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protocols::flexpep_docking::FlexPepDockingFlags Class Reference

#include <FlexPepDockingFlags.hh>

Inheritance diagram for protocols::flexpep_docking::FlexPepDockingFlags:
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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
 
char receptor_chain () const
 
char peptide_chain () const
 
void set_receptor_chain (char ch)
 
void set_peptide_chain (char ch)
 
int receptor_first_res () const
 
int receptor_last_res () const
 
int receptor_nres () const
 
int peptide_first_res () const
 
int peptide_last_res () const
 
int peptide_nres () const
 
std::string ref_start_struct () const
 
bool valid_ref_start_struct () const
 

Public Attributes

bool pep_fold_only
 
int receptor_anchor_pos
 
std::map< int, int > peptide_cuts
 
std::map< int, int > peptide_anchors
 
std::string params_file
 
bool lowres_abinitio
 
bool lowres_preoptimize
 
bool min_only
 
bool pep_refine
 
bool random_phi_psi_pert
 
double random_phi_psi_pert_size
 
bool extend
 
bool randomRBstart
 
bool rbMCM
 
double rb_trans_size
 
double rb_rot_size
 
bool torsionsMCM
 
bool peptide_loop_model
 
double 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 use_cen_score
 
bool ppk_only
 
bool no_prepack1
 
bool no_prepack2
 
double score_filter
 
int hb_filter
 
int hotspot_filter
 
double frag3_weight
 
double frag5_weight
 
double frag9_weight
 
bool pSer2Asp_centroid
 
bool pSer2Glu_centroid
 
bool dumpPDB_abinitio
 
bool dumpPDB_lowres
 
bool dumpPDB_hires
 

Private Attributes

char receptor_chain_
 
char peptide_chain_
 
int receptor_first_res_
 
int receptor_nres_
 
int peptide_first_res_
 
int peptide_nres_
 
bool valid_receptor_chain_
 
bool valid_peptide_chain_
 
bool valid_chain_bounds_
 
std::string ref_start_struct_
 
bool valid_ref_start_struct_
 

Detailed Description

Definition at line 34 of file FlexPepDockingFlags.hh.

Constructor & Destructor Documentation

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

initialize all flags from cmd-line options

ctr

Definition at line 50 of file FlexPepDockingFlags.cc.

References core::io::serialization::at(), and protocols::loops::extend.

Referenced by clone().

Member Function Documentation

FlexPepDockingFlagsOP protocols::flexpep_docking::FlexPepDockingFlags::clone ( ) const
inline

Definition at line 46 of file FlexPepDockingFlags.hh.

References FlexPepDockingFlags().

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::apply().

bool FlexPepDockingFlags::is_ligand_present ( core::pose::Pose const &  pose) const

Definition at line 161 of file FlexPepDockingFlags.cc.

References peptide_nres_, receptor_nres_, core::pose::Pose::total_residue(), and valid_chain_bounds_.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::setup_foldtree().

char FlexPepDockingFlags::peptide_chain ( ) const

Definition at line 181 of file FlexPepDockingFlags.cc.

References peptide_chain_, and valid_chain_info().

int FlexPepDockingFlags::peptide_first_res ( ) const

Definition at line 215 of file FlexPepDockingFlags.cc.

References peptide_first_res_, and valid_chain_info().

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::backrub_move(), protocols::flexpep_docking::FlexPepDockingProtocol::extend_peptide(), protocols::flexpep_docking::FlexPepDockingProtocol::markNativeInterface(), protocols::flexpep_docking::FlexPepDockingProtocol::peptide_random_loop_model(), protocols::flexpep_docking::FlexPepDockingProtocol::polyAla(), protocols::flexpep_docking::FlexPepDockingProtocol::random_peptide_phi_psi_perturbation(), protocols::flexpep_docking::FlexPepDockingProtocol::randomlySlidePeptideJump(), and protocols::flexpep_docking::FlexPepDockingProtocol::set_allowed_moves().

int FlexPepDockingFlags::peptide_last_res ( ) const

Definition at line 223 of file FlexPepDockingFlags.cc.

