 |
Rosetta
3.8
|
All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
|
Rosetta
3.8
|
#include <BundleGridSampler.hh>
Public Member Functions | |
| BundleGridSampler () | |
| Creator for BundleGridSampler mover. More... | |
| BundleGridSampler (BundleGridSampler const &src) | |
| Copy constructor for BundleGridSampler mover. More... | |
| ~BundleGridSampler () override | |
| Destructor for BundleGridSampler mover. More... | |
| protocols::moves::MoverOP | clone () const override |
| Clone operator to create a pointer to a fresh BundleGridSampler object that copies this one. More... | |
| protocols::moves::MoverOP | fresh_instance () const override |
| Fresh_instance operator to create a pointer to a fresh BundleGridSampler object that does NOT copy this one. More... | |
| void | apply (core::pose::Pose &pose) override |
| Actually apply the mover to the pose. More... | |
| void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, core::pose::Pose const &) override |
| Returns the name of this mover ("BundleGridSampler"). More... | |
| void | set_reset_mode (bool const val) |
| Set the reset mode. More... | |
| bool | reset_mode () const |
| Get the reset mode. More... | |
| PerturbBundleOptionsOP | r0 (core::Size const index) |
| Access the r0_ BundleOptions object, by index. More... | |
| PerturbBundleOptionsCOP | r0 (core::Size const index) const |
| Access the r0_ BundleOptions object, by index. This provides const access. More... | |
| PerturbBundleOptionsOP | omega0 (core::Size const index) |
| Access the omega0_ BundleOptions object, by index. More... | |
| PerturbBundleOptionsCOP | omega0 (core::Size const index) const |
| Access the omega0_ BundleOptions object, by index. This provides const access. More... | |
| PerturbBundleOptionsOP | delta_omega0 (core::Size const index) |
| Access the delta_omega0_ BundleOptions object, by index. More... | |
| PerturbBundleOptionsCOP | delta_omega0 (core::Size const index) const |
| Access the delta_omega0_ BundleOptions object, by index. This provides const access. More... | |
| PerturbBundleOptionsOP | delta_omega1 (core::Size const index) |
| Access the delta_omega1_ BundleOptions object, by index. More... | |
| PerturbBundleOptionsCOP | delta_omega1 (core::Size const index) const |
| Access the delta_omega1_ BundleOptions object, by index. This provides const access. More... | |
| PerturbBundleOptionsOP | delta_t (core::Size const index) |
| Access the delta_t_ BundleOptions object, by index. More... | |
| PerturbBundleOptionsCOP | delta_t (core::Size const index) const |
| Access the delta_t_ BundleOptions object, by index. This provides const access. More... | |
| PerturbBundleOptionsOP | z1_offset (core::Size const index) |
| Access the z1_offset_ BundleOptions object, by index. More... | |
| PerturbBundleOptionsCOP | z1_offset (core::Size const index) const |
| Access the z1_offset_ BundleOptions object, by index. This provides const access. More... | |
| PerturbBundleOptionsOP | z0_offset (core::Size const index) |
| Access the z0_offset_ BundleOptions object, by index. More... | |
| PerturbBundleOptionsCOP | z0_offset (core::Size const index) const |
| Access the z0_offset_ BundleOptions object, by index. This provides const access. More... | |
| PerturbBundleOptionsOP | epsilon (core::Size const index) |
| Access the epsilon_ BundleOptions object, by index. More... | |
| PerturbBundleOptionsCOP | epsilon (core::Size const index) const |
| Access the epsilon_ BundleOptions object, by index. This provides const access. More... | |
| PerturbBundleOptionsOP | default_r0 () |
| Access the default_r0_ BundleOptions object. More... | |
| PerturbBundleOptionsCOP | default_r0 () const |
| Access the default_r0_ BundleOptions object (const-access). More... | |
| PerturbBundleOptionsOP | default_omega0 () |
| Access the default_omega0_ BundleOptions object. More... | |
| PerturbBundleOptionsCOP | default_omega0 () const |
| Access the default_omega0_ BundleOptions object (const-access). More... | |
| PerturbBundleOptionsOP | default_delta_omega0 () |
| Access the default_delta_omega0_ BundleOptions object. More... | |
| PerturbBundleOptionsCOP | default_delta_omega0 () const |
| Access the default_delta_omega0_ BundleOptions object (const-access). More... | |
