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Public Member Functions | Public Attributes | Private Attributes | List of all members
protocols::flexpep_docking::FlexPepDockingFlags Class Reference

#include <FlexPepDockingFlags.hh>

Inheritance diagram for protocols::flexpep_docking::FlexPepDockingFlags:
Inheritance graph
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Public Member Functions

 FlexPepDockingFlags ()
 initialize all flags from cmd-line options More...
 
FlexPepDockingFlagsOP clone () const
 
void updateChains (core::pose::Pose const &pose)
 
void setDefaultAnchors (core::pose::Pose &pose)
 
void updateChainsAndAnchors_fromParamsFile (std::string const &params_file)
 
bool valid_chain_info () const
 
bool valid_receptor_chain () const
 
bool valid_peptide_chain () const
 
bool valid_anchors () const
 
bool is_ligand_present (core::pose::Pose const &pose) const
 
std::string receptor_chain () const
 
char peptide_chain () const
 
void set_receptor_chain (std::string ch)
 
void set_peptide_chain (char ch)
 
void set_user_defined_receptor (bool state)
 
void set_user_defined_peptide (bool state)
 
bool user_defined_receptor_chain () const
 
bool user_defined_peptide_chain () const
 
core::Size receptor_first_res () const
 
core::Size receptor_last_res () const
 
core::Size receptor_nres () const
 
core::Size peptide_first_res () const
 
core::Size peptide_last_res () const
 
core::Size peptide_nres () const
 
std::string ref_start_struct () const
 
bool valid_ref_start_struct () const
 

Public Attributes

bool pep_fold_only
 
core::Size receptor_anchor_pos
 
std::map< core::Size, core::Sizepeptide_cuts
 
std::map< core::Size, core::Sizepeptide_anchors
 
std::string params_file
 
bool lowres_abinitio
 
bool lowres_preoptimize
 
bool min_only
 
bool pep_refine
 
bool random_phi_psi_pert
 
core::Real random_phi_psi_pert_size
 
bool extend
 
bool place_peptide
 
int sample_pc
 
bool slideintocontact
 
bool randomRBstart
 
bool recal_foldtree
 
bool rbMCM
 
core::Real rb_trans_size
 
core::Real rb_rot_size
 
bool torsionsMCM
 
bool peptide_loop_model
 
core::Real smove_angle_range
 
bool design_peptide
 
bool backrub_opt
 
bool boost_fa_atr
 
bool ramp_fa_rep
 
bool ramp_rama
 
int rep_ramp_cycles
 
int mcm_cycles
 
bool min_receptor_bb
 
bool score_only
 
bool ppk_only
 
bool no_prepack1
 
bool no_prepack2
 
core::Real score_filter
 
int hb_filter
 
int hotspot_filter
 
core::Real frag3_weight
 
core::Real frag5_weight
 
core::Real frag9_weight
 
bool pSer2Asp_centroid
 
bool pSer2Glu_centroid
 
bool dumpPDB_abinitio
 
bool dumpPDB_lowres
 
bool dumpPDB_hires
 

Private Attributes

std::string receptor_chain_
 
char peptide_chain_
 
core::Size receptor_first_res_
 
core::Size receptor_nres_
 
core::Size peptide_first_res_
 
core::Size peptide_nres_
 
bool valid_receptor_chain_
 
bool valid_peptide_chain_
 
bool valid_chain_bounds_
 
std::string ref_start_struct_
 
bool valid_ref_start_struct_
 
bool user_set_receptor_chain_
 
bool user_set_peptide_chain_
 

Constructor & Destructor Documentation

protocols::flexpep_docking::FlexPepDockingFlags::FlexPepDockingFlags ( )

initialize all flags from cmd-line options

ctr

References protocols::loops::extend.

