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protocols::swa::StepWisePoseSetup Class Reference

#include <StepWisePoseSetup.hh>

Inheritance diagram for protocols::swa::StepWisePoseSetup:
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Public Member Functions

 StepWisePoseSetup (utility::vector1< core::Size > const &moving_res_list, std::string const &desired_sequence, utility::vector1< InputStreamWithResidueInfoOP > &input_streams_with_residue_info, utility::vector1< core::Size > const &cutpoint_open, utility::vector1< core::Size > const &cutpoint_closed)
 
 ~StepWisePoseSetup ()
 
virtual void apply (core::pose::Pose &pose_to_visualize)
 Apply the minimizer to one pose. More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
StepWiseJobParametersOPjob_parameters ()
 
void set_fixed_res (utility::vector1< core::Size > const &fixed_res)
 
void set_jump_res (utility::vector1< core::Size > const &jump_res)
 
void set_virtual_res (utility::vector1< core::Size > const &set_virtual_res_list)
 
void set_terminal_res (utility::vector1< core::Size > const &terminal_res)
 
void set_superimpose_res (utility::vector1< core::Size > const &superimpose_res)
 
void set_calc_rms_res (utility::vector1< core::Size > const &calc_rms_res)
 
void set_bulge_res (utility::vector1< core::Size > const &bulge_res)
 
void set_bridge_res (utility::vector1< core::Size > const &bridge_res)
 
void set_parin_favorite_output (bool const &setting)
 
void set_rsd_set (core::chemical::ResidueTypeSetCAP &rsd_set)
 
void set_cst_file (std::string const cst_file)
 
void set_disulfide_file (std::string const disulfide_file)
 
void set_align_file (std::string const align_file)
 
void set_add_peptide_plane_variants (bool const &setting)
 
void set_remove_nterminus_variant (bool const &setting)
 
void set_remove_cterminus_variant (bool const &setting)
 
void align_pose (core::pose::Pose &pose)
 
bool ready_to_align () const
 
void set_dump (bool const dump)
 
void set_secstruct (std::string const secstruct)
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
std::string const & type () const
 
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...
 
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)
 
virtual MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
virtual void parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool reinitialize_for_each_job () const
 this function informs 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
 this function informs 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...
 
virtual MoverOP fresh_instance () const
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Private Member Functions

void Import_pose (core::pose::Pose &import_pose, InputStreamWithResidueInfoOP &stream)
 
void check_moving_res_in_chain (Size const &start_chain, Size const &end_chain, Size const &num_chains, Size &which_chain_has_moving_res)
 
void figure_out_working_sequence_and_mapping ()
 
void setup_secstruct (core::pose::Pose &pose) const
 
void figure_out_jump_partners ()
 
Size which_chain (Size const &i)
 
bool already_connected (std::pair< Size, Size > const &potential_chain_partner, utility::vector1< std::pair< Size, Size > > const &chain_partners) const
 
bool already_connected (Size const start_chain, Size const stop_chain, utility::vector1< std::pair< Size, Size > > const &chain_partners, utility::vector1< bool > already_checked) const
 
void figure_out_cuts ()
 
void make_pose (core::pose::Pose &pose)
 
void make_full_pose (core::pose::Pose &pose)
 
void setup_constraints (core::pose::Pose &pose)
 
void setup_disulfides (core::pose::Pose &pose)
 
void initialize_pose_from_streams (core::pose::Pose &pose)
 
void figure_out_Prepend_Internal (core::pose::Pose const &pose)
 
void figure_out_partition_definition (core::pose::Pose const &pose)
 
void figure_out_gap_size_and_first_chain_break_res ()
 
void reroot_fold_tree (core::pose::Pose &pose)
 
void apply_cutpoint_variants (core::pose::Pose &pose) const
 
void check_close_chain_break (core::pose::Pose const &pose) const
 
void apply_bulge_variants (core::pose::Pose &pose) const
 
void apply_terminus_variants_at_protein_rna_boundaries (core::pose::Pose &pose) const
 
void setup_working_native_pose ()
 