| PerturbBundleOptionsOP | default_delta_omega1 () |
| Access the default_delta_omega1_ BundleOptions object. More... | |
| PerturbBundleOptionsCOP | default_delta_omega1 () const |
| Access the default_delta_omega1_ BundleOptions object (const-access). More... | |
| PerturbBundleOptionsOP | default_delta_t () |
| Access the default_delta_t_ BundleOptions object. More... | |
| PerturbBundleOptionsCOP | default_delta_t () const |
| Access the default_delta_t_ BundleOptions object (const-access). More... | |
| PerturbBundleOptionsOP | default_z1_offset () |
| Access the default_z1_offset_ BundleOptions object. More... | |
| PerturbBundleOptionsCOP | default_z1_offset () const |
| Access the default_z1_offset_ BundleOptions object (const-access). More... | |
| PerturbBundleOptionsOP | default_z0_offset () |
| Access the default_z0_offset_ BundleOptions object. More... | |
| PerturbBundleOptionsCOP | default_z0_offset () const |
| Access the default_z0_offset_ BundleOptions object (const-access). More... | |
| PerturbBundleOptionsOP | default_epsilon () |
| Access the default_epsilon_ BundleOptions object. More... | |
| PerturbBundleOptionsCOP | default_epsilon () const |
| Access the default_epsilon_ BundleOptions object (const-access). More... | |
| core::Size | add_helix () |
| Add options for a new helix. More... | |
| void | set_max_samples (core::Size const val) |
| Set the maximum number of samples for the mover. More... | |
| core::Size | max_samples () const |
| Get the maximum number of samples for the mover. More... | |
| void | increment_helix_count () |
| Increments the number of helices that have been defined. More... | |
| core::Size | n_helices () const |
| Returns the number of helices that have been defined. More... | |
| void | set_selection_low (bool const val) |
| Sets whether the selection should be for the lowest score value (true) or highest (false). More... | |
| bool | selection_low () |
| Returns whether the selection should be for the lowest score value (true) or highest (false). More... | |
| void | set_preselection_mover (protocols::moves::MoverOP mover) |
| Sets the mover that will be applied to all helical bundles generated prior to energy evaluation. More... | |
| void | set_preselection_filter (protocols::filters::FilterOP filter) |
| Sets the filter that will be applied to all helical bundles generated prior to energy evaluation. More... | |
| bool | preselection_mover_exists () const |
| Returns "true" if and only if a preselection mover has been assigned. More... | |
| bool | preselection_filter_exists () const |
| Returns "true" if and only if a preselection filter has been assigned. More... | |
| void | set_pdb_output (bool const val) |
| Set whether the mover dumps pdbs or not. More... | |
| bool | pdb_output () const |
| Returns whether the mover dumps pdbs or not. More... | |
| void | set_pdb_prefix (std::string const &prefix) |
| Sets the filename prefix for PDB output. More... | |
| std::string | pdb_prefix () |
| Access the filename prefix for PDB output. More... | |
| void | set_sfxn (core::scoring::ScoreFunctionOP sfxn_in) |
| Sets the scorefunction for this mover. More... | |
| bool | sfxn_set () const |
| Returns whether the scorefunction has been set. More... | |
| void | set_nstruct_mode (bool const &val) |
| Set the nstruct mode. More... | |
| bool | nstruct_mode () const |
| Get the nstruct mode. More... | |
| void | set_nstruct_repeats (core::Size const val) |
| Set the nstruct repeats. More... | |
| core::Size | nstruct_repeats () const |
| Get the nstruct repeats. More... | |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
 Public Member Functions inherited from protocols::moves::Mover | |
| Mover () | |
| ~Mover () override | |
| 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 type_name) | |
| sets the type for a mover; name_ has been removed (2010/05/14) More... | |
| Mover (Mover const &other) | |
| Mover & | operator= (Mover const &other) |
| assignment operator More... | |
| virtual core::Real | last_proposal_density_ratio () |
| std::string const & | type () const |
| void | set_type (std::string const &setting) |
| 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 | set_current_tag (std::string const &new_tag) |
| 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 |
