A mover that removes the connections to metals that were added by the SetupMetalsMover or by the -auto_setup_metals flag. More...
#include <RemoveMetalConnectionsMover.hh>
Public Member Functions | |
| RemoveMetalConnectionsMover () | |
| Constructors ///. More... | |
| ~RemoveMetalConnectionsMover () override | |
| Destructor (important for properly forward-declaring smart-pointer members) More... | |
| void | apply (core::pose::Pose &pose) override |
| Mover Methods ///. More... | |
| void | show (std::ostream &output=std::cout) const override |
| Summarize this mover's configuration. More... | |
| void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override |
| Rosetta Scripts Support ///. More... | |
| protocols::moves::MoverOP | fresh_instance () const override |
| required in the context of the parser/scripting scheme. More... | |
| protocols::moves::MoverOP | clone () const override |
| required in the context of the parser/scripting scheme. More... | |
| std::string | get_name () const override |
| Returns "RemoveMetalConnectionsMover". More... | |
| void | set_residue_selector (core::select::residue_selector::ResidueSelectorCOP const &selector_in) |
| Sets the residue selector for selecting residues from which metal bonds will be removed. More... | |
| core::select::residue_selector::ResidueSelectorCOP | residue_selector () const |
| Gets the residue selector for selecting residues from which metal bonds will be removed. More... | |
| void | provide_citation_info (basic::citation_manager::CitationCollectionList &citations) const override |
| Provide citations to the passed CitationCollectionList. 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 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... | |
Static Public Member Functions | |
| static std::string | mover_name () |
| Returns "RemoveMetalConnectionsMover". Useful in situations in which an instance is not available. More... | |
| static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
| Provide a user- or machine-readable description of this mover's XML interface. More... | |
| 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 Member Functions | |
| void | remove_variant_types_from_res (core::pose::Pose &pose, core::Size const resindex, std::string const &this_atom, bool const this_is_metal) const |
| Remove one or two variant types from a pose residue. More... | |
Private Attributes | |
| core::select::residue_selector::ResidueSelectorCOP | residue_selector_ |
| Residue selector for residues to remove bonds from. 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 removes the connections to metals that were added by the SetupMetalsMover or by the -auto_setup_metals flag.
This mover:
- Removes the bonds between metals and metal-binding residues.
- Reverts metal-liganding residues back to their pre-bonded types.
- Reverts metals back to their pre-bonded types.
Constructor & Destructor Documentation
◆ RemoveMetalConnectionsMover()
| protocols::metal_interface::RemoveMetalConnectionsMover::RemoveMetalConnectionsMover | ( | ) |
Constructors ///.
Default constructor
◆ ~RemoveMetalConnectionsMover()
|
overridedefault |
Destructor (important for properly forward-declaring smart-pointer members)
Member Function Documentation
◆ apply()
|
overridevirtual |
Mover Methods ///.
Apply the mover.
Apply the mover
Implements protocols::moves::Mover.
References core::chemical::ResidueType::atom_name(), core::chemical::ResidueTypeBase::base_name(), core::pose::Pose::conformation(), core::conformation::Residue::connected_residue_at_resconn(), core::conformation::Residue::connection_incomplete(), core::chemical::ResidueType::is_metal(), core::chemical::ResidueType::is_metalbinding(), remove_variant_types_from_res(), core::pose::Pose::residue(), core::chemical::ResidueType::residue_connect_atom_index(), core::conformation::Residue::residue_connection_conn_id(), residue_selector_, core::pose::Pose::residue_type(), core::conformation::Conformation::sever_chemical_bond(), core::pose::Pose::total_residue(), and protocols::TR().
◆ clone()
|
overridevirtual |
required in the context of the parser/scripting scheme.
required in the context of the parser/scripting scheme
Reimplemented from protocols::moves::Mover.
◆ fresh_instance()
|
overridevirtual |
required in the context of the parser/scripting scheme.
required in the context of the parser/scripting scheme
Reimplemented from protocols::moves::Mover.
◆ get_name()
|
overridevirtual |
◆ mover_name()
|
static |
Returns "RemoveMetalConnectionsMover". Useful in situations in which an instance is not available.
Referenced by get_name(), protocols::metal_interface::RemoveMetalConnectionsMoverCreator::keyname(), and provide_xml_schema().
◆ parse_my_tag()
|
overridevirtual |
Rosetta Scripts Support ///.
parse XML tag (to use this Mover in Rosetta Scripts)
Reimplemented from protocols::moves::Mover.
References core::select::residue_selector::parse_residue_selector(), and set_residue_selector().
◆ provide_citation_info()
|
overridevirtual |
Provide citations to the passed CitationCollectionList.
This mover is unpublished. It returns Vikram K. Mulligan as its author.
Reimplemented from protocols::moves::Mover.
References residue_selector_.
◆ provide_xml_schema()
|
static |
Provide a user- or machine-readable description of this mover's XML interface.
References core::select::residue_selector::attributes_for_parse_residue_selector(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().
Referenced by protocols::metal_interface::RemoveMetalConnectionsMoverCreator::provide_xml_schema().
◆ remove_variant_types_from_res()
|
private |
Remove one or two variant types from a pose residue.
Private methods ///.
Based on name lookup, so hopefully should work for on-the-fly variants.
Remove one or two variant types from a pose residue.
Based on name lookup, so hopefully should work for on-the-fly variants.
References core::chemical::ResidueTypeBase::base_name(), core::chemical::ResidueTypeBase::mode(), core::chemical::ResidueTypeBase::name(), core::pose::replace_pose_residue_copying_existing_coordinates(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_set_for_pose(), and protocols::TR().
Referenced by apply().
◆ residue_selector()
| core::select::residue_selector::ResidueSelectorCOP protocols::metal_interface::RemoveMetalConnectionsMover::residue_selector | ( | ) | const |
Gets the residue selector for selecting residues from which metal bonds will be removed.
If a polymer residue AND a metal that it binds are selected, the corresponding metal bonds and variants are removed.
References residue_selector_.
◆ set_residue_selector()
| void protocols::metal_interface::RemoveMetalConnectionsMover::set_residue_selector | ( | core::select::residue_selector::ResidueSelectorCOP const & | selector_in | ) |
Sets the residue selector for selecting residues from which metal bonds will be removed.
If a polymer residue AND a metal that it binds are selected, the corresponding metal bonds and variants are removed.
References residue_selector_.
Referenced by parse_my_tag().
◆ show()
|
overridevirtual |
Summarize this mover's configuration.
Show the contents of the Mover.
Reimplemented from protocols::moves::Mover.
References protocols::moves::Mover::show().
Referenced by protocols::metal_interface::operator<<().
Member Data Documentation
◆ residue_selector_
|
private |
Residue selector for residues to remove bonds from.
If a polymer residue AND a metal that it binds are selected, the corresponding metal bonds and variants are removed.
Referenced by apply(), provide_citation_info(), residue_selector(), and set_residue_selector().
The documentation for this class was generated from the following files:
- src/protocols/metal_interface/RemoveMetalConnectionsMover.hh
- src/protocols/metal_interface/RemoveMetalConnectionsMover.cc
