void | to_res (core::Size const t) |
| core::Size | to_res () const |
| std::string | source_pdb () const |
| void | source_pdb (std::string const s) |
| void | ccd (bool const c) |
| bool | ccd () const |
| void | scorefxn (core::scoring::ScoreFunctionOP sf) |
| core::scoring::ScoreFunctionOP | scorefxn () const |
| core::Real | rms_cutoff () const |
| void | rms_cutoff (core::Real const r) |
| void | res_move (core::Size const r) |
| core::Size | res_move () const |
| void | randomize_cut (bool const r) |
| bool | randomize_cut () const |
| void | cut_secondarystruc (bool const r) |
| bool | cut_secondarystruc () const |
| core::pack::task::TaskFactoryOP | task_factory () const |
| void | task_factory (core::pack::task::TaskFactoryOP tf) |
| core::pack::task::TaskFactoryOP | design_task_factory () const |
| void | design_task_factory (core::pack::task::TaskFactoryOP tf) |
| std::string | torsion_database_fname () const |
| void | torsion_database_fname (std::string const d) |
| core::Size | database_entry () const |
| void | database_entry (core::Size const d) |
| void | read_torsion_database () |
| utility::vector1< ResidueBBDofs > | torsion_database () const |
| void | torsion_database (utility::vector1< ResidueBBDofs > const d) |
| std::string | template_file () const |
| void | template_file (std::string const s) |
| void | poly_ala (bool const p) |
| bool | poly_ala () const |
| void | equal_length (bool const e) |
| bool | equal_length () const |
| void | fold_tree (core::pose::Pose &pose, core::Size const start, core::Size const stop, core::Size const cut) const |
| set the fold tree around start/stop/cut sites. presently makes a simple fold tree, but at one point may be a more complicated function to include two poses More... | |
| bool | design () const |
| void | design (bool const d) |
| void | delta_lengths (utility::vector1< int > const dl) |
| utility::vector1< int > | delta_lengths () |
| bool | dbase_iterate () const |
| void | dbase_iterate (bool const d) |
| utility::vector1< core::Size > ::const_iterator | dbase_begin () const |
| utility::vector1< core::Size > ::const_iterator | dbase_end () const |
| core::Size | find_dbase_entry (core::pose::Pose const &pose) |
| controls which dbase entry will be used. Three options: 1. specific one according to user instruction; 2. randomized out of a subset of the dbase with fitting sequence lengths (if user specified 0); 3. iterating over dbase subset More... | |
| core::Size | locked_res () const |
| void | locked_res (core::Size const r) |
| void | locked_res_id (char const c) |
| char | locked_res_id () const |
| std::string | checkpointing_file () const |
| void | checkpointing_file (std::string const cf) |
| void | load_from_checkpoint () |
| void | save_to_checkpoint () const |
| std::string | loop_dbase_file_name () const |
| void | loop_dbase_file_name (std::string const f) |
| void | loop_pdb_source (std::string const l) |
| std::string | loop_pdb_source () const |
| protocols::filters::FilterOP | splice_filter () const |
| void | splice_filter (protocols::filters::FilterOP f) |
| void | database_pdb_entry (std::string const s) |
| std::string | database_pdb_entry () const |
| void | read_splice_segments (std::string const segment_type, std::string const segment_name, std::string const file_name) |
| core::sequence::SequenceProfileOP | generate_sequence_profile () |
| void | load_pdb_segments_from_pose_comments (core::pose::Pose const &p) |
| void | modify_pdb_segments_with_current_segment (std::string const pdb_name) |
| void | add_sequence_constraints (core::pose::Pose &pose) |
| void | profile_weight_away_from_interface (core::Real const p) |
| core::Real | profile_weight_away_from_interface () const |
| Public Member Functions inherited from protocols::moves::Mover | |
| Mover () | |
| virtual | ~Mover () |
| virtual MoverSP | create () |
| virtual void | apply (core::io::serialization::PipeMap &pmap) |
| virtual void | parse_state (SerializableState const &state) |
| virtual void | parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache) |
| virtual void | save_state (SerializableState &state) |
| 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 |
| 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... | |
| 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 |
| this function informs 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 |
| this function informs 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 |
Private Member Functions | |
| void | save_values () |
| void | retrieve_values () |
Additional Inherited Members | |
| 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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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... | |
designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines.
| typedef utility::vector1< ResidueBBDofs >::const_iterator protocols::protein_interface_design::movers::Splice::dbase_const_iterator |
| protocols::protein_interface_design::movers::Splice::Splice | ( | ) |
Definition at line 100 of file Splice.cc.
