Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup Class Reference

#include <StepWiseProteinPoseSetup.hh>

Inheritance diagram for protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup:
Inheritance graph
[legend]

Public Member Functions

 StepWiseProteinPoseSetup (utility::vector1< core::Size > const &moving_res_list, std::string const &desired_sequence, utility::vector1< protocols::stepwise::modeler::protein::InputStreamWithResidueInfoOP > &input_streams_with_residue_info, utility::vector1< core::Size > const &cutpoint_open, utility::vector1< core::Size > const &cutpoint_closed)
 
 ~StepWiseProteinPoseSetup () override
 
void apply (core::pose::Pose &pose_to_visualize) override
 Apply the minimizer to one pose. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
stepwise::modeler::working_parameters::StepWiseWorkingParametersOPworking_parameters ()
 
void set_fixed_res (utility::vector1< core::Size > const &fixed_res)
 
void set_extra_minimize_res (utility::vector1< core::Size > const &setting)
 
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) const
 
bool ready_to_align () const
 
void set_dump (bool const dump)
 
void set_add_virt_res (bool const setting)
 
void set_secstruct (std::string const &secstruct)
 
- 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 MoverOP clone () const
 Return a clone of the Mover object. 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...
 
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. 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
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
std::string get_current_tag () const
 A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual core::Real last_proposal_density_ratio ()
 
virtual void clear_info ()
 Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
 
virtual Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Private Member Functions

void Import_pose (core::pose::Pose &import_pose, protocols::stepwise::modeler::protein::InputStreamWithResidueInfoOP &stream)
 
void check_moving_res_in_chain (core::Size const &start_chain, core::Size const &end_chain, core::Size const &num_chains, core::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 ()
 
core::Size which_chain (core::Size const &i)
 
bool already_connected (std::pair< core::Size, core::Size > const &potential_chain_partner, utility::vector1< std::pair< core::Size, core::Size > > const &chain_partners) const
 
bool already_connected (core::Size const start_chain, core::Size const stop_chain, utility::vector1< std::pair< core::Size, core::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< core::Size >
const 
apply_full_to_sub_mapping (utility::vector1< core::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 (core::Size const res, std::map< core::Size, core::Size > &full_to_sub) const
 
std::string get_stepwise_jump_atom (core::chemical::ResidueType const &rsd)
 
void add_aa_virt_rsd_as_root (core::pose::Pose &pose)
 
void setup_full_model_info (core::pose::Pose &pose) const
 

Private Attributes

utility::vector1< core::Size >
const & 
moving_res_list_
 
std::string const desired_sequence_
 
core::chemical::ResidueTypeSetCAP rsd_set_
 
utility::vector1
< protocols::stepwise::modeler::protein::InputStreamWithResidueInfoOP
input_streams_with_residue_info_
 
utility::vector1< core::Size >
const 
cutpoint_open_
 
utility::vector1< core::Size >
const 
cutpoint_closed_
 
ObjexxFCL::FArray1D< boolis_cutpoint_
 
std::string secstruct_
 
utility::vector1< core::Sizefixed_res_
 
utility::vector1< core::Sizevirtual_res_list_
 
utility::vector1< core::Sizeterminal_res_
 
utility::vector1< core::Sizesuperimpose_res_
 
utility::vector1< core::Sizecalc_rms_res_
 
utility::vector1< core::Sizebulge_res_
 
utility::vector1< core::Sizejump_res_
 
utility::vector1< core::Sizebridge_res_
 
stepwise::modeler::working_parameters::StepWiseWorkingParametersOP working_parameters_
 
ObjexxFCL::FArray1D< core::Realphi_offsets_
 
ObjexxFCL::FArray1D< core::Realpsi_offsets_
 
utility::vector1< std::pair
< core::Size, core::Size > > 
jump_partners_
 
utility::vector1< core::Sizecuts_
 
utility::vector1< core::Sizeextra_minimize_res_
 
bool virtualize_5prime_phosphates_
 
bool add_peptide_plane_variants_
 
bool remove_nterminus_variant_
 
bool remove_cterminus_variant_
 
bool parin_favorite_output_
 
bool add_virt_res_
 
std::string cst_file_
 
std::string disulfide_file_
 
core::scoring::constraints::ConstraintSetOP cst_set_
 
core::pose::PoseOP working_native_pose
 
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::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
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. 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::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::StepWiseProteinPoseSetup ( utility::vector1< core::Size > const &  moving_res_list,
std::string const &  desired_sequence,
utility::vector1< protocols::stepwise::modeler::protein::InputStreamWithResidueInfoOP > &  input_streams_with_residue_info,
utility::vector1< core::Size > const &  cutpoint_open,
utility::vector1< core::Size > const &  cutpoint_closed 
)
protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::~StepWiseProteinPoseSetup ( )
overridedefault