References peptide_first_res_, peptide_nres_, and valid_chain_info().

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::markNativeInterface(), protocols::flexpep_docking::FlexPepDockingProtocol::peptide_random_loop_model(), protocols::flexpep_docking::FlexPepDockingProtocol::set_allowed_moves(), and protocols::flexpep_docking::FlexPepDockingProtocol::setup_foldtree().

int FlexPepDockingFlags::peptide_nres ( ) const

Definition at line 232 of file FlexPepDockingFlags.cc.

References peptide_nres_, and valid_chain_info().

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::backrub_move(), protocols::flexpep_docking::FlexPepDockingProtocol::extend_peptide(), protocols::flexpep_docking::FlexPepDockingProtocol::peptide_random_loop_model(), protocols::flexpep_docking::FlexPepDockingProtocol::polyAla(), protocols::flexpep_docking::FlexPepDockingProtocol::random_peptide_phi_psi_perturbation(), protocols::flexpep_docking::FlexPepDockingProtocol::randomlySlidePeptideJump(), protocols::flexpep_docking::FlexPepDockingProtocol::setup_foldtree(), and protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics().

char FlexPepDockingFlags::receptor_chain ( ) const

Definition at line 173 of file FlexPepDockingFlags.cc.

References pep_fold_only, receptor_chain_, and valid_chain_info().

int FlexPepDockingFlags::receptor_first_res ( ) const

Definition at line 189 of file FlexPepDockingFlags.cc.

References pep_fold_only, receptor_first_res_, and valid_chain_info().

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::hires_fpdock_protocol(), protocols::flexpep_docking::FlexPepDockingProtocol::set_allowed_moves(), and protocols::flexpep_docking::FlexPepDockingProtocol::set_receptor_constraints().

int FlexPepDockingFlags::receptor_last_res ( ) const

Definition at line 197 of file FlexPepDockingFlags.cc.

References pep_fold_only, receptor_first_res_, receptor_nres_, and valid_chain_info().

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::hires_fpdock_protocol(), protocols::flexpep_docking::FlexPepDockingProtocol::set_allowed_moves(), protocols::flexpep_docking::FlexPepDockingProtocol::set_receptor_constraints(), and protocols::flexpep_docking::FlexPepDockingProtocol::setup_foldtree().

int FlexPepDockingFlags::receptor_nres ( ) const

Definition at line 206 of file FlexPepDockingFlags.cc.

References pep_fold_only, receptor_nres_, and valid_chain_info().

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::prepack_only(), and protocols::flexpep_docking::FlexPepDockingProtocol::setup_foldtree().

std::string FlexPepDockingFlags::ref_start_struct ( ) const

Definition at line 240 of file FlexPepDockingFlags.cc.

References ref_start_struct_, and valid_ref_start_struct().

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::apply().

void protocols::flexpep_docking::FlexPepDockingFlags::set_peptide_chain ( char  ch)
inline

Definition at line 102 of file FlexPepDockingFlags.hh.

References peptide_chain_, and valid_peptide_chain_.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag().

void protocols::flexpep_docking::FlexPepDockingFlags::set_receptor_chain ( char  ch)
inline

Definition at line 98 of file FlexPepDockingFlags.hh.

References receptor_chain_, and valid_receptor_chain_.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag().

void FlexPepDockingFlags::setDefaultAnchors ( core::pose::Pose &  pose)

Definition at line 340 of file FlexPepDockingFlags.cc.

References core::conformation::Residue::atom(), core::pose::Pose::residue(), core::conformation::symmetry::residue_center_of_mass(), core::conformation::symmetry::return_nearest_residue(), protocols::TR(), and core::conformation::Atom::xyz().

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::apply().

void FlexPepDockingFlags::updateChains ( core::pose::Pose const &  pose)

Definition at line 263 of file FlexPepDockingFlags.cc.