void get_working_pose (core::pose::Pose const &pose, core::pose::Pose &working_pose)
 
void align_poses (core::pose::Pose &pose)
 
utility::vector1< Size > const apply_full_to_sub_mapping (utility::vector1< Size > &res_vector) const
 
void apply_virtual_phosphate_variants (core::pose::Pose &pose) const
 
void apply_peptide_plane_variants_OLD (core::pose::Pose &pose) const
 
void apply_peptide_plane_variants (core::pose::Pose &pose) const
 
void add_terminal_res_repulsion (core::pose::Pose &pose) const
 
void apply_virtual_res_variant (core::pose::Pose &pose) const
 
void initialize_phi_psi_offsets (core::pose::Pose const &pose)
 
void save_phi_psi_offsets (core::pose::Pose const &start_pose, utility::vector1< core::Size > const &input_res, utility::vector1< core::Size > const &slice_res)
 
void fix_phi_psi_offsets (core::pose::Pose &pose) const
 
void copy_rna_chi (core::pose::Pose &pose, core::pose::Pose const import_pose, utility::vector1< core::Size > const &input_res, utility::vector1< core::Size > const &slice_res)
 
void check_superimpose_res (core::pose::Pose const &pose)
 
bool is_working_cutpoint_closed (Size const res, std::map< Size, Size > &full_to_sub) const
 
std::string get_swa_jump_atom (core::conformation::Residue const &rsd)
 

Private Attributes

utility::vector1< core::Size >
const & 
moving_res_list_
 
std::string const desired_sequence_
 
core::chemical::ResidueTypeSetCAP rsd_set_
 
utility::vector1
< InputStreamWithResidueInfoOP
input_streams_with_residue_info_
 
utility::vector1< Size > const cutpoint_open_
 
utility::vector1< Size > const cutpoint_closed_
 
utility::vector1< Sizefixed_res_
 
utility::vector1< Sizevirtual_res_list_
 
utility::vector1< Sizeterminal_res_
 
utility::vector1< Sizesuperimpose_res_
 
utility::vector1< Sizecalc_rms_res_
 
utility::vector1< Sizebulge_res_
 
utility::vector1< Sizejump_res_
 
utility::vector1< Sizebridge_res_
 
ObjexxFCL::FArray1D< boolis_cutpoint_
 
std::string secstruct_
 
ObjexxFCL::FArray1D< core::Realphi_offsets_
 
ObjexxFCL::FArray1D< core::Realpsi_offsets_
 
utility::vector1< std::pair
< core::Size, core::Size > > 
jump_partners_
 
utility::vector1< core::Sizecuts_
 
StepWiseJobParametersOP job_parameters_
 
bool virtualize_5prime_phosphates_
 
bool add_peptide_plane_variants_
 
bool remove_nterminus_variant_
 
bool remove_cterminus_variant_
 
bool parin_favorite_output_
 
std::string cst_file_
 
std::string disulfide_file_
 
core::scoring::constraints::ConstraintSetOP cst_set_
 
core::pose::PoseOP working_native_pose
 
Size const BRIDGE_RES_
 
std::string align_file_
 
bool ready_to_align_
 
core::pose::PoseOP working_align_pose_
 
core::id::AtomID_Map
< core::id::AtomID
alignment_atom_id_map_
 
bool dump_
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::string > Strings
 
- 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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...
 
- 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

protocols::swa::StepWisePoseSetup::StepWisePoseSetup ( utility::vector1< core::Size > const &  moving_res_list,
std::string const &  desired_sequence,
utility::vector1< InputStreamWithResidueInfoOP > &  input_streams_with_residue_info,
utility::vector1< core::Size > const &  cutpoint_open,
utility::vector1< core::Size > const &  cutpoint_closed 
)
protocols::swa::StepWisePoseSetup::~StepWisePoseSetup ( )