Member Function Documentation

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::add_aa_virt_rsd_as_root ( core::pose::Pose pose)
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::add_terminal_res_repulsion ( core::pose::Pose pose) const
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::align_pose ( core::pose::Pose pose) const
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::align_poses ( core::pose::Pose pose)
private
bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::already_connected ( std::pair< core::Size, core::Size > const &  potential_chain_partner,
utility::vector1< std::pair< core::Size, core::Size > > const &  chain_partners 
) const
private
bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::already_connected ( core::Size const  start_chain,
core::Size const  stop_chain,
utility::vector1< std::pair< core::Size, core::Size > > const &  chain_partners,
utility::vector1< bool already_checked 
) const
private

References already_connected().

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply ( core::pose::Pose pose_to_visualize)
overridevirtual
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_bulge_variants ( core::pose::Pose pose) const
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_cutpoint_variants ( core::pose::Pose pose) const
private
utility::vector1< core::Size > const protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_full_to_sub_mapping ( utility::vector1< core::Size > &  res_vector) const
private

References working_parameters_.

Referenced by apply().

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_peptide_plane_variants ( core::pose::Pose pose) const
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_peptide_plane_variants_OLD ( core::pose::Pose pose) const
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_terminus_variants_at_protein_rna_boundaries ( core::pose::Pose pose) const
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_virtual_phosphate_variants ( core::pose::Pose pose) const
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_virtual_res_variant ( core::pose::Pose pose) const
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::check_close_chain_break ( core::pose::Pose const &  pose) const
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::check_moving_res_in_chain ( core::Size const &  start_chain,
core::Size const &  end_chain,
core::Size const &  num_chains,
core::Size which_chain_has_moving_res 
)
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::check_superimpose_res ( core::pose::Pose const &  pose)
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::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::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_cuts ( )
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_gap_size_and_first_chain_break_res ( )
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_jump_partners ( )
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_partition_definition ( core::pose::Pose const &  pose)
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_Prepend_Internal ( core::pose::Pose const &  pose)
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_working_sequence_and_mapping ( )
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::fix_phi_psi_offsets ( core::pose::Pose pose) const
private
std::string protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

std::string protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::get_stepwise_jump_atom ( core::chemical::ResidueType const &  rsd)
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::get_working_pose ( core::pose::Pose const &  pose,
core::pose::Pose working_pose 
)
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::Import_pose ( core::pose::Pose import_pose,
protocols::stepwise::modeler::protein::InputStreamWithResidueInfoOP stream 
)
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::initialize_phi_psi_offsets ( core::pose::Pose const &  pose)
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::initialize_pose_from_streams ( core::pose::Pose pose)
private
bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::is_working_cutpoint_closed ( core::Size const  res,
std::map< core::Size, core::Size > &  full_to_sub 
) const
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::make_full_pose ( core::pose::Pose pose)
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::make_pose ( core::pose::Pose pose)
private
bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::ready_to_align ( ) const

References ready_to_align_.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::reroot_fold_tree ( core::pose::Pose pose)
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::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::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_add_peptide_plane_variants ( bool const &  setting)
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_add_virt_res ( bool const  setting)

References add_virt_res_.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_align_file ( std::string const &  align_file)

References align_file_.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_bridge_res ( utility::vector1< core::Size > const &  bridge_res)

References bridge_res_.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_bulge_res ( utility::vector1< core::Size > const &  bulge_res)

References bulge_res_.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_calc_rms_res ( utility::vector1< core::Size > const &  calc_rms_res)

References calc_rms_res_.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_cst_file ( std::string const &  cst_file)

