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protocols::ligand_docking::Transform Class Reference

#include <Transform.hh>

Inheritance diagram for protocols::ligand_docking::Transform:
Inheritance graph
[legend]

Public Member Functions

 Transform ()
 
 Transform (qsar::scoring_grid::GridSetCOP grid_prototype, std::string const &chain, core::Real const &box_size, core::Real const &move_distance, core::Real const &angle, core::Size const &cycles, core::Real const &temp)
 
 Transform (Transform const &other)
 
 ~Transform () 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 &data_map) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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 randomize_ligand (core::conformation::UltraLightResidue &residue, core::Real distance, core::Real angle)
 Performa a randomization of the ligand residue, translating by some random value within a uniform distribution with a max of distance, and rotating around a random axis with a uniformly random angle of between -angle/2 and +angle/2 (in degrees). Also randomizes starting conformer if available. More...
 
void transform_ligand (core::conformation::UltraLightResidue &residue)
 translate and rotate a random value by the distances specified in the Transform_info object, using a gaussian distribution More...
 
void setup_conformers (core::pose::Pose &pose, core::Size begin)
 setup conformers for use More...
 
bool check_conformers (core::conformation::UltraLightResidue &starting_residue) const
 Check that conformers are safely within the grids. Returns true if good, false if bad. More...
 
core::Real recommended_grid_size (core::Real success_rate=-1) const
 Return the recommended minimum size of the ligand grids for this particular setup. More...
 
core::Real recommended_box_size (core::Real success_rate=-1) const
 Return the recommended minimum box size for this particular setup. More...
 
void change_conformer (core::conformation::UltraLightResidue &residue)
 randomly change the ligand conformation More...
 
void dump_conformer (core::conformation::UltraLightResidue &residue, utility::io::ozstream &output)
 output the ligand residues to a pdb file More...
 
bool check_rmsd (core::conformation::UltraLightResidue const &start, core::conformation::UltraLightResidue const &current) const
 return true if the rmsd is within the specified cutoff More...
 
bool check_grid (core::conformation::UltraLightResidue &ligand_residue, core::Real distance=0)
 check ligand still inside the grid More...
 
core::Real score_ligand (core::conformation::UltraLightResidue &ligand_residue)
 Calculate unconstrained score for given ligand. More...
 
core::Real score_constraints (core::pose::Pose &pose, core::conformation::UltraLightResidue &residue, core::scoring::ScoreFunctionOP &sfxn)
 score constraints by updating pose and applying score_function_ More...
 
void make_multi_pose_grids (core::Vector center)
 Generate all extra grids. More...
 
core::Real convert_to_full_pose (core::pose::Pose &pose, core::conformation::UltraLightResidue &residue, core::Size chain_id)
 copy the ligand into the desired receptor model and update conformation using the best model More...
 
bool mover_provides_citation_info () const override
 Does this mover provide information about how to cite it? More...
 
utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const override
 Provide the citation. 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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor 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...
 

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 Member Functions

core::Real estimate_mc_travel (core::Real success_rate=-1) const
 Estimate how much the ligand will travel during the MC translation. More...
 

Private Attributes

Transform_info transform_info_
 
utility::vector1< std::pair
< std::string,
qsar::scoring_grid::GridSetCOP > > 
grid_sets_
 
std::map< std::string,
core::pose::Pose
grid_set_poses_
 
utility::vector1
< core::conformation::UltraLightResidueOP
ligand_conformers_
 
protocols::qsar::scoring_grid::GridSetCOP grid_set_prototype_
 
bool optimize_until_score_is_negative_ = false
 
bool output_sampled_space_ = false
 
bool check_rmsd_ = false
 
bool use_conformers_ = true
 
bool use_constraints_ = false
 
bool use_main_model_ = false
 
std::string ensemble_proteins_ = ""
 
std::string cst_fa_file_ = ""
 
core::Real cst_fa_weight_ = 1.0
 
std::string sampled_space_file_
 
core::Real initial_perturb_ = 0.0
 
core::Real initial_angle_perturb_ = -360.0
 

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...
 

Constructor & Destructor Documentation

protocols::ligand_docking::Transform::Transform ( )
protocols::ligand_docking::Transform::Transform ( qsar::scoring_grid::GridSetCOP  grid_prototype,
std::string const &  chain,
core::Real const &  box_size,
core::Real const &  move_distance,
core::Real const &  angle,
core::Size const &  cycles,
core::Real const &  temp 
)
protocols::ligand_docking::Transform::Transform ( Transform const &  other)
default
protocols::ligand_docking::Transform::~Transform ( )
overridedefault

Member Function Documentation

void protocols::ligand_docking::Transform::apply ( core::pose::Pose )
overridevirtual

Main Method.

