a mover that sets a user-defined atom tree More...
#include <SetAtomTree.hh>
Public Member Functions | |
| SetAtomTree () | |
| ~SetAtomTree () override | |
| Commenting out to fix PyRosetta build SetAtomTree( core::kinematics::FoldTreeOP ft );. More... | |
| void | apply (core::pose::Pose &pose) override |
| protocols::moves::MoverOP | clone () const override |
| Return a clone of the Mover object. More... | |
| protocols::moves::MoverOP | fresh_instance () const override |
| Generates a new Mover object freshly created with the default ctor. More... | |
| void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
| core::kinematics::FoldTreeOP | create_atom_tree (core::pose::Pose const &pose, core::Size const host_chain, core::Size const resnum, core::Size const anchor_num_=0, std::string const &connect_to="", std::string const &connect_from="") |
| bool | simple_ft () const |
| void | simple_ft (bool const s) |
| void | set_ab_fold_tree (core::pose::Pose &pose) |
| void | two_parts_chain1 (bool const t) |
| bool | two_parts_chain1 () const |
| core::kinematics::FoldTreeOP | fold_tree () const |
| void | fold_tree (core::kinematics::FoldTreeOP ft_) |
| char | start_tree_at_chain () const |
| void | start_tree_at_chain (char const c) |
| void | ab_fold_tree (bool b) |
| bool | ab_fold_tree () |
| void | update_residue_variants (bool b) |
| bool | update_residue_variants () |
| void | add_cutpoint_variants (core::pose::Pose &pose) |
| void | chain (core::Size i) |
| core::Size | chain () |
| 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... | |
| 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... | |
Private Attributes | |
| bool | docking_ft_ |
| bool | simple_ft_ |
| bool | two_parts_chain1_ |
| char | start_tree_at_chain_ |
| core::Size | jump_ |
| std::string | partners_ |
| std::string | resnum_ |
| std::string | connect_to_ |
| std::string | anchor_res_ |
| std::string | connect_from_ |
| core::Size | host_chain_ |
| core::kinematics::FoldTreeOP | fold_tree_ |
| bool | ab_fold_tree_ |
| bool | update_residue_variants_ |
| std::string | remark_foldtree_ |
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 sets a user-defined atom tree
Constructor & Destructor Documentation
◆ SetAtomTree()
| protocols::protein_interface_design::movers::SetAtomTree::SetAtomTree | ( | ) |
References start_tree_at_chain_.
◆ ~SetAtomTree()
|
overridedefault |
Commenting out to fix PyRosetta build SetAtomTree( core::kinematics::FoldTreeOP ft );.
Member Function Documentation
◆ ab_fold_tree() [1/2]
|
inline |
References ab_fold_tree_.
Referenced by parse_my_tag().
◆ ab_fold_tree() [2/2]
|
inline |
References ab_fold_tree_, and protocols::match::upstream::b.
Referenced by protocols::splice::SpliceInAntibody::adjust_template_jump().
◆ add_cutpoint_variants()
| void protocols::protein_interface_design::movers::SetAtomTree::add_cutpoint_variants | ( | core::pose::Pose & | pose | ) |
References core::pose::correctly_add_cutpoint_variants(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::chemical::UPPER_TERMINUS_VARIANT.
Referenced by apply().
◆ apply()
|
overridevirtual |
Commenting out to fix PyRosetta build void fold_tree( core::kinematics::FoldTreeOP ft ); Commenting out to fix PyRosetta build core::kinematics::FoldTreeOP fold_tree() const;
Implements protocols::moves::Mover.
References ab_fold_tree_, add_cutpoint_variants(), core::kinematics::FoldTree::add_edge(), protocols::protein_interface_design::movers::anchor_num, anchor_res_, protocols::simple_moves::CutChainMover::bond_length(), chain(), core::conformation::Conformation::chain_begin(), protocols::simple_moves::CutChainMover::chain_cut(), core::conformation::Conformation::chain_end(), protocols::simple_moves::CutChainMover::chain_id(), core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), protocols::protein_interface_design::movers::connect_from(), connect_from_, protocols::protein_interface_design::movers::connect_to(), connect_to_, create_atom_tree(), core::kinematics::FoldTree::delete_self_edges(), docking_ft_, core::pose::PDBPoseMap::find(), core::pose::Pose::fold_tree(), fold_tree_, core::pose::get_comment(), host_chain_, jump_, protocols::mean_field::max(), protocols::mean_field::min(), core::conformation::Residue::name3(), core::conformation::Conformation::num_chains(), protocols::protein_interface_design::optimal_connection_point(), core::pose::parse_resnum(), partners_, core::pose::Pose::pdb_info(), remark_foldtree_, core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), core::conformation::symmetry::residue_center_of_mass(), core::pose::residue_center_of_mass(), resnum_, set_ab_fold_tree(), protocols::docking::setup_foldtree(), simple_ft(), start_tree_at_chain(), protocols::protein_interface_design::movers::TR(), two_parts_chain1(), and update_residue_variants_.
Referenced by protocols::splice::SpliceInAntibody::adjust_template_jump(), and protocols::splice::DesignInterfacesOperation::apply().
◆ chain() [1/2]
|
inline |
References host_chain_.
Referenced by apply().
◆ chain() [2/2]
|
inline |
References host_chain_.
Referenced by protocols::splice::SpliceInAntibody::adjust_template_jump().
