protocols::loop_grower::LoopGrower Member List

This is the complete list of members for protocols::loop_grower::LoopGrower, including all inherited members.

add_fragment_csts(core::pose::Pose &pose, core::Size startfasta, core::Size endfasta, core::Size natstoplow, core::Size natstarthi, core::Size startlower)	protocols::loop_grower::LoopGrower
add_user_csts(core::pose::Pose &pose)	protocols::loop_grower::LoopGrower
addnativesolution(LoopPartialSolutionStore &solutionset, core::pose::Pose &fa_pose, core::pose::Pose &cen_pose, int natlowerstart, int natlowerstop, int natupperstart, int natupperstop, int lower_pose, core::Size torsionrangelo, core::Size torsionrangehi)	protocols::loop_grower::LoopGrower
apply(core::pose::Pose &pose) override	protocols::loop_grower::LoopGrower	virtual
asymmdump_	protocols::loop_grower::LoopGrower	private
atomGDTha(core::Vector atom1, core::Vector atom2, core::Size &GDTha)	protocols::loop_grower::LoopGrower
auto_stop_	protocols::loop_grower::LoopGrower	private
beamscorecutoff_	protocols::loop_grower::LoopGrower	private
beamwidth_	protocols::loop_grower::LoopGrower	private
cen_seqpose_	protocols::loop_grower::LoopGrower	private
cen_sf_	protocols::loop_grower::LoopGrower	private
cenrot_	protocols::loop_grower::LoopGrower	private
cenrot_sf_	protocols::loop_grower::LoopGrower	private
cenrotfilter_	protocols::loop_grower::LoopGrower	private
censtartingscore_	protocols::loop_grower::LoopGrower	private
chainbreak_	protocols::loop_grower::LoopGrower	private
check_auto_stop(core::pose::Pose &pose, core::Size lower_res, core::Size upper_res)	protocols::loop_grower::LoopGrower
check_coordinates(core::pose::Pose &pose, core::Size lower_pose, core::Size upper_pose, core::Size lower_fasta, core::Real radius)	protocols::loop_grower::LoopGrower
checksymm_	protocols::loop_grower::LoopGrower	private
clear_info()	protocols::moves::Mover	inlinevirtual
clone() const override	protocols::loop_grower::LoopGrower	virtual
clustercheck_	protocols::loop_grower::LoopGrower	private
continuous_sheets_	protocols::loop_grower::LoopGrower	private
continuous_weight_	protocols::loop_grower::LoopGrower	private
coordfile_	protocols::loop_grower::LoopGrower	private
coordinate_filter(LoopPartialSolutionStore &solutionset, core::pose::Pose pose, bool lower, core::Size lower_fasta, core::Size upper_fasta, core::Size lower_pose, core::Size rangehi)	protocols::loop_grower::LoopGrower
create()	protocols::moves::Mover	virtual
debug_	protocols::loop_grower::LoopGrower	private
direction_	protocols::loop_grower::LoopGrower	private
dumpbeam_	protocols::loop_grower::LoopGrower	private
dumperrors_	protocols::loop_grower::LoopGrower	private
dumpfinalbeam_	protocols::loop_grower::LoopGrower	private
dumprms_	protocols::loop_grower::LoopGrower	private
fa_seqpose_	protocols::loop_grower::LoopGrower	private
fafilter(LoopPartialSolutionStore &solutionset, core::pose::Pose &fapose, core::pose::Pose &cenpose, core::Size total_lower, core::Size torsionrangelo, core::Size torsionrangehi, core::Size cycle, core::Size lower_fasta, core::Size upper_fasta, core::Size lower_pose)	protocols::loop_grower::LoopGrower
fafilter_	protocols::loop_grower::LoopGrower	private
fafilter_pmcycles_	protocols::loop_grower::LoopGrower	private
famin_	protocols::loop_grower::LoopGrower	private
filterbeams_	protocols::loop_grower::LoopGrower	private
filterprevious_	protocols::loop_grower::LoopGrower	private
fragmelt_	protocols::loop_grower::LoopGrower	private
fragments_	protocols::loop_grower::LoopGrower	private
fragtrials_	protocols::loop_grower::LoopGrower	private
fresh_instance() const override	protocols::loop_grower::LoopGrower	virtual