| 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... | |
| void | type (const std::string &type_in) |
| std::string | get_type () const |
| 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... | |
| 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... | |
| 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... | |
| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
| jobdist::BasicJobCOP | get_current_job () const |
| virtual void | show (std::ostream &output=std::cout) const |
| Outputs details about the Mover, including current settings. 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 | |
| bool | is_in_list (core::Size const val, utility::vector1< core::Size > const &list) const |
| Is a value in a list? More... | |
| core::Size | calculate_total_samples () const |
| Calculate the number of grid points that will be sampled, based on the options set by the user. More... | |
Private Attributes | |
| bool | reset_mode_ |
| Should the pose be reset before applying the GridSampler? Default true. More... | |
| bool | nstruct_mode_ |
| Should the parallel sampling be done based on the job (nstruct number)? More... | |
| core::Size | nstruct_mode_repeats_ |
| If nstruct_mode_ is true, how many times should each set of Crick parameters be repeated? More... | |
| bool | select_low_ |
| The selection type. If false, the pose with the highest score value is selected. If true, the pose with the lowest score value is selected. True by default. More... | |
| core::Size | n_helices_ |
| The number of helices that have been defined. More... | |
| core::Size | max_samples_ |
| The maximum number of gridpoints allowed. More... | |
| PerturbBundleOptionsOP | default_r0_ |
| Default options for sampling r0. More... | |
| PerturbBundleOptionsOPs | r0_ |
| Helix-by-helix options for sampling r0. More... | |
| PerturbBundleOptionsOP | default_omega0_ |
| Default options for sampling omega0. More... | |
| PerturbBundleOptionsOPs | omega0_ |
| Helix-by-helix options for sampling omega0. More... | |
| PerturbBundleOptionsOP | default_delta_omega0_ |
| Default options for sampling delta_omega0. More... | |
| PerturbBundleOptionsOPs | delta_omega0_ |
| Helix-by-helix options for sampling delta_omega0. More... | |
| PerturbBundleOptionsOP | default_delta_omega1_ |
| Default options for sampling delta_omega1. More... | |
| PerturbBundleOptionsOPs | delta_omega1_ |
| Helix-by-helix options for sampling delta_omega1. More... | |
| PerturbBundleOptionsOP | default_delta_t_ |
| Default options for sampling delta_t. More... | |
| PerturbBundleOptionsOPs | delta_t_ |
| Helix-by-helix options for sampling delta_t. More... | |
| PerturbBundleOptionsOP | default_z1_offset_ |
| Default options for sampling z1_offset. More... | |
| PerturbBundleOptionsOPs | z1_offset_ |
| Helix-by-helix options for sampling z1_offset. More... | |
| PerturbBundleOptionsOP | default_z0_offset_ |
| Default options for sampling z0_offset. More... | |
| PerturbBundleOptionsOPs | z0_offset_ |
| Helix-by-helix options for sampling z0_offset. More... | |
| PerturbBundleOptionsOP | default_epsilon_ |
| Default options for sampling epsilon. More... | |
| PerturbBundleOptionsOPs | epsilon_ |
| Helix-by-helix options for sampling epsilon. More... | |
| MakeBundleOP | make_bundle_ |
| A MakeBundle mover that this mover will call. More... | |
| protocols::moves::MoverOP | pre_selection_mover_ |
| Owning pointer for an (optional) pre-selection mover applied to all helical bundles before energy evaluation. More... | |
| bool | pre_selection_mover_exists_ |
| Bool determining whether there exists a pre-selection mover that wlil be applied. More... | |
| protocols::filters::FilterOP | pre_selection_filter_ |
| Owning pointer for an (optional) pre-selection filter applied to all helical bundles after the pre-selection mover but before picking the lowest-energy solution. If PDBs are dumped, only those passing filters are dumped. More... | |
| bool | pre_selection_filter_exists_ |
| Bool determining whether a pre-selection filter has been set. More... | |
| bool | dump_pdbs_ |
| Dump a PDB file for each bundle generated? False by default. More... | |
| std::string | pdb_prefix_ |
| PDB filename prefix. Filename will be of the form <prefix>_#####.pdb. More... | |