Member Function Documentation

void protocols::swa::StepWisePoseSetup::add_terminal_res_repulsion ( core::pose::Pose pose) const
private
void protocols::swa::StepWisePoseSetup::align_pose ( core::pose::Pose pose)
void protocols::swa::StepWisePoseSetup::align_poses ( core::pose::Pose pose)
private
bool protocols::swa::StepWisePoseSetup::already_connected ( std::pair< Size, Size > const &  potential_chain_partner,
utility::vector1< std::pair< Size, Size > > const &  chain_partners 
) const
private
bool protocols::swa::StepWisePoseSetup::already_connected ( Size const  start_chain,
Size const  stop_chain,
utility::vector1< std::pair< Size, Size > > const &  chain_partners,
utility::vector1< bool already_checked 
) const
private

References already_connected().

void protocols::swa::StepWisePoseSetup::apply ( core::pose::Pose pose_to_visualize)
virtual
void protocols::swa::StepWisePoseSetup::apply_bulge_variants ( core::pose::Pose pose) const
private
void protocols::swa::StepWisePoseSetup::apply_cutpoint_variants ( core::pose::Pose pose) const
private
utility::vector1< Size > const protocols::swa::StepWisePoseSetup::apply_full_to_sub_mapping ( utility::vector1< Size > &  res_vector) const
private

References job_parameters_.

Referenced by apply().

void protocols::swa::StepWisePoseSetup::apply_peptide_plane_variants ( core::pose::Pose pose) const
private
void protocols::swa::StepWisePoseSetup::apply_peptide_plane_variants_OLD ( core::pose::Pose pose) const
private
void protocols::swa::StepWisePoseSetup::apply_terminus_variants_at_protein_rna_boundaries ( core::pose::Pose pose) const
private
void protocols::swa::StepWisePoseSetup::apply_virtual_phosphate_variants ( core::pose::Pose pose) const
private
void protocols::swa::StepWisePoseSetup::apply_virtual_res_variant ( core::pose::Pose pose) const
private
void protocols::swa::StepWisePoseSetup::check_close_chain_break ( core::pose::Pose const &  pose) const
private
void protocols::swa::StepWisePoseSetup::check_moving_res_in_chain ( Size const &  start_chain,
Size const &  end_chain,
Size const &  num_chains,
Size which_chain_has_moving_res 
)
private
void protocols::swa::StepWisePoseSetup::check_superimpose_res ( core::pose::Pose const &  pose)
private
void protocols::swa::StepWisePoseSetup::copy_rna_chi ( core::pose::Pose pose,
core::pose::Pose const  import_pose,
utility::vector1< core::Size > const &  input_res,
utility::vector1< core::Size > const &  slice_res 
)
private
void protocols::swa::StepWisePoseSetup::figure_out_cuts ( )
private

References cuts_, and job_parameters_.

Referenced by apply().

void protocols::swa::StepWisePoseSetup::figure_out_gap_size_and_first_chain_break_res ( )
private

References BRIDGE_RES_, cutpoint_open_, and job_parameters_.

Referenced by apply().

void protocols::swa::StepWisePoseSetup::figure_out_jump_partners ( )
private
void protocols::swa::StepWisePoseSetup::figure_out_partition_definition ( core::pose::Pose const &  pose)
private
void protocols::swa::StepWisePoseSetup::figure_out_Prepend_Internal ( core::pose::Pose const &  pose)
private
void protocols::swa::StepWisePoseSetup::figure_out_working_sequence_and_mapping ( )
private
void protocols::swa::StepWisePoseSetup::fix_phi_psi_offsets ( core::pose::Pose pose) const
private
std::string protocols::swa::StepWisePoseSetup::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

std::string protocols::swa::StepWisePoseSetup::get_swa_jump_atom ( core::conformation::Residue const &  rsd)
private
void protocols::swa::StepWisePoseSetup::get_working_pose ( core::pose::Pose const &  pose,
core::pose::Pose working_pose 
)
private
void protocols::swa::StepWisePoseSetup::Import_pose ( core::pose::Pose import_pose,
InputStreamWithResidueInfoOP stream 
)
private
void protocols::swa::StepWisePoseSetup::initialize_phi_psi_offsets ( core::pose::Pose const &  pose)
private
void protocols::swa::StepWisePoseSetup::initialize_pose_from_streams ( core::pose::Pose pose)
private
bool protocols::swa::StepWisePoseSetup::is_working_cutpoint_closed ( Size const  res,
std::map< Size, Size > &  full_to_sub 
) const
private
StepWiseJobParametersOP & protocols::swa::StepWisePoseSetup::job_parameters ( )

