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Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Attributes | List of all members
protocols::drug_design::bcl::BCLFragmentBaseMover Class Reference

#include <BCLFragmentBaseMover.hh>

Inheritance diagram for protocols::drug_design::bcl::BCLFragmentBaseMover:
Inheritance graph
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Public Member Functions

 BCLFragmentBaseMover ()
 default constructor More...
 
protocols::moves::MoverOP clone () const override
 create copy constructor More...
 
protocols::moves::MoverOP fresh_instance () const override
 create this type of objectt More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void apply (core::pose::Pose &POSE) override
 apply BCLFragmentBaseMover More...
 
void set_ligand (std::string const &ligand_chain_id)
 set the residue ID of the ligand to be mutated More...
 
void set_conf_comparer (std::string const &conformation_comparer)
 set the fragment conformation comparer type More...
 
void set_conf_tolerance (double const tolerance)
 set the tolerance for different conformers More...
 
void set_n_max_confs (size_t const n_confs)
 set the max number of desired fragment conformers More...
 
void set_n_max_conf_iterations (size_t const n_max_iterations)
 set the max number of iterations for conformer sampling More...
 
void set_sample_chirality (bool const change_chirality)
 allow R/S sampling at chiral centers More...
 
void set_rand_dihed_prob (double const random_dihedral_change_prob)
 set the probability of accepting a random dihedral More...
 
void set_conf_generate_3d (bool const generate_3d)
 set de novo conformer generation More...
 
void set_conf_clash_tolerance (double const clash_tolerance)
 set the conformer clash tolerance More...
 
void set_conf_cluster (bool const cluster)
 set leader-follower clustering during conf generation More...
 
void set_conf_clash_resolution (double const clash_resolution)
 set the conformer clash resolution More...
 
void set_conf_sample_dihed (bool const sample_dihed)
 set dihedral bin sampling preference More...
 
void set_conf_sample_rings (bool const sample_rings)
 set ring sampling preference More...
 
void set_conf_sample_bond_angles (bool const sample_bonds)
 set bond angle/length sampling preference More...
 
void init_fragment_sample_confs ()
 initial setup of conformer sampler upon object construction More...
 
void parse_my_tag (TagCOP TAG, basic::datacache::DataMap &data) override
 parse xml file 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 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...
 

Static Public Member Functions

static std::string mover_name ()
 
static void base_attributes (utility::tag::AttributeList &attlist)
 set xml options 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...
 

Protected Member Functions

core::chemical::bcl::BCLFragmentHandlerget_base_handler ()
 
std::string & get_base_ligand_chain ()
 
std::string & get_base_conf_comparer ()
 
double & get_base_conf_tolerance ()
 
core::Sizeget_base_n_max_confs ()
 
core::Sizeget_base_n_max_conf_iterations ()
 
bool & get_base_conf_sample_chirality ()
 
double & get_base_conf_rand_dihedral_prob ()
 
bool & get_base_conf_generate_3d ()
 
double & get_base_conf_clash_tolerance ()
 
bool & get_base_conf_cluster ()
 
double & get_base_conf_clash_resolution ()
 
- 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...
 

Private Attributes

core::chemical::bcl::BCLFragmentHandler handler_
 the handler to convert between BCL and Rosetta small molecule objects More...
 
std::string ligand_chain_
 the pose residue chain ID of the ligand to be mutated More...
 
std::string conf_comparer_
 conformation comparer tells us how to distinguish conformers More...
 
double conf_tolerance_
 tolerance tells us how far away two potential conformers must be in conf_comparer space to be different More...
 
core::Size n_max_confs_
 max number of conformers to generate More...
 
core::Size n_max_conf_iterations_
 max number of conformer generation iterations More...
 
bool conf_sample_chirality_
 whether to sample chirality or not More...
 
double conf_rand_dihedral_prob_
 probability of including a randomly selected dihedral for inclusion in conformer More...
 
bool conf_generate_3d_
 create a 3D conformer from scratch; no input coordinate info is used More...
 