References dbase_subset_, delta_lengths_, end_dbase_subset_, pdb_segments_, splice_segments_, and torsion_database_.
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| void protocols::protein_interface_design::movers::Splice::add_sequence_constraints | ( | core::pose::Pose & | pose) |
Definition at line 1139 of file Splice.cc.
References core::pose::Pose::add_constraint(), core::pack::dunbrack::c, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), protocols::protein_interface_design::movers::find_residues_on_chain1_outside_interface(), core::pose::Pose::remove_constraint(), and core::scoring::res_type_constraint.
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Implements protocols::moves::Mover.
Definition at line 310 of file Splice.cc.
References core::chemical::aa_from_name(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::simple_moves::PackRotamersMover::apply(), protocols::protein_interface_design::movers::ResidueBBDofs::clear(), core::io::serialization::clone(), core::pose::Pose::conformation(), protocols::protein_interface_design::movers::copy_stretch(), protocols::toolbox::task_operations::DesignAroundOperation::design_shell(), core::conformation::Conformation::detect_disulfides(), core::chemical::DISULFIDE, core::scoring::dssp::Dssp::dssp_reduced(), protocols::moves::FAIL_DO_NOT_RETRY, protocols::moves::FAIL_RETRY, protocols::rosetta_scripts::find_nearest_res(), core::pose::Pose::fold_tree(), core::scoring::dssp::Dssp::get_dssp_secstruct(), core::conformation::Residue::has_variant_type(), protocols::toolbox::task_operations::DesignAroundOperation::include_residue(), protocols::protein_interface_design::movers::LoopLengthChange::loop_start(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::move_map(), protocols::moves::MS_SUCCESS, core::conformation::Residue::name1(), core::conformation::Residue::name3(), core::conformation::Conformation::num_chains(), protocols::protein_interface_design::movers::BBDofs::omega(), core::scoring::omega, core::pose::Pose::omega(), core::chemical::oneletter_code_from_aa(), protocols::protein_interface_design::movers::BBDofs::phi(), protocols::swa::phi(), core::pose::Pose::phi(), core::import_pose::pose_from_pdb(), protocols::protein_interface_design::movers::BBDofs::psi(), protocols::swa::psi(), core::pose::Pose::psi(), protocols::protein_interface_design::movers::BBDofs::resid(), core::pose::Pose::residue(), protocols::rosetta_scripts::residue_packer_states(), protocols::protein_interface_design::movers::BBDofs::resn(), protocols::protein_interface_design::movers::AddChainBreak::resnum(), core::scoring::rms, core::kinematics::MoveMap::set_chi(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_task_factory(), protocols::toolbox::task_operations::ThreadSequenceOperation::target_sequence(), protocols::protein_interface_design::filters::Torsion::task_factory(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::temp_final(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::temp_initial(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().
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Definition at line 112 of file Splice.hh.
References core::pack::dunbrack::c, and ccd_.
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| std::string protocols::protein_interface_design::movers::Splice::checkpointing_file | ( | ) | const |
| void protocols::protein_interface_design::movers::Splice::checkpointing_file | ( | std::string const | cf) |
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clone has to be overridden only if clone invocation is expected.
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.
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Definition at line 122 of file Splice.hh.
References cut_secondarystruc_.
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Definition at line 123 of file Splice.hh.
References cut_secondarystruc_.
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Definition at line 131 of file Splice.hh.
References database_entry_.
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Definition at line 132 of file Splice.hh.
References database_entry_.
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Definition at line 168 of file Splice.hh.
References database_pdb_entry_.
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Definition at line 169 of file Splice.hh.
References database_pdb_entry_.
| utility::vector1< core::Size >::const_iterator protocols::protein_interface_design::movers::Splice::dbase_begin | ( | ) | const |
| utility::vector1< core::Size >::const_iterator protocols::protein_interface_design::movers::Splice::dbase_end | ( | ) | const |
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Definition at line 147 of file Splice.hh.
References dbase_iterate_.
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Definition at line 148 of file Splice.hh.
References dbase_iterate_.
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Definition at line 145 of file Splice.hh.
References delta_lengths_.
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Definition at line 146 of file Splice.hh.
References delta_lengths_.
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| core::pack::task::TaskFactoryOP protocols::protein_interface_design::movers::Splice::design_task_factory | ( | ) | const |
| void protocols::protein_interface_design::movers::Splice::design_task_factory | ( | core::pack::task::TaskFactoryOP | tf) |
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Definition at line 140 of file Splice.hh.