References core::pose::Pose::pdb_info(), core::pose::Pose::total_residue(), and protocols::TR().

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::apply().

void FlexPepDockingFlags::updateChainsAndAnchors_fromParamsFile ( std::string const &  params_file)

Definition at line 390 of file FlexPepDockingFlags.cc.

References protocols::TR().

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

Definition at line 78 of file FlexPepDockingFlags.hh.

References pep_fold_only, peptide_anchors, peptide_cuts, and receptor_anchor_pos.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::apply().

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

Definition at line 66 of file FlexPepDockingFlags.hh.

References pep_fold_only, valid_chain_bounds_, valid_peptide_chain_, and valid_receptor_chain_.

Referenced by peptide_chain(), peptide_first_res(), peptide_last_res(), peptide_nres(), receptor_chain(), receptor_first_res(), receptor_last_res(), and receptor_nres().

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

Definition at line 74 of file FlexPepDockingFlags.hh.

References valid_peptide_chain_.

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

Definition at line 71 of file FlexPepDockingFlags.hh.

References valid_receptor_chain_.

bool FlexPepDockingFlags::valid_ref_start_struct ( ) const

Definition at line 248 of file FlexPepDockingFlags.cc.

References valid_ref_start_struct_.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::apply(), and ref_start_struct().

Member Data Documentation

bool protocols::flexpep_docking::FlexPepDockingFlags::backrub_opt

Definition at line 158 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::apply(), and protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag().

bool protocols::flexpep_docking::FlexPepDockingFlags::boost_fa_atr

Definition at line 159 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::hires_fpdock_protocol(), and protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag().

bool protocols::flexpep_docking::FlexPepDockingFlags::design_peptide

Definition at line 157 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::apply(), protocols::flexpep_docking::FlexPepDockingProtocol::hires_fpdock_protocol(), protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag(), and protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics().

bool protocols::flexpep_docking::FlexPepDockingFlags::dumpPDB_abinitio

Definition at line 178 of file FlexPepDockingFlags.hh.

bool protocols::flexpep_docking::FlexPepDockingFlags::dumpPDB_hires

Definition at line 180 of file FlexPepDockingFlags.hh.

bool protocols::flexpep_docking::FlexPepDockingFlags::dumpPDB_lowres

Definition at line 179 of file FlexPepDockingFlags.hh.

bool protocols::flexpep_docking::FlexPepDockingFlags::extend

Definition at line 149 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::apply(), and protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag().

double protocols::flexpep_docking::FlexPepDockingFlags::frag3_weight

Definition at line 173 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag().

double protocols::flexpep_docking::FlexPepDockingFlags::frag5_weight

Definition at line 174 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag().

double protocols::flexpep_docking::FlexPepDockingFlags::frag9_weight

Definition at line 175 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag().

int protocols::flexpep_docking::FlexPepDockingFlags::hb_filter

Definition at line 171 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::check_filters(), and protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag().

int protocols::flexpep_docking::FlexPepDockingFlags::hotspot_filter

Definition at line 172 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::check_filters(), and protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag().

bool protocols::flexpep_docking::FlexPepDockingFlags::lowres_abinitio

Definition at line 143 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::apply(), protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag(), and protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics().

bool protocols::flexpep_docking::FlexPepDockingFlags::lowres_preoptimize

Definition at line 144 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::apply(), protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag(), and protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics().

int protocols::flexpep_docking::FlexPepDockingFlags::mcm_cycles

Definition at line 163 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::hires_fpdock_protocol(), and protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag().

bool protocols::flexpep_docking::FlexPepDockingFlags::min_only

Definition at line 145 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::apply(), and protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag().

bool protocols::flexpep_docking::FlexPepDockingFlags::min_receptor_bb

Definition at line 164 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::apply(), protocols::flexpep_docking::FlexPepDockingProtocol::hires_fpdock_protocol(), protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag(), and protocols::flexpep_docking::FlexPepDockingProtocol::set_allowed_moves().

