protocols::flexpep_docking::FlexPepDockingFlags Class Reference

#include <FlexPepDockingFlags.hh>

Inheritance diagram for protocols::flexpep_docking::FlexPepDockingFlags:

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::Size >	peptide_cuts
std::map< core::Size, core::Size >	peptide_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
core::Size	hb_filter
core::Size	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

FlexPepDockingFlags()

protocols::flexpep_docking::FlexPepDockingFlags::FlexPepDockingFlags

(

)

initialize all flags from cmd-line options

ctr

References protocols::loops::extend.

Member Function Documentation

clone()

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

inline

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

is_ligand_present()

bool FlexPepDockingFlags::is_ligand_present

(

core::pose::Pose const &

pose

)

const

References peptide_nres_, receptor_nres_, core::pose::Pose::size(), protocols::TR(), and valid_chain_bounds_.

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

peptide_chain()

char FlexPepDockingFlags::peptide_chain

(

)

const

References peptide_chain_, protocols::TR(), and valid_chain_info().

peptide_first_res()

core::Size FlexPepDockingFlags::peptide_first_res

(

)

const

References peptide_first_res_, protocols::TR(), and valid_chain_info().

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::backrub_move(), protocols::flexpep_docking::FlexPepDockingProtocol::extend_peptide(), protocols::flexpep_docking::FlexPepDockingProtocol::flip_in_pcs(), protocols::flexpep_docking::FlexPepDockingAbInitio::loopclosure_monte_carlo(), protocols::flexpep_docking::FlexPepDockingLowRes::loopclosure_monte_carlo(), protocols::flexpep_docking::FlexPepDockingProtocol::markInterfaceBySideChainContacts(), protocols::flexpep_docking::FlexPepDockingProtocol::markNativeInterface(), protocols::flexpep_docking::FlexPepDockingProtocol::peptide_random_loop_model(), protocols::flexpep_docking::FlexPepDockingProtocol::place_peptide_on_binding_site(), protocols::flexpep_docking::FlexPepDockingProtocol::polyAla(), protocols::flexpep_docking::FlexPepDockingProtocol::random_peptide_phi_psi_perturbation(), protocols::flexpep_docking::FlexPepDockingProtocol::randomlySlidePeptideJump(), protocols::flexpep_docking::FlexPepDockingProtocol::set_allowed_moves(), and setDefaultAnchors().

peptide_last_res()

core::Size FlexPepDockingFlags::peptide_last_res

(

)

const

References peptide_first_res_, peptide_nres_, protocols::TR(), and valid_chain_info().

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::flip_in_pcs(), protocols::flexpep_docking::FlexPepDockingAbInitio::loopclosure_monte_carlo(), protocols::flexpep_docking::FlexPepDockingLowRes::loopclosure_monte_carlo(), protocols::flexpep_docking::FlexPepDockingProtocol::markInterfaceBySideChainContacts(), protocols::flexpep_docking::FlexPepDockingProtocol::markNativeInterface(), protocols::flexpep_docking::FlexPepDockingProtocol::peptide_random_loop_model(), protocols::flexpep_docking::FlexPepDockingProtocol::place_peptide_on_binding_site(), protocols::flexpep_docking::FlexPepDockingProtocol::set_allowed_moves(), setDefaultAnchors(), and protocols::flexpep_docking::FlexPepDockingProtocol::setup_foldtree().

peptide_nres()

core::Size FlexPepDockingFlags::peptide_nres

(

)

const

References peptide_nres_, protocols::TR(), and valid_chain_info().

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::backrub_move(), protocols::flexpep_docking::FlexPepDockingProtocol::extend_peptide(), protocols::flexpep_docking::FlexPepDockingAbInitio::loopclosure_monte_carlo(), protocols::flexpep_docking::FlexPepDockingLowRes::loopclosure_monte_carlo(), 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().

receptor_chain()

std::string FlexPepDockingFlags::receptor_chain

(

)

const

References pep_fold_only, receptor_chain_, protocols::TR(), and valid_chain_info().

