#include <BCLFragmentBaseMover.hh>
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 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 | 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::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... | |
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()
|
overridevirtual |
apply BCLFragmentBaseMover
Implements protocols::moves::Mover.
Reimplemented in protocols::drug_design::bcl::BCLFragmentMutateMover.
References core::chemical::bcl::require_bcl().
◆ base_attributes()
|
static |
set xml options
Referenced by protocols::drug_design::bcl::BCLFragmentMutateMover::provide_xml_schema().
◆ clone()
|
overridevirtual |
create copy constructor
default full constructor
clone this object
Reimplemented from protocols::moves::Mover.
Reimplemented in protocols::drug_design::bcl::BCLFragmentMutateMover.
◆ fresh_instance()
|
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()
|
protected |
References conf_clash_resolution_.
◆ get_base_conf_clash_tolerance()
|
protected |
References conf_clash_tolerance_.
◆ get_base_conf_cluster()
|
protected |
References conf_cluster_.
◆ get_base_conf_comparer()
|
protected |
References conf_comparer_.
◆ get_base_conf_generate_3d()
|
protected |
References conf_generate_3d_.
◆ get_base_conf_rand_dihedral_prob()
|
protected |
References conf_rand_dihedral_prob_.
◆ get_base_conf_sample_chirality()
|
protected |
References conf_sample_chirality_.
◆ get_base_conf_tolerance()
|
protected |
References conf_tolerance_.
◆ get_base_handler()
|
protected |
References handler_.
◆ get_base_ligand_chain()
|
protected |
References ligand_chain_.
◆ get_base_n_max_conf_iterations()
|
protected |
References n_max_conf_iterations_.
◆ get_base_n_max_confs()
|
protected |
References n_max_confs_.
◆ get_name()
|
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 | ( | ) |
initial setup of conformer sampler upon object construction
References conf_clash_resolution_, conf_clash_tolerance_, conf_cluster_, conf_comparer_, conf_generate_3d_, conf_rand_dihedral_prob_, conf_sample_bond_angles_, conf_sample_chirality_, conf_sample_dihed_, conf_sample_rings_, conf_tolerance_, n_max_conf_iterations_, and n_max_confs_.
Referenced by BCLFragmentBaseMover().
◆ mover_name()
|
static |
Referenced by get_name().
◆ parse_my_tag()
|
overridevirtual |
parse xml file
Reimplemented from protocols::moves::Mover.
Reimplemented in protocols::drug_design::bcl::BCLFragmentMutateMover.
References conf_clash_resolution_, conf_clash_tolerance_, conf_cluster_, conf_comparer_, conf_generate_3d_, conf_rand_dihedral_prob_, conf_sample_bond_angles_, conf_sample_chirality_, conf_sample_dihed_, conf_sample_rings_, conf_tolerance_, ligand_chain_, n_max_conf_iterations_, n_max_confs_, core::chemical::bcl::require_bcl(), set_conf_clash_resolution(), set_conf_clash_tolerance(), set_conf_cluster(), set_conf_comparer(), set_conf_generate_3d(), set_conf_sample_bond_angles(), set_conf_sample_dihed(), set_conf_sample_rings(), set_conf_tolerance(), set_ligand(), set_n_max_conf_iterations(), set_n_max_confs(), set_rand_dihed_prob(), and set_sample_chirality().
Referenced by protocols::drug_design::bcl::BCLFragmentMutateMover::parse_my_tag().
◆ 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::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_conf_clash_tolerance()
| void protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_clash_tolerance | ( | double const | clash_tolerance | ) |
◆ 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_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_conf_sample_rings()
| void protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_sample_rings | ( | bool const | sample_rings | ) |
◆ 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_
|
private |
clash resolution in Angstroms
Referenced by get_base_conf_clash_resolution(), init_fragment_sample_confs(), parse_my_tag(), and set_conf_clash_resolution().
◆ conf_clash_tolerance_
|
private |
clash tolerance in Angstroms
Referenced by get_base_conf_clash_tolerance(), init_fragment_sample_confs(), parse_my_tag(), and set_conf_clash_tolerance().
◆ 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_
|
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_
|
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_
|
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_
|
private |
skip bond angle/length sampling
Referenced by init_fragment_sample_confs(), parse_my_tag(), and set_conf_sample_bond_angles().
◆ conf_sample_chirality_
|
private |
whether to sample chirality or not
Referenced by get_base_conf_sample_chirality(), init_fragment_sample_confs(), parse_my_tag(), and set_sample_chirality().
◆ conf_sample_dihed_
|
private |
skip dihedral sampling
Referenced by init_fragment_sample_confs(), parse_my_tag(), and set_conf_sample_dihed().
◆ conf_sample_rings_
|
private |
skip ring sampling
Referenced by init_fragment_sample_confs(), parse_my_tag(), and set_conf_sample_rings().
◆ 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_
|
private |
the handler to convert between BCL and Rosetta small molecule objects
Referenced by get_base_handler().
◆ 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_
|
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_
|
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:
- src/protocols/drug_design/bcl/BCLFragmentBaseMover.hh
- src/protocols/drug_design/bcl/BCLFragmentBaseMover.cc