References equal_length_.
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Definition at line 141 of file Splice.hh.
References equal_length_.
| core::Size protocols::protein_interface_design::movers::Splice::find_dbase_entry | ( | core::pose::Pose const & | pose) |
controls which dbase entry will be used. Three options: 1. specific one according to user instruction; 2. randomized out of a subset of the dbase with fitting sequence lengths (if user specified 0); 3. iterating over dbase subset
Definition at line 246 of file Splice.cc.
References protocols::rosetta_scripts::find_nearest_res(), protocols::protein_interface_design::movers::RG(), protocols::protein_interface_design::movers::ResidueBBDofs::size(), protocols::protein_interface_design::movers::ResidueBBDofs::start_loop(), and protocols::protein_interface_design::movers::ResidueBBDofs::stop_loop().
| void protocols::protein_interface_design::movers::Splice::fold_tree | ( | core::pose::Pose & | pose, |
| core::Size const | start, | ||
| core::Size const | stop, | ||
| core::Size const | cut | ||
| ) | const |
set the fold tree around start/stop/cut sites. presently makes a simple fold tree, but at one point may be a more complicated function to include two poses
Definition at line 930 of file Splice.cc.
References core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), core::chemical::DISULFIDE, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::name3(), protocols::protein_interface_design::optimal_connection_point(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().
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this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).
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.
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| core::sequence::SequenceProfileOP protocols::protein_interface_design::movers::Splice::generate_sequence_profile | ( | ) |
Definition at line 1085 of file Splice.cc.
References protocols::protein_interface_design::movers::concatenate_profiles().
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Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
Definition at line 718 of file Splice.cc.
References protocols::protein_interface_design::movers::SpliceCreator::mover_name().
| void protocols::protein_interface_design::movers::Splice::load_from_checkpoint | ( | ) |
The checkpointing file has the following structure: the first line contains an ordered list of the dbase_subset_ for splice to iterate over the loop database. The second line contains the last element tested (the loop-entry number in the database; not the iterator to it!) and the third line contains the best element tested (again, the loop number from the database, not the iterator!). To recover from a checkpoint the following reads the dbase_subset_ then, if this is a first_pass_ the best entry becomes current, and if it is not a first_pass then the current entry is current.
| void protocols::protein_interface_design::movers::Splice::load_pdb_segments_from_pose_comments | ( | core::pose::Pose const & | p) |
Definition at line 1101 of file Splice.cc.
References core::pose::get_all_comments().
| core::Size protocols::protein_interface_design::movers::Splice::locked_res | ( | ) | const |
| void protocols::protein_interface_design::movers::Splice::locked_res | ( | core::Size const | r) |
| void protocols::protein_interface_design::movers::Splice::locked_res_id | ( | char const | c) |
Definition at line 1037 of file Splice.cc.
References core::pack::dunbrack::c.
| char protocols::protein_interface_design::movers::Splice::locked_res_id | ( | ) | const |
| std::string protocols::protein_interface_design::movers::Splice::loop_dbase_file_name | ( | ) | const |
| void protocols::protein_interface_design::movers::Splice::loop_dbase_file_name | ( | std::string const | f) |
| void protocols::protein_interface_design::movers::Splice::loop_pdb_source | ( | std::string const | l) |
| std::string protocols::protein_interface_design::movers::Splice::loop_pdb_source | ( | ) | const |
| void protocols::protein_interface_design::movers::Splice::modify_pdb_segments_with_current_segment | ( | std::string const | pdb_name) |
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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 stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.
Reimplemented from protocols::moves::Mover.
Definition at line 723 of file Splice.cc.
References protocols::moves::DataMap::add(), protocols::moves::DataMap::get(), protocols::moves::get_set_from_datamap(), protocols::moves::DataMap::has(), core::conformation::Residue::name1(), protocols::rosetta_scripts::parse_filter(), core::pose::parse_resnum(), protocols::rosetta_scripts::parse_score_function(), protocols::rosetta_scripts::parse_task_operations(), core::import_pose::pose_from_pdb(), and core::pose::Pose::residue().
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| void protocols::protein_interface_design::movers::Splice::profile_weight_away_from_interface | ( | core::Real const | p) |
| core::Real protocols::protein_interface_design::movers::Splice::profile_weight_away_from_interface | ( | ) | const |
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Definition at line 120 of file Splice.hh.