double conf_clash_tolerance_
 clash tolerance in Angstroms More...
 
bool conf_cluster_
 leader-follower clustering during conf sampling More...
 
double conf_clash_resolution_
 clash resolution in Angstroms More...
 
bool conf_sample_dihed_
 skip dihedral sampling More...
 
bool conf_sample_rings_
 skip ring sampling More...
 
bool conf_sample_bond_angles_
 skip bond angle/length sampling 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
 

Constructor & Destructor Documentation

◆ BCLFragmentBaseMover()

protocols::drug_design::bcl::BCLFragmentBaseMover::BCLFragmentBaseMover ( )

default constructor

References init_fragment_sample_confs().

Member Function Documentation

◆ apply()

void protocols::drug_design::bcl::BCLFragmentBaseMover::apply ( core::pose::Pose POSE)
overridevirtual

◆ base_attributes()

void protocols::drug_design::bcl::BCLFragmentBaseMover::base_attributes ( utility::tag::AttributeList &  attlist)
static

◆ clone()

protocols::moves::MoverOP protocols::drug_design::bcl::BCLFragmentBaseMover::clone ( ) const
overridevirtual

create copy constructor

default full constructor

clone this object

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::drug_design::bcl::BCLFragmentMutateMover.

◆ fresh_instance()

protocols::moves::MoverOP protocols::drug_design::bcl::BCLFragmentBaseMover::fresh_instance ( ) const
overridevirtual

create this type of objectt

create this type of object

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::drug_design::bcl::BCLFragmentMutateMover.

◆ get_base_conf_clash_resolution()

double & protocols::drug_design::bcl::BCLFragmentBaseMover::get_base_conf_clash_resolution ( )
protected

◆ get_base_conf_clash_tolerance()

double & protocols::drug_design::bcl::BCLFragmentBaseMover::get_base_conf_clash_tolerance ( )
protected

References conf_clash_tolerance_.

◆ get_base_conf_cluster()

bool & protocols::drug_design::bcl::BCLFragmentBaseMover::get_base_conf_cluster ( )
protected

References conf_cluster_.

◆ get_base_conf_comparer()

std::string & protocols::drug_design::bcl::BCLFragmentBaseMover::get_base_conf_comparer ( )
protected

References conf_comparer_.

◆ get_base_conf_generate_3d()

bool & protocols::drug_design::bcl::BCLFragmentBaseMover::get_base_conf_generate_3d ( )
protected

References conf_generate_3d_.

◆ get_base_conf_rand_dihedral_prob()

double & protocols::drug_design::bcl::BCLFragmentBaseMover::get_base_conf_rand_dihedral_prob ( )
protected

◆ get_base_conf_sample_chirality()

bool & protocols::drug_design::bcl::BCLFragmentBaseMover::get_base_conf_sample_chirality ( )
protected

◆ get_base_conf_tolerance()

double & protocols::drug_design::bcl::BCLFragmentBaseMover::get_base_conf_tolerance ( )
protected

References conf_tolerance_.

◆ get_base_handler()

core::chemical::bcl::BCLFragmentHandler & protocols::drug_design::bcl::BCLFragmentBaseMover::get_base_handler ( )
protected

References handler_.

◆ get_base_ligand_chain()

std::string & protocols::drug_design::bcl::BCLFragmentBaseMover::get_base_ligand_chain ( )
protected

References ligand_chain_.

◆ get_base_n_max_conf_iterations()

core::Size & protocols::drug_design::bcl::BCLFragmentBaseMover::get_base_n_max_conf_iterations ( )
protected

◆ get_base_n_max_confs()

core::Size & protocols::drug_design::bcl::BCLFragmentBaseMover::get_base_n_max_confs ( )
protected

References n_max_confs_.

◆ get_name()

std::string protocols::drug_design::bcl::BCLFragmentBaseMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::drug_design::bcl::BCLFragmentMutateMover.

References mover_name().