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

receptor_first_res()

core::Size FlexPepDockingFlags::receptor_first_res

(

)

const

References pep_fold_only, receptor_first_res_, protocols::TR(), and valid_chain_info().

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::markInterfaceBySideChainContacts(), protocols::flexpep_docking::FlexPepDockingProtocol::markNativeInterface(), protocols::flexpep_docking::FlexPepDockingProtocol::set_allowed_moves(), protocols::flexpep_docking::FlexPepDockingProtocol::set_receptor_constraints(), and setDefaultAnchors().

receptor_last_res()

core::Size FlexPepDockingFlags::receptor_last_res

(

)

const

References pep_fold_only, receptor_first_res_, receptor_nres_, protocols::TR(), and valid_chain_info().

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::markInterfaceBySideChainContacts(), protocols::flexpep_docking::FlexPepDockingProtocol::markNativeInterface(), protocols::flexpep_docking::FlexPepDockingProtocol::set_allowed_moves(), protocols::flexpep_docking::FlexPepDockingProtocol::set_receptor_constraints(), setDefaultAnchors(), and protocols::flexpep_docking::FlexPepDockingProtocol::setup_foldtree().

receptor_nres()

core::Size FlexPepDockingFlags::receptor_nres

(

)

const

References pep_fold_only, receptor_nres_, protocols::TR(), and valid_chain_info().

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

ref_start_struct()

std::string FlexPepDockingFlags::ref_start_struct

(

)

const

References ref_start_struct_, protocols::TR(), and valid_ref_start_struct().

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

set_peptide_chain()

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(), and updateChains().

set_receptor_chain()

void protocols::flexpep_docking::FlexPepDockingFlags::set_receptor_chain ( std::string  ch )

inline

References receptor_chain_, and valid_receptor_chain_.

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

set_user_defined_peptide()

void protocols::flexpep_docking::FlexPepDockingFlags::set_user_defined_peptide ( bool  state )

inline

References user_set_peptide_chain_.

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

set_user_defined_receptor()

void protocols::flexpep_docking::FlexPepDockingFlags::set_user_defined_receptor ( bool  state )

inline

References user_set_receptor_chain_.

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

setDefaultAnchors()

void FlexPepDockingFlags::setDefaultAnchors

(

core::pose::Pose &

pose

)

References core::conformation::Residue::atom(), peptide_anchors, peptide_cuts, peptide_first_res(), peptide_last_res(), receptor_anchor_pos, receptor_first_res(), receptor_last_res(), core::pose::Pose::residue(), core::pose::residue_center_of_mass(), core::pose::return_nearest_residue(), protocols::TR(), valid_receptor_chain_, and core::conformation::Atom::xyz().

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

updateChains()

void FlexPepDockingFlags::updateChains

(

core::pose::Pose const &

pose

)

References core::pose::Pose::pdb_info(), pep_fold_only, peptide_chain_, peptide_first_res_, peptide_nres_, receptor_chain_, receptor_first_res_, receptor_nres_, set_peptide_chain(), core::pose::Pose::size(), protocols::TR(), user_defined_peptide_chain(), user_defined_receptor_chain(), valid_chain_bounds_, and valid_receptor_chain_.

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

updateChainsAndAnchors_fromParamsFile()

void FlexPepDockingFlags::updateChainsAndAnchors_fromParamsFile

(

std::string const &

params_file

)

References core::sequence::end, params_file, peptide_anchors, peptide_cuts, peptide_first_res_, peptide_nres_, receptor_anchor_pos, receptor_first_res_, receptor_nres_, protocols::TR(), valid_anchors(), valid_chain_bounds_, valid_peptide_chain_, and valid_receptor_chain_.

user_defined_peptide_chain()

bool protocols::flexpep_docking::FlexPepDockingFlags::user_defined_peptide_chain ( ) const

inline

References user_set_peptide_chain_.

Referenced by updateChains().

user_defined_receptor_chain()

bool protocols::flexpep_docking::FlexPepDockingFlags::user_defined_receptor_chain ( ) const

inline

References user_set_receptor_chain_.