| bool | sfxn_set_ |
| Has the scorefunction been set? More... | |
| core::scoring::ScoreFunctionOP | sfxn_ |
| The scorefunction that this mover will use to pick the lowest-energy bundle. More... | |
Additional Inherited Members | |
| 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... | |
| typedef protocols::helical_bundle::parameters::BundleParameters protocols::helical_bundle::BundleGridSampler::BundleParameters |
| typedef protocols::helical_bundle::parameters::BundleParametersCOP protocols::helical_bundle::BundleGridSampler::BundleParametersCOP |
| typedef protocols::helical_bundle::parameters::BundleParametersOP protocols::helical_bundle::BundleGridSampler::BundleParametersOP |
| typedef protocols::helical_bundle::parameters::BundleParametersSet protocols::helical_bundle::BundleGridSampler::BundleParametersSet |
| typedef protocols::helical_bundle::parameters::BundleParametersSetCOP protocols::helical_bundle::BundleGridSampler::BundleParametersSetCOP |
| typedef protocols::helical_bundle::parameters::BundleParametersSetOP protocols::helical_bundle::BundleGridSampler::BundleParametersSetOP |
| typedef core::conformation::parametric::Parameters protocols::helical_bundle::BundleGridSampler::Parameters |
| typedef core::conformation::parametric::ParametersOP protocols::helical_bundle::BundleGridSampler::ParametersOP |
| typedef core::conformation::parametric::ParametersSet protocols::helical_bundle::BundleGridSampler::ParametersSet |
| typedef core::conformation::parametric::ParametersSetOP protocols::helical_bundle::BundleGridSampler::ParametersSetOP |
| protocols::helical_bundle::BundleGridSampler::BundleGridSampler | ( | ) |
| protocols::helical_bundle::BundleGridSampler::BundleGridSampler | ( | BundleGridSampler const & | src | ) |
Copy constructor for BundleGridSampler mover.
References delta_omega0_, delta_omega1_, delta_t_, epsilon_, omega0_, r0_, z0_offset_, and z1_offset_.
|
overridedefault |
Destructor for BundleGridSampler mover.
| core::Size protocols::helical_bundle::BundleGridSampler::add_helix | ( | ) |
Add options for a new helix.
Return value is the current total number of helices after the addition.
References delta_omega0(), delta_omega0_, delta_omega1(), delta_omega1_, delta_t(), delta_t_, epsilon(), epsilon_, increment_helix_count(), make_bundle_, n_helices(), omega0(), omega0_, r0(), r0_, z0_offset(), z0_offset_, z1_offset(), and z1_offset_.
Referenced by parse_my_tag().
|
overridevirtual |
Actually apply the mover to the pose.
Implements protocols::moves::Mover.
References protocols::helical_bundle::bgsh_delta_omega0, protocols::helical_bundle::bgsh_delta_omega1, protocols::helical_bundle::bgsh_delta_t, protocols::helical_bundle::bgsh_epsilon, protocols::helical_bundle::bgsh_omega0, protocols::helical_bundle::bgsh_r0, protocols::helical_bundle::bgsh_z0_offset, protocols::helical_bundle::bgsh_z1_offset, calculate_total_samples(), protocols::nonlocal::current_job(), default_delta_omega0(), default_delta_omega1(), default_delta_t(), default_epsilon(), default_omega0(), default_r0(), default_z0_offset(), default_z1_offset(), delta_omega0(), delta_omega1(), delta_t(), core::pose::Pose::dump_scored_pdb(), core::pose::Pose::energies(), epsilon(), protocols::moves::FAIL_RETRY, protocols::jd2::JobDistributor::get_instance(), protocols::jd2::JD2_BOGUS_JOB, protocols::jd2::jd2_used(), make_bundle_, max_samples(), protocols::moves::MS_SUCCESS, n_helices(), nstruct_mode(), nstruct_repeats(), omega0(), pdb_output(), pdb_prefix(), pre_selection_filter_, pre_selection_mover_, preselection_filter_exists(), preselection_mover_exists(), r0(), reset_mode(), selection_low(), protocols::moves::Mover::set_last_move_status(), sfxn_, sfxn_set(), core::scoring::Energies::total_energy(), protocols::helical_bundle::TR(), z0_offset(), and z1_offset().
|
private |
Calculate the number of grid points that will be sampled, based on the options set by the user.
References default_delta_omega0(), default_delta_omega1(), default_delta_t(), default_epsilon(), default_omega0(), default_r0(), default_z0_offset(), default_z1_offset(), delta_omega0(), delta_omega0_, delta_omega1(), delta_omega1_, delta_t(), delta_t_, epsilon(), epsilon_, n_helices(), omega0(), omega0_, r0(), r0_, z0_offset(), z0_offset_, z1_offset(), and z1_offset_.