References job_parameters_.

void protocols::swa::StepWisePoseSetup::make_full_pose ( core::pose::Pose pose)
private
void protocols::swa::StepWisePoseSetup::make_pose ( core::pose::Pose pose)
private
bool protocols::swa::StepWisePoseSetup::ready_to_align ( ) const

References ready_to_align_.

void protocols::swa::StepWisePoseSetup::reroot_fold_tree ( core::pose::Pose pose)
private
void protocols::swa::StepWisePoseSetup::save_phi_psi_offsets ( core::pose::Pose const &  start_pose,
utility::vector1< core::Size > const &  input_res,
utility::vector1< core::Size > const &  slice_res 
)
private
void protocols::swa::StepWisePoseSetup::set_add_peptide_plane_variants ( bool const &  setting)
void protocols::swa::StepWisePoseSetup::set_align_file ( std::string const  align_file)

References align_file_.

void protocols::swa::StepWisePoseSetup::set_bridge_res ( utility::vector1< core::Size > const &  bridge_res)

References bridge_res_.

void protocols::swa::StepWisePoseSetup::set_bulge_res ( utility::vector1< core::Size > const &  bulge_res)

References bulge_res_.

void protocols::swa::StepWisePoseSetup::set_calc_rms_res ( utility::vector1< core::Size > const &  calc_rms_res)

References calc_rms_res_.

void protocols::swa::StepWisePoseSetup::set_cst_file ( std::string const  cst_file)

References cst_file_.

void protocols::swa::StepWisePoseSetup::set_disulfide_file ( std::string const  disulfide_file)

References disulfide_file_.

void protocols::swa::StepWisePoseSetup::set_dump ( bool const  dump)

References dump_.

void protocols::swa::StepWisePoseSetup::set_fixed_res ( utility::vector1< core::Size > const &  fixed_res)

References fixed_res_.

void protocols::swa::StepWisePoseSetup::set_jump_res ( utility::vector1< core::Size > const &  jump_res)

References jump_res_.

void protocols::swa::StepWisePoseSetup::set_parin_favorite_output ( bool const &  setting)
inline
void protocols::swa::StepWisePoseSetup::set_remove_cterminus_variant ( bool const &  setting)
inline
void protocols::swa::StepWisePoseSetup::set_remove_nterminus_variant ( bool const &  setting)
inline
void protocols::swa::StepWisePoseSetup::set_rsd_set ( core::chemical::ResidueTypeSetCAP rsd_set)

References rsd_set_.

void protocols::swa::StepWisePoseSetup::set_secstruct ( std::string const  secstruct)

References secstruct_.

void protocols::swa::StepWisePoseSetup::set_superimpose_res ( utility::vector1< core::Size > const &  superimpose_res)

References superimpose_res_.

void protocols::swa::StepWisePoseSetup::set_terminal_res ( utility::vector1< core::Size > const &  terminal_res)

References terminal_res_.

void protocols::swa::StepWisePoseSetup::set_virtual_res ( utility::vector1< core::Size > const &  set_virtual_res_list)

References virtual_res_list_.

void protocols::swa::StepWisePoseSetup::setup_constraints ( core::pose::Pose pose)
private
void protocols::swa::StepWisePoseSetup::setup_disulfides ( core::pose::Pose pose)
private
void protocols::swa::StepWisePoseSetup::setup_secstruct ( core::pose::Pose pose) const
private
void protocols::swa::StepWisePoseSetup::setup_working_native_pose ( )
private
Size protocols::swa::StepWisePoseSetup::which_chain ( Size const &  i)
private

References job_parameters_.

