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protocols::enzdes::RepackLigandSiteWithoutLigandMover Class Reference

class that will identify the region around the ligand, remove it, and then do a repack. It can also calculate the following parameters: E diff after the repack, (in essence a crude delta G calc) rmsd of the repacked site after the repack and rmsd of catalytic residues More...

#include <EnzdesMovers.hh>

Inheritance diagram for protocols::enzdes::RepackLigandSiteWithoutLigandMover:
Inheritance graph

Public Member Functions

 RepackLigandSiteWithoutLigandMover ()
 RepackLigandSiteWithoutLigandMover (core::scoring::ScoreFunctionCOP sfxn, bool calculate_silent_Es)
 ~RepackLigandSiteWithoutLigandMover () override
void apply (core::pose::Pose &pose) override
 Main Method. More...
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
void set_cstio (toolbox::match_enzdes_util::EnzConstraintIOCOP enzcst_io)
void set_sfxn (core::scoring::ScoreFunctionCOP sfxn)
void set_calculate_silent_Es (bool calculate)
void set_separate_prt_ligand (bool separate_prt_ligand)
< core::io::silent::SilentEnergy >
const & 
silent_Es ()
core::pack::task::PackerTaskCOP get_ptask () const
- 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 MoverOP clone () const
 Return a clone of the Mover object. 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
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
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...

Private Member Functions

void separate_protein_and_ligand (core::pose::Pose &pose) const

Private Attributes

core::scoring::ScoreFunctionCOP sfxn_
core::Size lig_seqpos_
toolbox::match_enzdes_util::EnzConstraintIOCOP enzcst_io_
bool calculate_silent_Es_
core::pack::task::PackerTaskOP ptask_
< core::io::silent::SilentEnergy
bool separate_prt_ligand_

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
- 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::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

class that will identify the region around the ligand, remove it, and then do a repack. It can also calculate the following parameters: E diff after the repack, (in essence a crude delta G calc) rmsd of the repacked site after the repack and rmsd of catalytic residues

Constructor & Destructor Documentation

protocols::enzdes::RepackLigandSiteWithoutLigandMover::RepackLigandSiteWithoutLigandMover ( )

References silent_Es_.

protocols::enzdes::RepackLigandSiteWithoutLigandMover::RepackLigandSiteWithoutLigandMover ( core::scoring::ScoreFunctionCOP  sfxn,
bool  calculate_silent_Es 

References silent_Es_.

protocols::enzdes::RepackLigandSiteWithoutLigandMover::~RepackLigandSiteWithoutLigandMover ( )

Member Function Documentation

void protocols::enzdes::RepackLigandSiteWithoutLigandMover::apply ( core::pose::Pose )
std::string protocols::enzdes::RepackLigandSiteWithoutLigandMover::get_name ( ) const

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

Implements protocols::moves::Mover.

core::pack::task::PackerTaskCOP protocols::enzdes::RepackLigandSiteWithoutLigandMover::get_ptask ( ) const
void protocols::enzdes::RepackLigandSiteWithoutLigandMover::separate_protein_and_ligand ( core::pose::Pose pose) const
void protocols::enzdes::RepackLigandSiteWithoutLigandMover::set_calculate_silent_Es ( bool  calculate)

References calculate_silent_Es_.

void protocols::enzdes::RepackLigandSiteWithoutLigandMover::set_cstio ( toolbox::match_enzdes_util::EnzConstraintIOCOP  enzcst_io)
void protocols::enzdes::RepackLigandSiteWithoutLigandMover::set_separate_prt_ligand ( bool  separate_prt_ligand)
void protocols::enzdes::RepackLigandSiteWithoutLigandMover::set_sfxn ( core::scoring::ScoreFunctionCOP  sfxn)

References sfxn_.

utility::vector1< core::io::silent::SilentEnergy > const& protocols::enzdes::RepackLigandSiteWithoutLigandMover::silent_Es ( )

Member Data Documentation

bool protocols::enzdes::RepackLigandSiteWithoutLigandMover::calculate_silent_Es_

Referenced by apply(), and set_calculate_silent_Es().

toolbox::match_enzdes_util::EnzConstraintIOCOP protocols::enzdes::RepackLigandSiteWithoutLigandMover::enzcst_io_

Referenced by apply(), and set_cstio().

core::Size protocols::enzdes::RepackLigandSiteWithoutLigandMover::lig_seqpos_
core::pack::task::PackerTaskOP protocols::enzdes::RepackLigandSiteWithoutLigandMover::ptask_

Referenced by apply(), and get_ptask().

bool protocols::enzdes::RepackLigandSiteWithoutLigandMover::separate_prt_ligand_

Referenced by apply(), and set_separate_prt_ligand().

core::scoring::ScoreFunctionCOP protocols::enzdes::RepackLigandSiteWithoutLigandMover::sfxn_

Referenced by apply(), and set_sfxn().

utility::vector1< core::io::silent::SilentEnergy > protocols::enzdes::RepackLigandSiteWithoutLigandMover::silent_Es_

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