Referenced by apply().
|
overridevirtual |
Clone operator to create a pointer to a fresh BundleGridSampler object that copies this one.
Reimplemented from protocols::moves::Mover.
References BundleGridSampler().
Referenced by parse_my_tag().
|
inline |
Access the default_delta_omega0_ BundleOptions object.
References default_delta_omega0_.
Referenced by apply(), calculate_total_samples(), and parse_my_tag().
|
inline |
Access the default_delta_omega0_ BundleOptions object (const-access).
References default_delta_omega0_.
|
inline |
Access the default_delta_omega1_ BundleOptions object.
References default_delta_omega1_.
Referenced by apply(), calculate_total_samples(), and parse_my_tag().
|
inline |
Access the default_delta_omega1_ BundleOptions object (const-access).
References default_delta_omega1_.
|
inline |
Access the default_delta_t_ BundleOptions object.
References default_delta_t_.
Referenced by apply(), calculate_total_samples(), and parse_my_tag().
|
inline |
Access the default_delta_t_ BundleOptions object (const-access).
References default_delta_t_.
|
inline |
Access the default_epsilon_ BundleOptions object.
References default_epsilon_.
Referenced by apply(), calculate_total_samples(), and parse_my_tag().
|
inline |
Access the default_epsilon_ BundleOptions object (const-access).
References default_epsilon_.
|
inline |
Access the default_omega0_ BundleOptions object.
References default_omega0_.
Referenced by apply(), calculate_total_samples(), and parse_my_tag().
|
inline |
Access the default_omega0_ BundleOptions object (const-access).
References default_omega0_.
|
inline |
Access the default_r0_ BundleOptions object.
References default_r0_.
Referenced by apply(), calculate_total_samples(), and parse_my_tag().
|
inline |
Access the default_r0_ BundleOptions object (const-access).
References default_r0_.
|
inline |
Access the default_z0_offset_ BundleOptions object.
References default_z0_offset_.
Referenced by apply(), calculate_total_samples(), and parse_my_tag().
|
inline |
Access the default_z0_offset_ BundleOptions object (const-access).
References default_z0_offset_.
|
inline |
Access the default_z1_offset_ BundleOptions object.
References default_z1_offset_.
Referenced by apply(), calculate_total_samples(), and parse_my_tag().
|
inline |
Access the default_z1_offset_ BundleOptions object (const-access).
References default_z1_offset_.
|
inline |
Access the delta_omega0_ BundleOptions object, by index.
This is the index in order of helices added, NOT necessarily the index of the helix.
References delta_omega0_.
Referenced by add_helix(), apply(), calculate_total_samples(), and parse_my_tag().
|
inline |
Access the delta_omega0_ BundleOptions object, by index. This provides const access.
This is the index in order of helices added, NOT necessarily the index of the helix.
References delta_omega0_.
|
inline |
Access the delta_omega1_ BundleOptions object, by index.
This is the index in order of helices added, NOT necessarily the index of the helix.
References delta_omega1_.
Referenced by add_helix(), apply(), calculate_total_samples(), and parse_my_tag().
|
inline |
Access the delta_omega1_ BundleOptions object, by index. This provides const access.
This is the index in order of helices added, NOT necessarily the index of the helix.
References delta_omega1_.
|
inline |
Access the delta_t_ BundleOptions object, by index.
This is the index in order of helices added, NOT necessarily the index of the helix.
References delta_t_.
Referenced by add_helix(), apply(), calculate_total_samples(), and parse_my_tag().
|
inline |
Access the delta_t_ BundleOptions object, by index. This provides const access.
This is the index in order of helices added, NOT necessarily the index of the helix.
References delta_t_.
|
inline |
Access the epsilon_ BundleOptions object, by index.
This is the index in order of helices added, NOT necessarily the index of the helix.
References epsilon_.
Referenced by add_helix(), apply(), calculate_total_samples(), and parse_my_tag().
|
inline |
Access the epsilon_ BundleOptions object, by index. This provides const access.
This is the index in order of helices added, NOT necessarily the index of the helix.
References epsilon_.
|
overridevirtual |
Fresh_instance operator to create a pointer to a fresh BundleGridSampler object that does NOT copy this one.
Reimplemented from protocols::moves::Mover.