Referenced by figure_out_jump_partners().

Member Data Documentation

bool protocols::swa::StepWisePoseSetup::add_peptide_plane_variants_
private
std::string protocols::swa::StepWisePoseSetup::align_file_
private
core::id::AtomID_Map< core::id::AtomID > protocols::swa::StepWisePoseSetup::alignment_atom_id_map_
private

Referenced by align_pose(), and align_poses().

utility::vector1< Size > protocols::swa::StepWisePoseSetup::bridge_res_
private
Size const protocols::swa::StepWisePoseSetup::BRIDGE_RES_
private
utility::vector1< Size > protocols::swa::StepWisePoseSetup::bulge_res_
private
utility::vector1< Size > protocols::swa::StepWisePoseSetup::calc_rms_res_
private

Referenced by apply(), and set_calc_rms_res().

std::string protocols::swa::StepWisePoseSetup::cst_file_
private

Referenced by set_cst_file(), and setup_constraints().

core::scoring::constraints::ConstraintSetOP protocols::swa::StepWisePoseSetup::cst_set_
private

Referenced by setup_constraints().

utility::vector1< Size > const protocols::swa::StepWisePoseSetup::cutpoint_closed_
private
utility::vector1< Size > const protocols::swa::StepWisePoseSetup::cutpoint_open_
private
utility::vector1< core::Size > protocols::swa::StepWisePoseSetup::cuts_
private

Referenced by figure_out_cuts(), and make_pose().

std::string const protocols::swa::StepWisePoseSetup::desired_sequence_
private
std::string protocols::swa::StepWisePoseSetup::disulfide_file_
private
bool protocols::swa::StepWisePoseSetup::dump_
private
utility::vector1< Size > protocols::swa::StepWisePoseSetup::fixed_res_
private

Referenced by apply(), and set_fixed_res().

utility::vector1< InputStreamWithResidueInfoOP > protocols::swa::StepWisePoseSetup::input_streams_with_residue_info_
private
ObjexxFCL::FArray1D< bool > protocols::swa::StepWisePoseSetup::is_cutpoint_
private
StepWiseJobParametersOP protocols::swa::StepWisePoseSetup::job_parameters_
private
utility::vector1< std::pair< core::Size, core::Size > > protocols::swa::StepWisePoseSetup::jump_partners_
private
utility::vector1< Size > protocols::swa::StepWisePoseSetup::jump_res_
private
utility::vector1< core::Size > const& protocols::swa::StepWisePoseSetup::moving_res_list_
private
bool protocols::swa::StepWisePoseSetup::parin_favorite_output_
private
ObjexxFCL::FArray1D< core::Real > protocols::swa::StepWisePoseSetup::phi_offsets_
private
ObjexxFCL::FArray1D< core::Real > protocols::swa::StepWisePoseSetup::psi_offsets_
private
bool protocols::swa::StepWisePoseSetup::ready_to_align_
private
bool protocols::swa::StepWisePoseSetup::remove_cterminus_variant_
private
bool protocols::swa::StepWisePoseSetup::remove_nterminus_variant_
private
core::chemical::ResidueTypeSetCAP protocols::swa::StepWisePoseSetup::rsd_set_
private
std::string protocols::swa::StepWisePoseSetup::secstruct_
private

Referenced by set_secstruct(), and setup_secstruct().

utility::vector1< Size > protocols::swa::StepWisePoseSetup::superimpose_res_
private

Referenced by apply(), and set_superimpose_res().

utility::vector1< Size > protocols::swa::StepWisePoseSetup::terminal_res_
private

Referenced by apply(), and set_terminal_res().

utility::vector1< Size > protocols::swa::StepWisePoseSetup::virtual_res_list_
private
bool protocols::swa::StepWisePoseSetup::virtualize_5prime_phosphates_
private

Referenced by apply().

core::pose::PoseOP protocols::swa::StepWisePoseSetup::working_align_pose_
private

Referenced by align_pose(), and align_poses().

core::pose::PoseOP protocols::swa::StepWisePoseSetup::working_native_pose
private

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