Member Function Documentation

FlexPepDockingFlagsOP protocols::flexpep_docking::FlexPepDockingFlags::clone ( ) const
inline
bool FlexPepDockingFlags::is_ligand_present ( core::pose::Pose const &  pose) const
char FlexPepDockingFlags::peptide_chain ( ) const
core::Size FlexPepDockingFlags::peptide_first_res ( ) const
core::Size FlexPepDockingFlags::peptide_last_res ( ) const
core::Size FlexPepDockingFlags::peptide_nres ( ) const
std::string FlexPepDockingFlags::receptor_chain ( ) const
core::Size FlexPepDockingFlags::receptor_first_res ( ) const
core::Size FlexPepDockingFlags::receptor_last_res ( ) const
core::Size FlexPepDockingFlags::receptor_nres ( ) const
std::string FlexPepDockingFlags::ref_start_struct ( ) const
void protocols::flexpep_docking::FlexPepDockingFlags::set_peptide_chain ( char  ch)
inline
void protocols::flexpep_docking::FlexPepDockingFlags::set_receptor_chain ( std::string  ch)
inline
void protocols::flexpep_docking::FlexPepDockingFlags::set_user_defined_peptide ( bool  state)
inline
void protocols::flexpep_docking::FlexPepDockingFlags::set_user_defined_receptor ( bool  state)
inline
void FlexPepDockingFlags::setDefaultAnchors ( core::pose::Pose pose)
void FlexPepDockingFlags::updateChains ( core::pose::Pose const &  pose)
void FlexPepDockingFlags::updateChainsAndAnchors_fromParamsFile ( std::string const &  params_file)
bool protocols::flexpep_docking::FlexPepDockingFlags::user_defined_peptide_chain ( ) const
inline
bool protocols::flexpep_docking::FlexPepDockingFlags::user_defined_receptor_chain ( ) const
inline
bool protocols::flexpep_docking::FlexPepDockingFlags::valid_anchors ( ) const
inline
bool protocols::flexpep_docking::FlexPepDockingFlags::valid_chain_info ( ) const
inline
bool protocols::flexpep_docking::FlexPepDockingFlags::valid_peptide_chain ( ) const
inline

References valid_peptide_chain_.

bool protocols::flexpep_docking::FlexPepDockingFlags::valid_receptor_chain ( ) const
inline

References valid_receptor_chain_.

bool FlexPepDockingFlags::valid_ref_start_struct ( ) const

Member Data Documentation

bool protocols::flexpep_docking::FlexPepDockingFlags::backrub_opt
bool protocols::flexpep_docking::FlexPepDockingFlags::boost_fa_atr
bool protocols::flexpep_docking::FlexPepDockingFlags::design_peptide
bool protocols::flexpep_docking::FlexPepDockingFlags::dumpPDB_abinitio
bool protocols::flexpep_docking::FlexPepDockingFlags::dumpPDB_hires
bool protocols::flexpep_docking::FlexPepDockingFlags::dumpPDB_lowres
bool protocols::flexpep_docking::FlexPepDockingFlags::extend
core::Real protocols::flexpep_docking::FlexPepDockingFlags::frag3_weight
core::Real protocols::flexpep_docking::FlexPepDockingFlags::frag5_weight
core::Real protocols::flexpep_docking::FlexPepDockingFlags::frag9_weight
int protocols::flexpep_docking::FlexPepDockingFlags::hb_filter
int protocols::flexpep_docking::FlexPepDockingFlags::hotspot_filter
bool protocols::flexpep_docking::FlexPepDockingFlags::lowres_abinitio
bool protocols::flexpep_docking::FlexPepDockingFlags::lowres_preoptimize
int protocols::flexpep_docking::FlexPepDockingFlags::mcm_cycles
bool protocols::flexpep_docking::FlexPepDockingFlags::min_only
bool protocols::flexpep_docking::FlexPepDockingFlags::min_receptor_bb
bool protocols::flexpep_docking::FlexPepDockingFlags::no_prepack1
bool protocols::flexpep_docking::FlexPepDockingFlags::no_prepack2
std::string protocols::flexpep_docking::FlexPepDockingFlags::params_file
bool protocols::flexpep_docking::FlexPepDockingFlags::pep_fold_only
bool protocols::flexpep_docking::FlexPepDockingFlags::pep_refine
std::map< core::Size, core::Size > protocols::flexpep_docking::FlexPepDockingFlags::peptide_anchors
char protocols::flexpep_docking::FlexPepDockingFlags::peptide_chain_
private