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
References mover_name().
|
inline |
Increments the number of helices that have been defined.
References n_helices_.
Referenced by add_helix().
|
private |
Is a value in a list?
|
inline |
Get the maximum number of samples for the mover.
If the number of gridpoints based on user options exceeds this number, an error is thrown and the mover aborts. This is to prevent unreasonably large calculations from being attempted.
References max_samples_.
Referenced by apply().
|
static |
Referenced by get_name(), protocols::helical_bundle::BundleGridSamplerCreator::keyname(), and provide_xml_schema().
|
inline |
Returns the number of helices that have been defined.
References n_helices_.
Referenced by add_helix(), apply(), calculate_total_samples(), and parse_my_tag().
|
inline |
Get the nstruct mode.
If true, each job samples one set of Crick parameters. If false, every job samples every set of Crick parameters. False by default.
References nstruct_mode_.
Referenced by apply().
|
inline |
Get the nstruct repeats.
This is set to 1 by default, which means that each nstruct number correspnds to a different set of Crick parameters. If set greater than 1, then multiple consecutive nstruct numbers will correspond to the same Crick parameters. This allows combinatorially combining this mover's sampling with another, similar mover's sampling.
References nstruct_mode_repeats_.
Referenced by apply().
|
inline |
Access the omega0_ BundleOptions object, by index.
This is the index in order of helices added, NOT necessarily the index of the helix.
References omega0_.
Referenced by add_helix(), apply(), calculate_total_samples(), and parse_my_tag().
|
inline |
Access the omega0_ BundleOptions object, by index. This provides const access.
This is the index in order of helices added, NOT necessarily the index of the helix.
References omega0_.
|
overridevirtual |
Returns the name of this mover ("BundleGridSampler").
parse XML (specifically in the context of the parser/Rosetta_scripting scheme)
Reimplemented from protocols::moves::Mover.
References add_helix(), clone(), default_delta_omega0(), default_delta_omega1(), default_delta_t(), default_epsilon(), default_omega0(), default_r0(), default_z0_offset(), default_z1_offset(), delta_omega0(), delta_omega1(), delta_t(), epsilon(), make_bundle_, n_helices(), omega0(), protocols::rosetta_scripts::parse_filter(), protocols::rosetta_scripts::parse_mover(), protocols::rosetta_scripts::parse_score_function(), r0(), reset_mode(), set_max_samples(), set_nstruct_mode(), set_nstruct_repeats(), set_pdb_output(), set_pdb_prefix(), set_preselection_filter(), set_preselection_mover(), set_reset_mode(), set_selection_low(), set_sfxn(), protocols::helical_bundle::TR(), protocols::hybridization::val, z0_offset(), and z1_offset().
|
inline |
|
inline |
Access the filename prefix for PDB output.
PDB files are of the form <prefix>_#####.pdb.
References pdb_prefix_.
Referenced by apply().
|
inline |
Returns "true" if and only if a preselection filter has been assigned.
References pre_selection_filter_exists_.
Referenced by apply().
|
inline |
Returns "true" if and only if a preselection mover has been assigned.
References pre_selection_mover_exists_.
Referenced by apply().
|
static |
References protocols::helical_bundle::add_attributes_for_helix_params(), protocols::helical_bundle::add_attributes_for_make_bundle_dofs(), protocols::helical_bundle::add_attributes_for_make_bundle_minorhelix_defaults(), protocols::helical_bundle::add_attributes_for_make_bundle_other_defaults(), protocols::helical_bundle::add_attributes_for_make_bundle_symmetry(), protocols::helical_bundle::add_attributes_for_minor_helix_params(), protocols::helical_bundle::add_attributes_for_other_helix_params(), protocols::rosetta_scripts::attributes_for_parse_score_function(), mover_name(), protocols::helical_bundle::subtag_for_bundgrid(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().
Referenced by protocols::helical_bundle::BundleGridSamplerCreator::provide_xml_schema().
|
inline |
Access the r0_ BundleOptions object, by index.
This is the index in order of helices added, NOT necessarily the index of the helix.
References r0_.
Referenced by add_helix(), apply(), calculate_total_samples(), and parse_my_tag().
|
inline |
Access the r0_ BundleOptions object, by index. This provides const access.
This is the index in order of helices added, NOT necessarily the index of the helix.
