#include <BCLFragmentMutateMover.hh>
Inheritance diagram for protocols::drug_design::bcl::BCLFragmentMutateMover:
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 Strings & | info () |
| 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::BCLFragmentHandler & | get_base_handler () |
| std::string & | get_base_ligand_chain () |
| std::string & | get_base_conf_comparer () |
| double & | get_base_conf_tolerance () |
| core::Size & | get_base_n_max_confs () |
| core::Size & | get_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()
|
overridevirtual |
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()
|
overridevirtual |
create copy constructor
default sample confs constructor
clone this object
Reimplemented from protocols::drug_design::bcl::BCLFragmentBaseMover.
◆ fresh_instance()
|
overridevirtual |
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 |
References core::chemical::bcl::require_bcl().
◆ get_name()
|
overridevirtual |
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 |
References core::pose::Pose::pdb_info().
◆ mover_name()
|
static |
◆ parse_my_tag()
|
overridevirtual |
parse xml file
Reimplemented from protocols::drug_design::bcl::BCLFragmentBaseMover.
References max_mutate_retry_, protocols::drug_design::bcl::BCLFragmentBaseMover::parse_my_tag(), core::chemical::bcl::require_bcl(), set_mutate(), and set_n_max_mutate_attempts().
◆ provide_citation_info()
|
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::drug_design::bcl::BCLFragmentBaseMover.
◆ provide_xml_schema()
|
static |
◆ 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_
|
private |
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:
- src/protocols/drug_design/bcl/BCLFragmentMutateMover.hh
- src/protocols/drug_design/bcl/BCLFragmentMutateMover.cc
