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

#include <BCLFragmentMutateMover.hh>

Inheritance diagram for protocols::drug_design::bcl::BCLFragmentMutateMover:
Inheritance graph

Public Member Functions

 BCLFragmentMutateMover ()
 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...
std::string get_tag (Pose &pose, core::Size resid) const
void get_mutate_label () const
void apply (core::pose::Pose &pose) override
 apply BCLFragmentMutateMover More...
void set_n_max_mutate_attempts (core::Size const &n_max_mutate_attempts)
 set the maximum number of mutate attempts More...
void set_mutate (std::string const &object_data_label)
 set the mutate using a BCL object data label string 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::drug_design::bcl::BCLFragmentBaseMover
 BCLFragmentBaseMover ()
 default constructor 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...
- 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 provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 set xml options More...
- Static Public Member Functions inherited from protocols::drug_design::bcl::BCLFragmentBaseMover
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...

Private Attributes

core::Size max_mutate_retry_

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::drug_design::bcl::BCLFragmentBaseMover
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...

Constructor & Destructor Documentation

◆ BCLFragmentMutateMover()

protocols::drug_design::bcl::BCLFragmentMutateMover::BCLFragmentMutateMover ( )

default constructor

Member Function Documentation

◆ apply()

void protocols::drug_design::bcl::BCLFragmentMutateMover::apply ( core::pose::Pose pose)

apply BCLFragmentMutateMover

extract ligand residue from pose, apply mutate, add mutated ligand back to the pose; additional protein-ligand interface optimization NOT included; I recommend repacking/minimization

Reimplemented from protocols::drug_design::bcl::BCLFragmentBaseMover.

References protocols::indexed_structure_store::filters::First, core::pose::get_resnums_for_chain(), core::chemical::ResidueType::make(), core::chemical::bcl::require_bcl(), and protocols::drug_design::bcl::TR().

◆ clone()

protocols::moves::MoverOP protocols::drug_design::bcl::BCLFragmentMutateMover::clone ( ) const

create copy constructor

default sample confs constructor

clone this object

Reimplemented from protocols::drug_design::bcl::BCLFragmentBaseMover.

◆ fresh_instance()

protocols::moves::MoverOP protocols::drug_design::bcl::BCLFragmentMutateMover::fresh_instance ( ) const

create this type of objectt

create this type of object

Reimplemented from protocols::drug_design::bcl::BCLFragmentBaseMover.

◆ get_mutate_label()

void protocols::drug_design::bcl::BCLFragmentMutateMover::get_mutate_label ( ) const

◆ get_name()

std::string protocols::drug_design::bcl::BCLFragmentMutateMover::get_name ( ) const

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

Reimplemented from protocols::drug_design::bcl::BCLFragmentBaseMover.

References mover_name().

◆ get_tag()

std::string protocols::drug_design::bcl::BCLFragmentMutateMover::get_tag ( Pose pose,
core::Size  resid 
) const

◆ mover_name()

std::string protocols::drug_design::bcl::BCLFragmentMutateMover::mover_name ( )

◆ parse_my_tag()

void protocols::drug_design::bcl::BCLFragmentMutateMover::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap data 

◆ provide_citation_info()

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

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::drug_design::bcl::BCLFragmentBaseMover.

◆ provide_xml_schema()

void protocols::drug_design::bcl::BCLFragmentMutateMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)

◆ set_mutate()

void protocols::drug_design::bcl::BCLFragmentMutateMover::set_mutate ( std::string const &  object_data_label)

set the mutate using a BCL object data label string

References core::chemical::bcl::require_bcl().

Referenced by parse_my_tag().

◆ set_n_max_mutate_attempts()

void protocols::drug_design::bcl::BCLFragmentMutateMover::set_n_max_mutate_attempts ( core::Size const &  n_max_mutate_attempts)

set the maximum number of mutate attempts

References max_mutate_retry_.

Referenced by parse_my_tag().

Member Data Documentation

◆ max_mutate_retry_

core::Size protocols::drug_design::bcl::BCLFragmentMutateMover::max_mutate_retry_

maximum number of times to retry a particular mutate if it fails. if the mutate fails for any reason, e.g. the mutated molecule failed the druglikeness filter or 3D coordinates could not be generated, then the mutate returns a null pointer, so we will just return the initial fragment

Referenced by parse_my_tag(), and set_n_max_mutate_attempts().

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