bool protocols::flexpep_docking::FlexPepDockingFlags::no_prepack1

Definition at line 168 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::apply(), and protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag().

bool protocols::flexpep_docking::FlexPepDockingFlags::no_prepack2

Definition at line 169 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::apply(), and protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag().

std::string protocols::flexpep_docking::FlexPepDockingFlags::params_file

Definition at line 142 of file FlexPepDockingFlags.hh.

bool protocols::flexpep_docking::FlexPepDockingFlags::pep_fold_only

Definition at line 138 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::apply(), protocols::flexpep_docking::FlexPepDockingProtocol::hires_fpdock_protocol(), protocols::flexpep_docking::FlexPepDockingProtocol::markNativeInterface(), protocols::flexpep_docking::FlexPepDockingProtocol::prepack_only(), receptor_chain(), receptor_first_res(), receptor_last_res(), receptor_nres(), protocols::flexpep_docking::FlexPepDockingProtocol::set_allowed_moves(), protocols::flexpep_docking::FlexPepDockingProtocol::set_default(), protocols::flexpep_docking::FlexPepDockingProtocol::setup_foldtree(), protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics(), valid_anchors(), and valid_chain_info().

bool protocols::flexpep_docking::FlexPepDockingFlags::pep_refine

Definition at line 146 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::apply(), and protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag().

std::map<int,int> protocols::flexpep_docking::FlexPepDockingFlags::peptide_anchors

Definition at line 141 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::setup_foldtree(), and valid_anchors().

char protocols::flexpep_docking::FlexPepDockingFlags::peptide_chain_
private

Definition at line 127 of file FlexPepDockingFlags.hh.

Referenced by peptide_chain(), and set_peptide_chain().

std::map<int,int> protocols::flexpep_docking::FlexPepDockingFlags::peptide_cuts

Definition at line 140 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::setup_foldtree(), and valid_anchors().

int protocols::flexpep_docking::FlexPepDockingFlags::peptide_first_res_
private

Definition at line 130 of file FlexPepDockingFlags.hh.

Referenced by peptide_first_res(), and peptide_last_res().

bool protocols::flexpep_docking::FlexPepDockingFlags::peptide_loop_model

Definition at line 155 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingLowRes::apply(), protocols::flexpep_docking::FlexPepDockingProtocol::apply(), protocols::flexpep_docking::FlexPepDockingProtocol::hires_fpdock_protocol(), and protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag().

int protocols::flexpep_docking::FlexPepDockingFlags::peptide_nres_
private

Definition at line 131 of file FlexPepDockingFlags.hh.

Referenced by is_ligand_present(), peptide_last_res(), and peptide_nres().

bool protocols::flexpep_docking::FlexPepDockingFlags::ppk_only

Definition at line 167 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::apply(), and protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag().

bool protocols::flexpep_docking::FlexPepDockingFlags::pSer2Asp_centroid

Definition at line 176 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag().

bool protocols::flexpep_docking::FlexPepDockingFlags::pSer2Glu_centroid

Definition at line 177 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag().

bool protocols::flexpep_docking::FlexPepDockingFlags::ramp_fa_rep

Definition at line 160 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::hires_fpdock_protocol(), and protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag().

bool protocols::flexpep_docking::FlexPepDockingFlags::ramp_rama

Definition at line 161 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::hires_fpdock_protocol(), and protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag().

bool protocols::flexpep_docking::FlexPepDockingFlags::random_phi_psi_pert

Definition at line 147 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::apply(), and protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag().

double protocols::flexpep_docking::FlexPepDockingFlags::random_phi_psi_pert_size

Definition at line 148 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag(), and protocols::flexpep_docking::FlexPepDockingProtocol::random_peptide_phi_psi_perturbation().

bool protocols::flexpep_docking::FlexPepDockingFlags::randomRBstart

Definition at line 150 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::apply(), and protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag().