full_atom_beam(LoopPartialSolutionStore &solutionset, core::pose::Pose &fa_pose, core::pose::Pose &cen_pose, core::Size lower_pos, core::Size upper_pos)	protocols::loop_grower::LoopGrower
GDThatonative(core::pose::Pose const &pose, int natlow, int nathi, int natstoplow, int natstarthi, int startlow, int stoplow, int starthi, int stophi)	protocols::loop_grower::LoopGrower
get_additional_output()	protocols::moves::Mover	virtual
get_current_job() const	protocols::moves::Mover
get_current_tag() const	protocols::moves::Mover	inline
get_input_pose() const	protocols::moves::Mover
get_last_move_status() const	protocols::moves::Mover
get_name() const override	protocols::loop_grower::LoopGrower	inlinevirtual
get_native_pose() const	protocols::moves::Mover
get_resrange_hbond_energy(core::pose::Pose &pose, core::Size lower, core::Size upper)	protocols::loop_grower::LoopGrower
get_self_ptr() const	protocols::moves::Mover	inline
get_self_ptr()	protocols::moves::Mover	inline
get_self_weak_ptr() const	protocols::moves::Mover	inline
get_self_weak_ptr()	protocols::moves::Mover	inline
get_type() const	protocols::moves::Mover	inline
getSolutionSet()	protocols::loop_grower::LoopGrower	inline
greedy_	protocols::loop_grower::LoopGrower	private
info()	protocols::moves::Mover	inlinevirtual
info() const	protocols::moves::Mover	inlinevirtual
insert_pose_	protocols::loop_grower::LoopGrower	private
is_beta(core::Real phi, core::Real psi)	protocols::loop_grower::LoopGrower
last_proposal_density_ratio()	protocols::moves::Mover	inlinevirtual
library_	protocols::loop_grower::LoopGrower	private
loop_	protocols::loop_grower::LoopGrower	private
LoopGrower()=default	protocols::loop_grower::LoopGrower
LoopGrower(core::sequence::SequenceOP seq, protocols::loops::Loop loop, int resstart, int resstop, utility::vector1< core::fragment::FragSetOP > const &fragments)	protocols::loop_grower::LoopGrower	inline
loopnumber_	protocols::loop_grower::LoopGrower	private
lower_fasta_	protocols::loop_grower::LoopGrower	private
lowest_ranked_native_	protocols::loop_grower::LoopGrower	private
master_beam_cutoff_	protocols::loop_grower::LoopGrower	private
master_beam_width_	protocols::loop_grower::LoopGrower	private
maxfrag_	protocols::loop_grower::LoopGrower	private
minimize_	protocols::loop_grower::LoopGrower	private
minmelt_	protocols::loop_grower::LoopGrower	private
modifieddensity(core::pose::Pose &pose, core::Size rangelo, core::Size rangehi, core::Real density_weight, core::Size &includesheets)	protocols::loop_grower::LoopGrower
modifiedscore(core::pose::Pose &fapose, core::pose::Pose &cen_pose, core::Size rangelo, core::Size rangehi)	protocols::loop_grower::LoopGrower
Mover()	protocols::moves::Mover
Mover(std::string const &type_name)	protocols::moves::Mover
name()	protocols::moves::Mover	inlinestatic
native_	protocols::loop_grower::LoopGrower	private
nativegrow_	protocols::loop_grower::LoopGrower	private
nton3_hbond_score(core::pose::Pose &pose)	protocols::loop_grower::LoopGrower
numjumps_	protocols::loop_grower::LoopGrower	private
pack_min_cycles_	protocols::loop_grower::LoopGrower	private
parallelcount_	protocols::loop_grower::LoopGrower	private
parametercheck_	protocols::loop_grower::LoopGrower	private
parse_my_tag(TagCOP tag, basic::datacache::DataMap &data)	protocols::moves::Mover	virtual
Pose typedef	protocols::moves::Mover
PoseCOP typedef	protocols::moves::Mover
provide_citation_info(basic::citation_manager::CitationCollectionList &) const override	protocols::loop_grower::LoopGrower	virtual
read_coordfile()	protocols::loop_grower::LoopGrower
read_from_disk(LoopPartialSolutionStore &solutionset, int &cycle, bool &lower, bool filterbeams)	protocols::loop_grower::LoopGrower
