protocols::flexpep_docking::FlexPepDockingFlags Class Reference

#include <FlexPepDockingFlags.hh>

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)
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
std::string	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 at(), boost_fa_atr, design_peptide, dumpPDB_abinitio, dumpPDB_hires, dumpPDB_lowres, protocols::loops::extend, frag3_weight, frag5_weight, frag9_weight, hb_filter, hotspot_filter, lowres_abinitio, lowres_preoptimize, mcm_cycles, min_receptor_bb, option, params_file, pep_fold_only, pep_refine, peptide_loop_model, pSer2Asp_centroid, pSer2Glu_centroid, ramp_fa_rep, ramp_rama, rbMCM, rep_ramp_cycles, runtime_assert_msg, score_filter, score_only, smove_angle_range, torsionsMCM, use_cen_score, and user.

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 exit, 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 exit, peptide_chain_, and valid_chain_info().

int FlexPepDockingFlags::peptide_first_res

(

)

const

References exit, 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 exit, 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 exit, 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().

std::string FlexPepDockingFlags::receptor_chain

(

)

const

References exit, pep_fold_only, receptor_chain_, and valid_chain_info().

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

int FlexPepDockingFlags::receptor_first_res

(

)

const

References exit, 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 exit, 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 exit, 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 exit, 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 ( std::string  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(), option, core::pose::Pose::residue(), core::pose::residue_center_of_mass(), core::pose::return_nearest_residue(), runtime_assert_msg, protocols::TR, user, 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(), pep_fold_only, resi, 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 exit, getline(), l, pep_anchor, tag, and 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().

std::string 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:

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