References r0_.
|
inline |
Get the reset mode.
If true (default), the pose is reset before generating bundles. If false, it is not.
References reset_mode_.
Referenced by apply(), and parse_my_tag().
|
inline |
Returns whether the selection should be for the lowest score value (true) or highest (false).
References select_low_.
Referenced by apply().
|
inline |
Set the maximum number of samples for the mover.
If the number of gridpoints based on user options exceeds this number, an error is thrown and the mover aborts. This is to prevent unreasonably large calculations from being attempted.
References max_samples_, and protocols::hybridization::val.
Referenced by parse_my_tag().
|
inline |
Set the nstruct mode.
If true, each job samples one set of Crick parameters. If false, every job samples every set of Crick parameters. False by default.
References nstruct_mode_, and protocols::hybridization::val.
Referenced by parse_my_tag().
|
inline |
Set the nstruct repeats.
This is set to 1 by default, which means that each nstruct number correspnds to a different set of Crick parameters. If set greater than 1, then multiple consecutive nstruct numbers will correspond to the same Crick parameters. This allows combinatorially combining this mover's sampling with another, similar mover's sampling.
References nstruct_mode_repeats_, and protocols::hybridization::val.
Referenced by parse_my_tag().
|
inline |
Set whether the mover dumps pdbs or not.
References dump_pdbs_, and protocols::hybridization::val.
Referenced by parse_my_tag().
|
inline |
Sets the filename prefix for PDB output.
PDB files are of the form <prefix>_#####.pdb.
References pdb_prefix_.
Referenced by parse_my_tag().
| void protocols::helical_bundle::BundleGridSampler::set_preselection_filter | ( | protocols::filters::FilterOP | filter | ) |
Sets the filter that will be applied to all helical bundles generated prior to energy evaluation.
See the pre_selection_filter_ private member variable for details.
References pre_selection_filter_, and pre_selection_filter_exists_.
Referenced by parse_my_tag().
| void protocols::helical_bundle::BundleGridSampler::set_preselection_mover | ( | protocols::moves::MoverOP | mover | ) |
Sets the mover that will be applied to all helical bundles generated prior to energy evaluation.
Note: if this is used, there is no guarantee that the resulting geometry will still lie within the parameter space. (That is, this mover could move the backbone.)
References pre_selection_mover_, and pre_selection_mover_exists_.
Referenced by parse_my_tag().
|
inline |
Set the reset mode.
If true (default), the pose is reset before generating bundles. If false, it is not.
References reset_mode_, and protocols::hybridization::val.
Referenced by parse_my_tag().
|
inline |
Sets whether the selection should be for the lowest score value (true) or highest (false).
References select_low_, and protocols::hybridization::val.
Referenced by parse_my_tag().
|
inline |
Sets the scorefunction for this mover.
This must be done before calling the apply() function.
References sfxn_, and sfxn_set_.
Referenced by parse_my_tag().
|
inline |
|
inline |
Access the z0_offset_ BundleOptions object, by index.
This is the index in order of helices added, NOT necessarily the index of the helix.
References z0_offset_.
Referenced by add_helix(), apply(), calculate_total_samples(), and parse_my_tag().
|
inline |
Access the z0_offset_ BundleOptions object, by index. This provides const access.
This is the index in order of helices added, NOT necessarily the index of the helix.
References z0_offset_.
|
inline |
Access the z1_offset_ BundleOptions object, by index.
This is the index in order of helices added, NOT necessarily the index of the helix.
References z1_offset_.
Referenced by add_helix(), apply(), calculate_total_samples(), and parse_my_tag().
|
inline |
Access the z1_offset_ BundleOptions object, by index. This provides const access.
This is the index in order of helices added, NOT necessarily the index of the helix.
References z1_offset_.
|
private |
Default options for sampling delta_omega0.
May be overridden on a helix-by-helix basis.
Referenced by default_delta_omega0().
|
private |
Default options for sampling delta_omega1.
May be overridden on a helix-by-helix basis.
Referenced by default_delta_omega1().
|
private |
Default options for sampling delta_t.
May be overridden on a helix-by-helix basis.
Referenced by default_delta_t().
|
private |
Default options for sampling epsilon.
May be overridden on a helix-by-helix basis.
Referenced by BundleGridSampler(), and default_epsilon().
|
private |
Default options for sampling omega0.