Referenced by peptide_chain(), and set_peptide_chain().

std::map< core::Size, core::Size > protocols::flexpep_docking::FlexPepDockingFlags::peptide_cuts
core::Size protocols::flexpep_docking::FlexPepDockingFlags::peptide_first_res_
private
bool protocols::flexpep_docking::FlexPepDockingFlags::peptide_loop_model
core::Size protocols::flexpep_docking::FlexPepDockingFlags::peptide_nres_
private
bool protocols::flexpep_docking::FlexPepDockingFlags::place_peptide
bool protocols::flexpep_docking::FlexPepDockingFlags::ppk_only
bool protocols::flexpep_docking::FlexPepDockingFlags::pSer2Asp_centroid
bool protocols::flexpep_docking::FlexPepDockingFlags::pSer2Glu_centroid
bool protocols::flexpep_docking::FlexPepDockingFlags::ramp_fa_rep
bool protocols::flexpep_docking::FlexPepDockingFlags::ramp_rama
bool protocols::flexpep_docking::FlexPepDockingFlags::random_phi_psi_pert
core::Real protocols::flexpep_docking::FlexPepDockingFlags::random_phi_psi_pert_size
bool protocols::flexpep_docking::FlexPepDockingFlags::randomRBstart
core::Real protocols::flexpep_docking::FlexPepDockingFlags::rb_rot_size
core::Real protocols::flexpep_docking::FlexPepDockingFlags::rb_trans_size
bool protocols::flexpep_docking::FlexPepDockingFlags::rbMCM
bool protocols::flexpep_docking::FlexPepDockingFlags::recal_foldtree
core::Size protocols::flexpep_docking::FlexPepDockingFlags::receptor_anchor_pos
std::string protocols::flexpep_docking::FlexPepDockingFlags::receptor_chain_
private
core::Size protocols::flexpep_docking::FlexPepDockingFlags::receptor_first_res_
private
core::Size protocols::flexpep_docking::FlexPepDockingFlags::receptor_nres_
private
std::string protocols::flexpep_docking::FlexPepDockingFlags::ref_start_struct_
private

Referenced by ref_start_struct().

int protocols::flexpep_docking::FlexPepDockingFlags::rep_ramp_cycles
int protocols::flexpep_docking::FlexPepDockingFlags::sample_pc
core::Real protocols::flexpep_docking::FlexPepDockingFlags::score_filter
bool protocols::flexpep_docking::FlexPepDockingFlags::score_only
bool protocols::flexpep_docking::FlexPepDockingFlags::slideintocontact
core::Real protocols::flexpep_docking::FlexPepDockingFlags::smove_angle_range
bool protocols::flexpep_docking::FlexPepDockingFlags::torsionsMCM
bool protocols::flexpep_docking::FlexPepDockingFlags::user_set_peptide_chain_
private
bool protocols::flexpep_docking::FlexPepDockingFlags::user_set_receptor_chain_
private
bool protocols::flexpep_docking::FlexPepDockingFlags::valid_chain_bounds_
private
bool protocols::flexpep_docking::FlexPepDockingFlags::valid_peptide_chain_
private
bool protocols::flexpep_docking::FlexPepDockingFlags::valid_receptor_chain_
private
bool protocols::flexpep_docking::FlexPepDockingFlags::valid_ref_start_struct_
private

Referenced by valid_ref_start_struct().


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