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protocols::flexpep_docking::FlexPepDockingFlags Class Reference

#include <FlexPepDockingFlags.hh>

Inheritance diagram for protocols::flexpep_docking::FlexPepDockingFlags:
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Collaboration 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_
 

Constructor & Destructor Documentation

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

initialize all flags from cmd-line options

ctr

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

Referenced by clone().

Member Function Documentation

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

References FlexPepDockingFlags().

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

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

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

References peptide_chain_, and valid_chain_info().

int FlexPepDockingFlags::peptide_first_res ( ) const

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

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

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

References pep_fold_only, receptor_chain_, and valid_chain_info().

int FlexPepDockingFlags::receptor_first_res ( ) const

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

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

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

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

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

References receptor_chain_, and valid_receptor_chain_.

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

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

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)

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)

References protocols::TR().

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

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

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

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

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

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

bool protocols::flexpep_docking::FlexPepDockingFlags::boost_fa_atr

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

bool protocols::flexpep_docking::FlexPepDockingFlags::design_peptide

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
bool protocols::flexpep_docking::FlexPepDockingFlags::dumpPDB_hires
bool protocols::flexpep_docking::FlexPepDockingFlags::dumpPDB_lowres
bool protocols::flexpep_docking::FlexPepDockingFlags::extend

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

double protocols::flexpep_docking::FlexPepDockingFlags::frag3_weight

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

double protocols::flexpep_docking::FlexPepDockingFlags::frag5_weight

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

double protocols::flexpep_docking::FlexPepDockingFlags::frag9_weight

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

int protocols::flexpep_docking::FlexPepDockingFlags::hb_filter

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

int protocols::flexpep_docking::FlexPepDockingFlags::hotspot_filter

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

bool protocols::flexpep_docking::FlexPepDockingFlags::lowres_abinitio

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

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

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

bool protocols::flexpep_docking::FlexPepDockingFlags::min_only

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

bool protocols::flexpep_docking::FlexPepDockingFlags::min_receptor_bb

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

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

bool protocols::flexpep_docking::FlexPepDockingFlags::no_prepack2

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

std::string protocols::flexpep_docking::FlexPepDockingFlags::params_file
bool protocols::flexpep_docking::FlexPepDockingFlags::pep_fold_only

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

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

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

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

Referenced by peptide_chain(), and set_peptide_chain().

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

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

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

Referenced by peptide_first_res(), and peptide_last_res().

bool protocols::flexpep_docking::FlexPepDockingFlags::peptide_loop_model

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

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

bool protocols::flexpep_docking::FlexPepDockingFlags::ppk_only

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

bool protocols::flexpep_docking::FlexPepDockingFlags::pSer2Asp_centroid

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

bool protocols::flexpep_docking::FlexPepDockingFlags::pSer2Glu_centroid

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

bool protocols::flexpep_docking::FlexPepDockingFlags::ramp_fa_rep

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

bool protocols::flexpep_docking::FlexPepDockingFlags::ramp_rama

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

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

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

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

double protocols::flexpep_docking::FlexPepDockingFlags::rb_rot_size

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

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

bool protocols::flexpep_docking::FlexPepDockingFlags::rbMCM

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

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

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

Referenced by receptor_chain(), and set_receptor_chain().

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

Referenced by receptor_first_res(), and receptor_last_res().

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

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

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

Referenced by ref_start_struct().

int protocols::flexpep_docking::FlexPepDockingFlags::rep_ramp_cycles

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

double protocols::flexpep_docking::FlexPepDockingFlags::score_filter

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

bool protocols::flexpep_docking::FlexPepDockingFlags::score_only

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

double protocols::flexpep_docking::FlexPepDockingFlags::smove_angle_range

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

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

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

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

Referenced by is_ligand_present(), and valid_chain_info().

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

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

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

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

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:
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