Implements protocols::moves::Mover.

References protocols::jd2::add_string_real_pair_to_current_job(), core::scoring::angle_constraint, core::scoring::atom_pair_constraint, protocols::ligand_docking::Transform_info::box_size, core::conformation::membrane::center, protocols::ligand_docking::Transform_info::chain, core::conformation::Conformation::chain_begin(), change_conformer(), check_conformers(), check_grid(), check_rmsd(), check_rmsd_, core::pose::Pose::clone(), core::pose::Pose::conformation(), convert_to_full_pose(), core::scoring::coordinate_constraint, cst_fa_file_, cst_fa_weight_, protocols::ligand_docking::Transform_info::cycles, core::scoring::dihedral_constraint, core::kinematics::distance(), protocols::geometry::downstream_centroid_by_jump(), dump_conformer(), ensemble_proteins_, protocols::moves::FAIL_RETRY, core::pose::get_chain_id_from_chain(), core::pose::get_jump_id_from_chain_id(), core::conformation::Residue::get_self_ptr(), grid_set_prototype_, grid_sets_, initial_angle_perturb_, initial_perturb_, ligand_conformers_, make_multi_pose_grids(), optimize_until_score_is_negative_, output_sampled_space_, protocols::simple_moves::bb_sampler::probability, randomize_ligand(), recommended_box_size(), recommended_grid_size(), protocols::ligand_docking::Transform_info::repeats, core::pose::Pose::residue(), core::scoring::rg, sampled_space_file_, score_constraints(), score_ligand(), protocols::moves::Mover::set_last_move_status(), setup_conformers(), protocols::ligand_docking::Transform_info::temperature, protocols::ligand_docking::TR(), transform_info_, transform_ligand(), use_conformers_, and use_constraints_.

void protocols::ligand_docking::Transform::change_conformer ( core::conformation::UltraLightResidue residue)

randomly change the ligand conformation

References core::conformation::UltraLightResidue::align_to_residue(), ligand_conformers_, and core::scoring::rg.

Referenced by apply().

bool protocols::ligand_docking::Transform::check_conformers ( core::conformation::UltraLightResidue starting_residue) const

Check that conformers are safely within the grids. Returns true if good, false if bad.

References core::conformation::UltraLightResidue::align_to_residue(), grid_sets_, ligand_conformers_, recommended_grid_size(), and protocols::ligand_docking::TR().

Referenced by apply().

bool protocols::ligand_docking::Transform::check_grid ( core::conformation::UltraLightResidue ligand_residue,
core::Real  distance = 0 
)

check ligand still inside the grid

References protocols::ligand_docking::Transform_info::box_size, grid_sets_, and transform_info_.

Referenced by apply().

bool protocols::ligand_docking::Transform::check_rmsd ( core::conformation::UltraLightResidue const &  start,
core::conformation::UltraLightResidue const &  current 
) const

return true if the rmsd is within the specified cutoff

References core::conformation::UltraLightResidue::natoms(), protocols::ligand_docking::Transform_info::rmsd, and transform_info_.

Referenced by apply().

protocols::moves::MoverOP protocols::ligand_docking::Transform::clone ( ) const
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.

core::Real protocols::ligand_docking::Transform::convert_to_full_pose ( core::pose::Pose pose,
core::conformation::UltraLightResidue residue,
core::Size  chain_id 
)
void protocols::ligand_docking::Transform::dump_conformer ( core::conformation::UltraLightResidue residue,
utility::io::ozstream &  output 
)
core::Real protocols::ligand_docking::Transform::estimate_mc_travel ( core::Real  success_rate = -1) const
private

Estimate how much the ligand will travel during the MC translation.

  • success_rate is the MC success rate. Will be bumped to a reasonable minimum

References protocols::ligand_docking::Transform_info::cycles, ligand_conformers_, protocols::ligand_docking::Transform_info::move_distance, transform_info_, and use_conformers_.

Referenced by recommended_box_size(), and recommended_grid_size().

protocols::moves::MoverOP protocols::ligand_docking::Transform::fresh_instance ( ) const
overridevirtual

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.

std::string protocols::ligand_docking::Transform::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

void protocols::ligand_docking::Transform::make_multi_pose_grids ( core::Vector  center)
std::string protocols::ligand_docking::Transform::mover_name ( )
static
bool protocols::ligand_docking::Transform::mover_provides_citation_info ( ) const
overridevirtual

Does this mover provide information about how to cite it?

Returns true.