◆ init_fragment_sample_confs()

void protocols::drug_design::bcl::BCLFragmentBaseMover::init_fragment_sample_confs ( )

◆ mover_name()

std::string protocols::drug_design::bcl::BCLFragmentBaseMover::mover_name ( )
static

Referenced by get_name().

◆ parse_my_tag()

void protocols::drug_design::bcl::BCLFragmentBaseMover::parse_my_tag ( TagCOP  TAG,
basic::datacache::DataMap data 
)
overridevirtual

◆ provide_citation_info()

void protocols::drug_design::bcl::BCLFragmentBaseMover::provide_citation_info ( basic::citation_manager::CitationCollectionList &  citations) const
overridevirtual

Provide citations to the passed CitationCollectionList.

This mover is unpublished. Hopefully we can publish it soon and I can change this to a citation for an actual manuscript

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::drug_design::bcl::BCLFragmentMutateMover.

◆ set_conf_clash_resolution()

void protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_clash_resolution ( double const  clash_resolution)

set the conformer clash resolution

References conf_clash_resolution_.

Referenced by parse_my_tag().

◆ set_conf_clash_tolerance()

void protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_clash_tolerance ( double const  clash_tolerance)

set the conformer clash tolerance

References conf_clash_tolerance_.

Referenced by parse_my_tag().

◆ set_conf_cluster()

void protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_cluster ( bool const  cluster)

set leader-follower clustering during conf generation

References conf_cluster_.

Referenced by parse_my_tag().

◆ set_conf_comparer()

void protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_comparer ( std::string const &  conformation_comparer)

set the fragment conformation comparer type

References conf_comparer_.

Referenced by parse_my_tag().

◆ set_conf_generate_3d()

void protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_generate_3d ( bool const  generate_3d)

set de novo conformer generation

References conf_generate_3d_.

Referenced by parse_my_tag().

◆ set_conf_sample_bond_angles()

void protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_sample_bond_angles ( bool const  sample_bonds)

set bond angle/length sampling preference

References conf_sample_bond_angles_.

Referenced by parse_my_tag().

◆ set_conf_sample_dihed()

void protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_sample_dihed ( bool const  sample_dihed)

set dihedral bin sampling preference

References conf_sample_dihed_.

Referenced by parse_my_tag().

◆ set_conf_sample_rings()

void protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_sample_rings ( bool const  sample_rings)

set ring sampling preference

References conf_sample_rings_.

Referenced by parse_my_tag().

◆ set_conf_tolerance()

void protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_tolerance ( double const  tolerance)

set the tolerance for different conformers

References conf_tolerance_.

Referenced by parse_my_tag().

◆ set_ligand()

void protocols::drug_design::bcl::BCLFragmentBaseMover::set_ligand ( std::string const &  ligand_chain_id)

set the residue ID of the ligand to be mutated

References ligand_chain_.

Referenced by parse_my_tag().

◆ set_n_max_conf_iterations()

void protocols::drug_design::bcl::BCLFragmentBaseMover::set_n_max_conf_iterations ( size_t const  n_max_iterations)

set the max number of iterations for conformer sampling

References n_max_conf_iterations_.

Referenced by parse_my_tag().

◆ set_n_max_confs()

void protocols::drug_design::bcl::BCLFragmentBaseMover::set_n_max_confs ( size_t const  n_confs)

set the max number of desired fragment conformers

References n_max_confs_.

Referenced by parse_my_tag().

◆ set_rand_dihed_prob()

void protocols::drug_design::bcl::BCLFragmentBaseMover::set_rand_dihed_prob ( double const  random_dihedral_change_prob)

set the probability of accepting a random dihedral

References conf_rand_dihedral_prob_.

Referenced by parse_my_tag().

◆ set_sample_chirality()

void protocols::drug_design::bcl::BCLFragmentBaseMover::set_sample_chirality ( bool const  change_chirality)

allow R/S sampling at chiral centers

References conf_sample_chirality_.

Referenced by parse_my_tag().