References cst_file_.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_disulfide_file ( std::string const &  disulfide_file)

References disulfide_file_.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_dump ( bool const  dump)

References dump_.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_extra_minimize_res ( utility::vector1< core::Size > const &  setting)
inline

References extra_minimize_res_.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_fixed_res ( utility::vector1< core::Size > const &  fixed_res)

References fixed_res_.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_jump_res ( utility::vector1< core::Size > const &  jump_res)

References jump_res_.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_parin_favorite_output ( bool const &  setting)
inline
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_remove_cterminus_variant ( bool const &  setting)
inline
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_remove_nterminus_variant ( bool const &  setting)
inline
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_rsd_set ( core::chemical::ResidueTypeSetCAP rsd_set)

References rsd_set_.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_secstruct ( std::string const &  secstruct)

References secstruct_.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_superimpose_res ( utility::vector1< core::Size > const &  superimpose_res)

References superimpose_res_.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_terminal_res ( utility::vector1< core::Size > const &  terminal_res)

References terminal_res_.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_virtual_res ( utility::vector1< core::Size > const &  set_virtual_res_list)

References virtual_res_list_.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::setup_constraints ( core::pose::Pose pose)
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::setup_disulfides ( core::pose::Pose pose)
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::setup_full_model_info ( core::pose::Pose pose) const
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::setup_secstruct ( core::pose::Pose pose) const
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::setup_working_native_pose ( )
private
Size protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::which_chain ( core::Size const &  i)
private
stepwise::modeler::working_parameters::StepWiseWorkingParametersOP & protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::working_parameters ( )

References working_parameters_.

Member Data Documentation

bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::add_peptide_plane_variants_
private
bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::add_virt_res_
private
std::string protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::align_file_
private
core::id::AtomID_Map< core::id::AtomID > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::alignment_atom_id_map_
private

Referenced by align_pose(), and align_poses().

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::bridge_res_
private
utility::vector1< core::Size > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::bulge_res_
private
utility::vector1< core::Size > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::calc_rms_res_
private
std::string protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::cst_file_
private

Referenced by set_cst_file(), and setup_constraints().

core::scoring::constraints::ConstraintSetOP protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::cst_set_
private

Referenced by setup_constraints().

utility::vector1< core::Size > const protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::cutpoint_closed_
private
utility::vector1< core::Size > const protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::cutpoint_open_
private
utility::vector1< core::Size > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::cuts_
private

Referenced by figure_out_cuts(), and make_pose().

std::string const protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::desired_sequence_
private
std::string protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::disulfide_file_
private
bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::dump_
private
utility::vector1< core::Size > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::extra_minimize_res_
private
utility::vector1< core::Size > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::fixed_res_
private
utility::vector1< protocols::stepwise::modeler::protein::InputStreamWithResidueInfoOP > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::input_streams_with_residue_info_
private
ObjexxFCL::FArray1D< bool > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::is_cutpoint_
private
utility::vector1< std::pair< core::Size, core::Size > > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::jump_partners_
private
utility::vector1< core::Size > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::jump_res_
private
utility::vector1< core::Size > const& protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::moving_res_list_
private
bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::parin_favorite_output_
private
ObjexxFCL::FArray1D< core::Real > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::phi_offsets_
private
ObjexxFCL::FArray1D< core::Real > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::psi_offsets_
private
bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::ready_to_align_
private
bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::remove_cterminus_variant_
private
bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::remove_nterminus_variant_
private
core::chemical::ResidueTypeSetCAP protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::rsd_set_
private
std::string protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::secstruct_
private

Referenced by set_secstruct(), and setup_secstruct().

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::superimpose_res_
private

Referenced by apply(), and set_superimpose_res().

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::terminal_res_
private

Referenced by set_terminal_res().

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::virtual_res_list_
private
bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::virtualize_5prime_phosphates_
private

Referenced by apply().

core::pose::PoseOP protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::working_align_pose_
private

Referenced by align_pose(), and align_poses().

core::pose::PoseOP protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::working_native_pose
private
stepwise::modeler::working_parameters::StepWiseWorkingParametersOP protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::working_parameters_
private

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