Referenced by updateChains().

valid_anchors()

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(), and updateChainsAndAnchors_fromParamsFile().

valid_chain_info()

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().

valid_peptide_chain()

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

inline

References valid_peptide_chain_.

valid_receptor_chain()

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

inline

References valid_receptor_chain_.

valid_ref_start_struct()

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

backrub_opt

bool protocols::flexpep_docking::FlexPepDockingFlags::backrub_opt

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

boost_fa_atr

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().

design_peptide

bool protocols::flexpep_docking::FlexPepDockingFlags::design_peptide

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

dumpPDB_abinitio

bool protocols::flexpep_docking::FlexPepDockingFlags::dumpPDB_abinitio

dumpPDB_hires

bool protocols::flexpep_docking::FlexPepDockingFlags::dumpPDB_hires

dumpPDB_lowres

bool protocols::flexpep_docking::FlexPepDockingFlags::dumpPDB_lowres

extend

bool protocols::flexpep_docking::FlexPepDockingFlags::extend

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

frag3_weight

core::Real protocols::flexpep_docking::FlexPepDockingFlags::frag3_weight

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

frag5_weight

core::Real protocols::flexpep_docking::FlexPepDockingFlags::frag5_weight

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

frag9_weight

core::Real protocols::flexpep_docking::FlexPepDockingFlags::frag9_weight

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

hb_filter

core::Size protocols::flexpep_docking::FlexPepDockingFlags::hb_filter

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

hotspot_filter

core::Size protocols::flexpep_docking::FlexPepDockingFlags::hotspot_filter

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

lowres_abinitio

bool protocols::flexpep_docking::FlexPepDockingFlags::lowres_abinitio

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

lowres_preoptimize

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().

mcm_cycles

int protocols::flexpep_docking::FlexPepDockingFlags::mcm_cycles

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

min_only

bool protocols::flexpep_docking::FlexPepDockingFlags::min_only

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

min_receptor_bb

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().

no_prepack1

bool protocols::flexpep_docking::FlexPepDockingFlags::no_prepack1

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

no_prepack2

bool protocols::flexpep_docking::FlexPepDockingFlags::no_prepack2

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

params_file

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

Referenced by updateChainsAndAnchors_fromParamsFile().

pep_fold_only

bool protocols::flexpep_docking::FlexPepDockingFlags::pep_fold_only

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::addLowResStatistics(), protocols::flexpep_docking::FlexPepDockingAbInitio::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(), updateChains(), valid_anchors(), and valid_chain_info().

pep_refine

bool protocols::flexpep_docking::FlexPepDockingFlags::pep_refine

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

peptide_anchors

std::map< core::Size, core::Size > protocols::flexpep_docking::FlexPepDockingFlags::peptide_anchors

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

peptide_chain_

char protocols::flexpep_docking::FlexPepDockingFlags::peptide_chain_

private

Referenced by peptide_chain(), set_peptide_chain(), and updateChains().

peptide_cuts

std::map< core::Size, core::Size > protocols::flexpep_docking::FlexPepDockingFlags::peptide_cuts

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

peptide_first_res_

core::Size protocols::flexpep_docking::FlexPepDockingFlags::peptide_first_res_

private

Referenced by peptide_first_res(), peptide_last_res(), updateChains(), and updateChainsAndAnchors_fromParamsFile().

peptide_loop_model

bool protocols::flexpep_docking::FlexPepDockingFlags::peptide_loop_model

Referenced by protocols::flexpep_docking::FlexPepDockingAbInitio::apply(), 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().

peptide_nres_

core::Size protocols::flexpep_docking::FlexPepDockingFlags::peptide_nres_

private

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

place_peptide

bool protocols::flexpep_docking::FlexPepDockingFlags::place_peptide

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

ppk_only

bool protocols::flexpep_docking::FlexPepDockingFlags::ppk_only

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

pSer2Asp_centroid

bool protocols::flexpep_docking::FlexPepDockingFlags::pSer2Asp_centroid

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

pSer2Glu_centroid

bool protocols::flexpep_docking::FlexPepDockingFlags::pSer2Glu_centroid

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

ramp_fa_rep

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().