Reimplemented from protocols::moves::Mover.

void protocols::ligand_docking::Transform::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
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 protocols::qsar::scoring_grid::parse_grid_set_from_tag(), core::import_pose::PDB_file, and core::import_pose::pose_from_file().

utility::vector1< basic::citation_manager::CitationCollectionCOP > protocols::ligand_docking::Transform::provide_citation_info ( ) const
overridevirtual

Provide the citation.

Returns
A vector of citation collections. This allows the mover to provide citations for itself and for any modules that it invokes.

Reimplemented from protocols::moves::Mover.

void protocols::ligand_docking::Transform::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::ligand_docking::Transform::randomize_ligand ( core::conformation::UltraLightResidue residue,
core::Real  distance,
core::Real  angle 
)

Performa a randomization of the ligand residue, translating by some random value within a uniform distribution with a max of distance, and rotating around a random axis with a uniformly random angle of between -angle/2 and +angle/2 (in degrees). Also randomizes starting conformer if available.

References core::conformation::UltraLightResidue::center(), core::scoring::rg, and core::conformation::UltraLightResidue::transform().

Referenced by apply().

core::Real protocols::ligand_docking::Transform::recommended_box_size ( core::Real  success_rate = -1) const

Return the recommended minimum box size for this particular setup.

  • success_rate is the MC success rate. Will be bumped to a reasonable minimum

References estimate_mc_travel(), and initial_perturb_.

Referenced by apply().

core::Real protocols::ligand_docking::Transform::recommended_grid_size ( core::Real  success_rate = -1) const

Return the recommended minimum size of the ligand grids for this particular setup.

  • success_rate is the MC success rate. Will be bumped to a reasonable minimum

References estimate_mc_travel(), initial_perturb_, and ligand_conformers_.

Referenced by apply(), and check_conformers().

core::Real protocols::ligand_docking::Transform::score_constraints ( core::pose::Pose pose,
core::conformation::UltraLightResidue residue,
core::scoring::ScoreFunctionOP sfxn 
)

score constraints by updating pose and applying score_function_

References core::pose::Pose::conformation(), and core::conformation::UltraLightResidue::update_conformation().

Referenced by apply().

core::Real protocols::ligand_docking::Transform::score_ligand ( core::conformation::UltraLightResidue ligand_residue)

Calculate unconstrained score for given ligand.

References grid_sets_, protocols::hybridization::score, and protocols::ligand_docking::TR().

Referenced by apply().

void protocols::ligand_docking::Transform::setup_conformers ( core::pose::Pose pose,
core::Size  begin 
)
void protocols::ligand_docking::Transform::transform_ligand ( core::conformation::UltraLightResidue residue)

Member Data Documentation

bool protocols::ligand_docking::Transform::check_rmsd_ = false
private

Referenced by apply().

std::string protocols::ligand_docking::Transform::cst_fa_file_ = ""
private

Referenced by apply().

core::Real protocols::ligand_docking::Transform::cst_fa_weight_ = 1.0
private

Referenced by apply().

std::string protocols::ligand_docking::Transform::ensemble_proteins_ = ""
private

Referenced by apply().

std::map<std::string, core::pose::Pose> protocols::ligand_docking::Transform::grid_set_poses_
private
protocols::qsar::scoring_grid::GridSetCOP protocols::ligand_docking::Transform::grid_set_prototype_
private

Referenced by apply(), and make_multi_pose_grids().

utility::vector1<std::pair<std::string, qsar::scoring_grid::GridSetCOP> > protocols::ligand_docking::Transform::grid_sets_
private
core::Real protocols::ligand_docking::Transform::initial_angle_perturb_ = -360.0
private

Referenced by apply().

core::Real protocols::ligand_docking::Transform::initial_perturb_ = 0.0
private
utility::vector1< core::conformation::UltraLightResidueOP > protocols::ligand_docking::Transform::ligand_conformers_
private
bool protocols::ligand_docking::Transform::optimize_until_score_is_negative_ = false
private

Referenced by apply().

bool protocols::ligand_docking::Transform::output_sampled_space_ = false
private

Referenced by apply().

std::string protocols::ligand_docking::Transform::sampled_space_file_
private

Referenced by apply().

Transform_info protocols::ligand_docking::Transform::transform_info_
private
bool protocols::ligand_docking::Transform::use_conformers_ = true
private

Referenced by apply(), and estimate_mc_travel().

bool protocols::ligand_docking::Transform::use_constraints_ = false
private

Referenced by apply().

bool protocols::ligand_docking::Transform::use_main_model_ = false
private

Referenced by convert_to_full_pose().


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