May be overridden on a helix-by-helix basis.
Referenced by default_omega0().
|
private |
Default options for sampling r0.
May be overridden on a helix-by-helix basis.
Referenced by default_r0().
|
private |
Default options for sampling z0_offset.
May be overridden on a helix-by-helix basis.
Referenced by default_z0_offset().
|
private |
Default options for sampling z1_offset.
May be overridden on a helix-by-helix basis.
Referenced by default_z1_offset().
|
private |
Helix-by-helix options for sampling delta_omega0.
Referenced by add_helix(), BundleGridSampler(), calculate_total_samples(), and delta_omega0().
|
private |
Helix-by-helix options for sampling delta_omega1.
Referenced by add_helix(), BundleGridSampler(), calculate_total_samples(), and delta_omega1().
|
private |
Helix-by-helix options for sampling delta_t.
Referenced by add_helix(), BundleGridSampler(), calculate_total_samples(), and delta_t().
|
private |
Dump a PDB file for each bundle generated? False by default.
Referenced by pdb_output(), and set_pdb_output().
|
private |
Helix-by-helix options for sampling epsilon.
Referenced by add_helix(), BundleGridSampler(), calculate_total_samples(), and epsilon().
|
private |
A MakeBundle mover that this mover will call.
Referenced by add_helix(), apply(), and parse_my_tag().
|
private |
The maximum number of gridpoints allowed.
If the number of gridpoints based on user options exceeds this number, an error is thrown and the mover aborts. This is to prevent unreasonably large calculations from being attempted. Default value is ten thousand (10,000).
Referenced by max_samples(), and set_max_samples().
|
private |
The number of helices that have been defined.
Referenced by increment_helix_count(), and n_helices().
|
private |
Should the parallel sampling be done based on the job (nstruct number)?
If true, each job samples one set of Crick parameters. If false, every job samples every set of Crick parameters. False by default.
Referenced by nstruct_mode(), and set_nstruct_mode().
|
private |
If nstruct_mode_ is true, how many times should each set of Crick parameters be repeated?
This is set to 1 by default, which means that each nstruct number correspnds to a different set of Crick parameters. If set greater than 1, then multiple consecutive nstruct numbers will correspond to the same Crick parameters. This allows combinatorially combining this mover's sampling with another, similar mover's sampling.
Referenced by nstruct_repeats(), and set_nstruct_repeats().
|
private |
Helix-by-helix options for sampling omega0.
Referenced by add_helix(), BundleGridSampler(), calculate_total_samples(), and omega0().
|
private |
PDB filename prefix. Filename will be of the form <prefix>_#####.pdb.
Defaults to "bgs_out".
Referenced by pdb_prefix(), and set_pdb_prefix().
|
private |
Owning pointer for an (optional) pre-selection filter applied to all helical bundles after the pre-selection mover but before picking the lowest-energy solution. If PDBs are dumped, only those passing filters are dumped.
Referenced by apply(), and set_preselection_filter().
|
private |
Bool determining whether a pre-selection filter has been set.
Referenced by preselection_filter_exists(), and set_preselection_filter().
|
private |
Owning pointer for an (optional) pre-selection mover applied to all helical bundles before energy evaluation.
Referenced by apply(), and set_preselection_mover().
|
private |
Bool determining whether there exists a pre-selection mover that wlil be applied.
Referenced by preselection_mover_exists(), and set_preselection_mover().
|
private |
Helix-by-helix options for sampling r0.
Referenced by add_helix(), BundleGridSampler(), calculate_total_samples(), and r0().
|
private |
Should the pose be reset before applying the GridSampler? Default true.
Referenced by reset_mode(), and set_reset_mode().
|
private |
The selection type. If false, the pose with the highest score value is selected. If true, the pose with the lowest score value is selected. True by default.
Referenced by selection_low(), and set_selection_low().
|
private |
The scorefunction that this mover will use to pick the lowest-energy bundle.
Must be set prior to calling apply() function.
Referenced by apply(), and set_sfxn().
|
private |
|
private |
Helix-by-helix options for sampling z0_offset.
Referenced by add_helix(), BundleGridSampler(), calculate_total_samples(), and z0_offset().
|
private |
Helix-by-helix options for sampling z1_offset.
Referenced by add_helix(), BundleGridSampler(), calculate_total_samples(), and z1_offset().
1.8.7