ramp_rama

bool protocols::flexpep_docking::FlexPepDockingFlags::ramp_rama

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

random_phi_psi_pert

bool protocols::flexpep_docking::FlexPepDockingFlags::random_phi_psi_pert

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

random_phi_psi_pert_size

core::Real 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().

randomRBstart

bool protocols::flexpep_docking::FlexPepDockingFlags::randomRBstart

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

rb_rot_size

core::Real protocols::flexpep_docking::FlexPepDockingFlags::rb_rot_size

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

rb_trans_size

core::Real protocols::flexpep_docking::FlexPepDockingFlags::rb_trans_size

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

rbMCM

bool protocols::flexpep_docking::FlexPepDockingFlags::rbMCM

Referenced by protocols::flexpep_docking::FlexPepDockingAbInitio::apply(), 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().

recal_foldtree

bool protocols::flexpep_docking::FlexPepDockingFlags::recal_foldtree

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

receptor_anchor_pos

core::Size protocols::flexpep_docking::FlexPepDockingFlags::receptor_anchor_pos

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

receptor_chain_

std::string protocols::flexpep_docking::FlexPepDockingFlags::receptor_chain_

private

Referenced by receptor_chain(), set_receptor_chain(), and updateChains().

receptor_first_res_

core::Size protocols::flexpep_docking::FlexPepDockingFlags::receptor_first_res_

private

Referenced by receptor_first_res(), receptor_last_res(), updateChains(), and updateChainsAndAnchors_fromParamsFile().

receptor_nres_

core::Size protocols::flexpep_docking::FlexPepDockingFlags::receptor_nres_

private

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

ref_start_struct_

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

private

Referenced by ref_start_struct().

rep_ramp_cycles

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().

sample_pc

int protocols::flexpep_docking::FlexPepDockingFlags::sample_pc

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

score_filter

core::Real protocols::flexpep_docking::FlexPepDockingFlags::score_filter

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

score_only

bool protocols::flexpep_docking::FlexPepDockingFlags::score_only

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

slideintocontact

bool protocols::flexpep_docking::FlexPepDockingFlags::slideintocontact

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

smove_angle_range

core::Real protocols::flexpep_docking::FlexPepDockingFlags::smove_angle_range

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

torsionsMCM

bool protocols::flexpep_docking::FlexPepDockingFlags::torsionsMCM

Referenced by protocols::flexpep_docking::FlexPepDockingAbInitio::apply(), 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().

user_set_peptide_chain_

bool protocols::flexpep_docking::FlexPepDockingFlags::user_set_peptide_chain_

private

Referenced by set_user_defined_peptide(), and user_defined_peptide_chain().

user_set_receptor_chain_

bool protocols::flexpep_docking::FlexPepDockingFlags::user_set_receptor_chain_

private

Referenced by set_user_defined_receptor(), and user_defined_receptor_chain().

valid_chain_bounds_

bool protocols::flexpep_docking::FlexPepDockingFlags::valid_chain_bounds_

private

Referenced by is_ligand_present(), updateChains(), updateChainsAndAnchors_fromParamsFile(), and valid_chain_info().

valid_peptide_chain_

bool protocols::flexpep_docking::FlexPepDockingFlags::valid_peptide_chain_

private

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

valid_receptor_chain_

bool protocols::flexpep_docking::FlexPepDockingFlags::valid_receptor_chain_

private

Referenced by set_receptor_chain(), setDefaultAnchors(), updateChains(), updateChainsAndAnchors_fromParamsFile(), valid_chain_info(), and valid_receptor_chain().

valid_ref_start_struct_

bool protocols::flexpep_docking::FlexPepDockingFlags::valid_ref_start_struct_

private

Referenced by valid_ref_start_struct().

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

• src/protocols/flexpep_docking/FlexPepDockingFlags.hh
• src/protocols/flexpep_docking/FlexPepDockingFlags.cc