Member Data Documentation

◆ conf_clash_resolution_

double protocols::drug_design::bcl::BCLFragmentBaseMover::conf_clash_resolution_
private

◆ conf_clash_tolerance_

double protocols::drug_design::bcl::BCLFragmentBaseMover::conf_clash_tolerance_
private

◆ conf_cluster_

bool protocols::drug_design::bcl::BCLFragmentBaseMover::conf_cluster_
private

leader-follower clustering during conf sampling

Referenced by get_base_conf_cluster(), init_fragment_sample_confs(), parse_my_tag(), and set_conf_cluster().

◆ conf_comparer_

std::string protocols::drug_design::bcl::BCLFragmentBaseMover::conf_comparer_
private

conformation comparer tells us how to distinguish conformers

Referenced by get_base_conf_comparer(), init_fragment_sample_confs(), parse_my_tag(), and set_conf_comparer().

◆ conf_generate_3d_

bool protocols::drug_design::bcl::BCLFragmentBaseMover::conf_generate_3d_
private

create a 3D conformer from scratch; no input coordinate info is used

Referenced by get_base_conf_generate_3d(), init_fragment_sample_confs(), parse_my_tag(), and set_conf_generate_3d().

◆ conf_rand_dihedral_prob_

double protocols::drug_design::bcl::BCLFragmentBaseMover::conf_rand_dihedral_prob_
private

probability of including a randomly selected dihedral for inclusion in conformer

Referenced by get_base_conf_rand_dihedral_prob(), init_fragment_sample_confs(), parse_my_tag(), and set_rand_dihed_prob().

◆ conf_sample_bond_angles_

bool protocols::drug_design::bcl::BCLFragmentBaseMover::conf_sample_bond_angles_
private

skip bond angle/length sampling

Referenced by init_fragment_sample_confs(), parse_my_tag(), and set_conf_sample_bond_angles().

◆ conf_sample_chirality_

bool protocols::drug_design::bcl::BCLFragmentBaseMover::conf_sample_chirality_
private

◆ conf_sample_dihed_

bool protocols::drug_design::bcl::BCLFragmentBaseMover::conf_sample_dihed_
private

skip dihedral sampling

Referenced by init_fragment_sample_confs(), parse_my_tag(), and set_conf_sample_dihed().

◆ conf_sample_rings_

bool protocols::drug_design::bcl::BCLFragmentBaseMover::conf_sample_rings_
private

skip ring sampling

Referenced by init_fragment_sample_confs(), parse_my_tag(), and set_conf_sample_rings().

◆ conf_tolerance_

double protocols::drug_design::bcl::BCLFragmentBaseMover::conf_tolerance_
private

tolerance tells us how far away two potential conformers must be in conf_comparer space to be different

Referenced by get_base_conf_tolerance(), init_fragment_sample_confs(), parse_my_tag(), and set_conf_tolerance().

◆ handler_

core::chemical::bcl::BCLFragmentHandler protocols::drug_design::bcl::BCLFragmentBaseMover::handler_
private

the handler to convert between BCL and Rosetta small molecule objects

Referenced by get_base_handler().

◆ ligand_chain_

std::string protocols::drug_design::bcl::BCLFragmentBaseMover::ligand_chain_
private

the pose residue chain ID of the ligand to be mutated

Referenced by get_base_ligand_chain(), parse_my_tag(), and set_ligand().

◆ n_max_conf_iterations_

core::Size protocols::drug_design::bcl::BCLFragmentBaseMover::n_max_conf_iterations_
private

max number of conformer generation iterations

Referenced by get_base_n_max_conf_iterations(), init_fragment_sample_confs(), parse_my_tag(), and set_n_max_conf_iterations().

◆ n_max_confs_

core::Size protocols::drug_design::bcl::BCLFragmentBaseMover::n_max_confs_
private

max number of conformers to generate

Referenced by get_base_n_max_confs(), init_fragment_sample_confs(), parse_my_tag(), and set_n_max_confs().


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