References randomize_cut_.
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Definition at line 121 of file Splice.hh.
References randomize_cut_.
| void protocols::protein_interface_design::movers::Splice::read_splice_segments | ( | std::string const | segment_type, |
| std::string const | segment_name, | ||
| std::string const | file_name | ||
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| void protocols::protein_interface_design::movers::Splice::read_torsion_database | ( | ) |
the torsion dbase should have the following structure: each line represents a single loop. Each four values represent <phi> <psi> <omega> <3-let resid>; the last entry in a line represents <loop start>=""> <loop stop>=""> <cut site>=""> cut; where cut signifies that this is the loop designator
Definition at line 892 of file Splice.cc.
References protocols::protein_interface_design::movers::ResidueBBDofs::clear(), protocols::protein_interface_design::movers::ResidueBBDofs::cut_site(), core::scoring::omega, protocols::swa::phi(), protocols::swa::psi(), protocols::protein_interface_design::movers::ResidueBBDofs::push_back(), protocols::protein_interface_design::movers::ResidueBBDofs::source_pdb(), protocols::protein_interface_design::movers::ResidueBBDofs::start_loop(), and protocols::protein_interface_design::movers::ResidueBBDofs::stop_loop().
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Definition at line 116 of file Splice.hh.
References rms_cutoff_.
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Definition at line 117 of file Splice.hh.
References rms_cutoff_.
| void protocols::protein_interface_design::movers::Splice::save_to_checkpoint | ( | ) | const |
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splice apply might change the from_res/to_res internals since they sometimes refer to the template file. If that happens, we want the values to revert to their original values before the end of the apply function (so retrieve_values) below must be called before return.
| void protocols::protein_interface_design::movers::Splice::scorefxn | ( | core::scoring::ScoreFunctionOP | sf) |
| core::scoring::ScoreFunctionOP protocols::protein_interface_design::movers::Splice::scorefxn | ( | ) | const |
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Definition at line 110 of file Splice.hh.
References source_pdb_.
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Definition at line 111 of file Splice.hh.
References source_pdb_.
| protocols::filters::FilterOP protocols::protein_interface_design::movers::Splice::splice_filter | ( | ) | const |
| void protocols::protein_interface_design::movers::Splice::splice_filter | ( | protocols::filters::FilterOP | f) |
| core::pack::task::TaskFactoryOP protocols::protein_interface_design::movers::Splice::task_factory | ( | ) | const |
| void protocols::protein_interface_design::movers::Splice::task_factory | ( | core::pack::task::TaskFactoryOP | tf) |
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Definition at line 136 of file Splice.hh.
References template_file_.
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Definition at line 137 of file Splice.hh.
References template_file_.
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Definition at line 108 of file Splice.hh.
References core::scoring::hbonds::t(), and to_res_.
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Definition at line 134 of file Splice.hh.
References torsion_database_.
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Definition at line 135 of file Splice.hh.
References torsion_database_.
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Definition at line 129 of file Splice.hh.
References torsion_database_fname_.
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Definition at line 130 of file Splice.hh.
References torsion_database_fname_.
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Definition at line 193 of file Splice.hh.
Referenced by cut_secondarystruc().
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Definition at line 197 of file Splice.hh.
Referenced by database_entry().
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Definition at line 198 of file Splice.hh.
Referenced by database_pdb_entry().
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Definition at line 207 of file Splice.hh.
Referenced by dbase_iterate().
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Definition at line 206 of file Splice.hh.
Referenced by delta_lengths(), and Splice().
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dflt true; thread ala residues in each position other than Gly/Pro or conserved in the source pdb. If false, keeps the input sequence (except Gly/Pro, which are replaced)
Definition at line 202 of file Splice.hh.
Referenced by equal_length().
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Definition at line 186 of file Splice.hh.
Referenced by from_res().
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Definition at line 201 of file Splice.hh.
Referenced by poly_ala().
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Definition at line 192 of file Splice.hh.
Referenced by randomize_cut().
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Definition at line 191 of file Splice.hh.
Referenced by res_move().
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Definition at line 190 of file Splice.hh.
Referenced by rms_cutoff().
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Definition at line 187 of file Splice.hh.
Referenced by source_pdb().
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Definition at line 200 of file Splice.hh.
Referenced by template_file().
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Definition at line 199 of file Splice.hh.
Referenced by Splice(), and torsion_database().
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Definition at line 196 of file Splice.hh.
Referenced by torsion_database_fname().
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1.8.4