double protocols::flexpep_docking::FlexPepDockingFlags::rb_rot_size

Definition at line 153 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag(), and protocols::flexpep_docking::FlexPepDockingProtocol::random_rb_pert().

double protocols::flexpep_docking::FlexPepDockingFlags::rb_trans_size

Definition at line 152 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag(), and protocols::flexpep_docking::FlexPepDockingProtocol::random_rb_pert().

bool protocols::flexpep_docking::FlexPepDockingFlags::rbMCM

Definition at line 151 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingLowRes::apply(), protocols::flexpep_docking::FlexPepDockingProtocol::apply(), protocols::flexpep_docking::FlexPepDockingProtocol::hires_fpdock_protocol(), and protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag().

int protocols::flexpep_docking::FlexPepDockingFlags::receptor_anchor_pos

Definition at line 139 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::setup_foldtree(), and valid_anchors().

char protocols::flexpep_docking::FlexPepDockingFlags::receptor_chain_
private

Definition at line 126 of file FlexPepDockingFlags.hh.

Referenced by receptor_chain(), and set_receptor_chain().

int protocols::flexpep_docking::FlexPepDockingFlags::receptor_first_res_
private

Definition at line 128 of file FlexPepDockingFlags.hh.

Referenced by receptor_first_res(), and receptor_last_res().

int protocols::flexpep_docking::FlexPepDockingFlags::receptor_nres_
private

Definition at line 129 of file FlexPepDockingFlags.hh.

Referenced by is_ligand_present(), receptor_last_res(), and receptor_nres().

std::string protocols::flexpep_docking::FlexPepDockingFlags::ref_start_struct_
private

Definition at line 135 of file FlexPepDockingFlags.hh.

Referenced by ref_start_struct().

int protocols::flexpep_docking::FlexPepDockingFlags::rep_ramp_cycles

Definition at line 162 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::hires_fpdock_protocol(), and protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag().

double protocols::flexpep_docking::FlexPepDockingFlags::score_filter

Definition at line 170 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::check_filters(), and protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag().

bool protocols::flexpep_docking::FlexPepDockingFlags::score_only

Definition at line 165 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag(), and protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics().

double protocols::flexpep_docking::FlexPepDockingFlags::smove_angle_range

Definition at line 156 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag(), protocols::flexpep_docking::FlexPepDockingProtocol::shear_moves(), and protocols::flexpep_docking::FlexPepDockingProtocol::small_moves().

bool protocols::flexpep_docking::FlexPepDockingFlags::torsionsMCM

Definition at line 154 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingLowRes::apply(), protocols::flexpep_docking::FlexPepDockingProtocol::apply(), protocols::flexpep_docking::FlexPepDockingProtocol::hires_fpdock_protocol(), and protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag().

bool protocols::flexpep_docking::FlexPepDockingFlags::use_cen_score

Definition at line 166 of file FlexPepDockingFlags.hh.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag().

bool protocols::flexpep_docking::FlexPepDockingFlags::valid_chain_bounds_
private

Definition at line 134 of file FlexPepDockingFlags.hh.

Referenced by is_ligand_present(), and valid_chain_info().

bool protocols::flexpep_docking::FlexPepDockingFlags::valid_peptide_chain_
private

Definition at line 133 of file FlexPepDockingFlags.hh.

Referenced by set_peptide_chain(), valid_chain_info(), and valid_peptide_chain().

bool protocols::flexpep_docking::FlexPepDockingFlags::valid_receptor_chain_
private

Definition at line 132 of file FlexPepDockingFlags.hh.

Referenced by set_receptor_chain(), valid_chain_info(), and valid_receptor_chain().

bool protocols::flexpep_docking::FlexPepDockingFlags::valid_ref_start_struct_
private

Definition at line 136 of file FlexPepDockingFlags.hh.

Referenced by valid_ref_start_struct().

The documentation for this class was generated from the following files:
Generated on Sat Jun 1 2013 12:37:11 for Rosetta 3.5 by   doxygen 1.8.4