◆ 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.
◆ create_atom_tree()
| core::kinematics::FoldTreeOP protocols::protein_interface_design::movers::SetAtomTree::create_atom_tree | ( | core::pose::Pose const & | pose, |
| core::Size const | host_chain, | ||
| core::Size const | resnum, | ||
| core::Size const | anchor_num_ = 0, |
||
| std::string const & | connect_to = "", |
||
| std::string const & | connect_from = "" |
||
| ) |
References protocols::protein_interface_design::movers::anchor_num, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), protocols::protein_interface_design::movers::connect_from(), protocols::protein_interface_design::movers::connect_to(), core::kinematics::distance(), core::sequence::end, fold_tree(), core::conformation::Residue::name3(), core::conformation::Residue::nbr_atom(), protocols::protein_interface_design::optimal_connection_point(), protocols::make_rot_lib::PEPTIDE, core::pose::Pose::residue(), core::pose::Pose::size(), protocols::protein_interface_design::movers::TR(), and core::conformation::Residue::xyz().
Referenced by apply(), and protocols::protein_interface_design::movers::PlaceStubMover::stub_based_atom_tree().
◆ fold_tree() [1/2]
| core::kinematics::FoldTreeOP protocols::protein_interface_design::movers::SetAtomTree::fold_tree | ( | ) | const |
References fold_tree_.
Referenced by create_atom_tree().
◆ fold_tree() [2/2]
| void protocols::protein_interface_design::movers::SetAtomTree::fold_tree | ( | core::kinematics::FoldTreeOP | ft_ | ) |
References fold_tree_.
◆ fresh_instance()
|
inlineoverridevirtual |
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.
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
References mover_name().
◆ 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 ab_fold_tree(), anchor_res_, connect_from_, connect_to_, docking_ft_, fold_tree_, host_chain_, jump_, partners_, remark_foldtree_, resnum_, simple_ft(), start_tree_at_chain(), protocols::protein_interface_design::movers::TR(), two_parts_chain1(), and update_residue_variants().
◆ provide_xml_schema()
|
static |
◆ set_ab_fold_tree()
| void protocols::protein_interface_design::movers::SetAtomTree::set_ab_fold_tree | ( | core::pose::Pose & | pose | ) |
References core::kinematics::FoldTree::add_edge(), core::conformation::Conformation::chain_begin(), protocols::simple_moves::CutChainMover::chain_cut(), core::conformation::Conformation::chain_end(), core::kinematics::FoldTree::check_fold_tree(), core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), core::kinematics::FoldTree::delete_self_edges(), core::chemical::DISULFIDE, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), host_chain_, core::conformation::Conformation::num_chains(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), core::pose::residue_center_of_mass(), and protocols::protein_interface_design::movers::TR().
Referenced by apply().
◆ simple_ft() [1/2]
|
inline |
References simple_ft_.
Referenced by apply(), and parse_my_tag().
◆ simple_ft() [2/2]
|
inline |
References simple_ft_.
◆ start_tree_at_chain() [1/2]
|
inline |
References start_tree_at_chain_.
Referenced by apply(), and parse_my_tag().
◆ start_tree_at_chain() [2/2]
|
inline |
References start_tree_at_chain_.
◆ two_parts_chain1() [1/2]
|
inline |
References two_parts_chain1_.
Referenced by apply(), and parse_my_tag().
◆ two_parts_chain1() [2/2]
|
inline |
References protocols::hybridization::t, and two_parts_chain1_.
Referenced by protocols::splice::DesignInterfacesOperation::apply().
◆ update_residue_variants() [1/2]
|
inline |
References update_residue_variants_.
Referenced by parse_my_tag().
◆ update_residue_variants() [2/2]
|
inline |
References protocols::match::upstream::b, and update_residue_variants_.
Member Data Documentation
◆ ab_fold_tree_
|
private |
Referenced by ab_fold_tree(), and apply().
◆ anchor_res_
|
private |
Referenced by apply(), and parse_my_tag().
◆ connect_from_
|
private |
Referenced by apply(), and parse_my_tag().
◆ connect_to_
|
private |
Referenced by apply(), and parse_my_tag().
◆ docking_ft_
|
private |
Referenced by apply(), and parse_my_tag().
◆ fold_tree_
|
private |
Referenced by apply(), fold_tree(), and parse_my_tag().
◆ host_chain_
|
private |
Referenced by apply(), chain(), parse_my_tag(), and set_ab_fold_tree().
◆ jump_
|
private |
Referenced by apply(), and parse_my_tag().
◆ partners_
|
private |
Referenced by apply(), and parse_my_tag().
◆ remark_foldtree_
|
private |
Referenced by apply(), and parse_my_tag().
◆ resnum_
|
private |
Referenced by apply(), and parse_my_tag().
◆ simple_ft_
|
private |
Referenced by simple_ft().
◆ start_tree_at_chain_
|
private |
Referenced by SetAtomTree(), and start_tree_at_chain().
◆ two_parts_chain1_
|
private |
Referenced by two_parts_chain1().
◆ update_residue_variants_
|
private |
Referenced by apply(), and update_residue_variants().
The documentation for this class was generated from the following files:
- src/protocols/protein_interface_design/movers/SetAtomTree.hh
- src/protocols/protein_interface_design/movers/SetAtomTree.cc