readbeams_	protocols::loop_grower::LoopGrower	private
refine_cycle(core::pose::Pose &pose, core::pose::Pose &cen_pose, int loop_start, int loop_end, bool finalrefinement, int cycle, int beam, int fragment, core::Size is_lower)	protocols::loop_grower::LoopGrower
register_options()	protocols::moves::Mover	inlinestatic
reinitialize_for_each_job() const	protocols::moves::Mover	virtual
reinitialize_for_new_input() const	protocols::moves::Mover	virtual
rephasemap_	protocols::loop_grower::LoopGrower	private
rescorebeams_	protocols::loop_grower::LoopGrower	private
rescoresolutionset(LoopPartialSolutionStore &solutionset, core::pose::Pose &fa_pose, core::pose::Pose &cen_pose, core::Size torsionrangelo, core::Size torsionrangehi)	protocols::loop_grower::LoopGrower
reset_status()	protocols::moves::Mover
resstart_	protocols::loop_grower::LoopGrower	private
resstop_	protocols::loop_grower::LoopGrower	private
rmscutoff_	protocols::loop_grower::LoopGrower	private
rmsrangehi_	protocols::loop_grower::LoopGrower	private
rmsrangelo_	protocols::loop_grower::LoopGrower	private
RMStonative(core::pose::Pose const &pose, int natlow, int nathi, int natstoplow, int natstarthi, int startlow, int stoplow, int starthi, int stophi)	protocols::loop_grower::LoopGrower
rmswindow_	protocols::loop_grower::LoopGrower	private
samplesheets_	protocols::loop_grower::LoopGrower	private
sc_scale_	protocols::loop_grower::LoopGrower	private
scoringcoords_	protocols::loop_grower::LoopGrower	private
seq_	protocols::loop_grower::LoopGrower	private
set_asymmdump(bool asymmdump)	protocols::loop_grower::LoopGrower	inline
set_auto_stop(bool auto_stop)	protocols::loop_grower::LoopGrower	inline
set_beamscorecutoff(core::Real beamscorecutoff)	protocols::loop_grower::LoopGrower	inline
set_beamwidth(core::Size beamwidth)	protocols::loop_grower::LoopGrower	inline
set_cen_scorefunction(core::scoring::ScoreFunctionOP sf)	protocols::loop_grower::LoopGrower	inline
set_cenrot(bool cenrot)	protocols::loop_grower::LoopGrower	inline
set_cenrot_scorefunction(core::scoring::ScoreFunctionOP sf)	protocols::loop_grower::LoopGrower	inline
set_chainbreak(core::Real chainbreak)	protocols::loop_grower::LoopGrower	inline
set_checksymm(bool checksymm)	protocols::loop_grower::LoopGrower	inline
set_clustercheck(bool clustercheck)	protocols::loop_grower::LoopGrower	inline
set_continuous_sheets(bool continuous_sheets)	protocols::loop_grower::LoopGrower	inline
set_continuous_weight(core::Real continuous_weight)	protocols::loop_grower::LoopGrower	inline
set_coordfile(std::string coordfile)	protocols::loop_grower::LoopGrower	inline
set_current_job(protocols::jobdist::BasicJobCOP job)	protocols::moves::Mover
set_current_tag(std::string const &new_tag)	protocols::moves::Mover	inlinevirtual
set_debug(bool debug)	protocols::loop_grower::LoopGrower	inline
set_direction(core::Size direction)	protocols::loop_grower::LoopGrower	inline
set_dumpbeam(bool dumpbeam)	protocols::loop_grower::LoopGrower	inline
set_dumperrors(bool dumperrors)	protocols::loop_grower::LoopGrower	inline
set_dumpfinalbeam(bool dumpfinalbeam)	protocols::loop_grower::LoopGrower	inline
set_dumprms(bool dumprms)	protocols::loop_grower::LoopGrower	inline
set_fafilter(bool fafilter)	protocols::loop_grower::LoopGrower	inline
set_famin(bool famin)	protocols::loop_grower::LoopGrower	inline
set_filterbeams(std::string filterbeams)	protocols::loop_grower::LoopGrower	inline
set_filterprevious(bool filterprevious)	protocols::loop_grower::LoopGrower	inline
set_fragmelt(core::Size fragmelt)	protocols::loop_grower::LoopGrower	inline
set_fragtrials(core::Size fragtrials)	protocols::loop_grower::LoopGrower	inline
set_greedy(bool greedy)	protocols::loop_grower::LoopGrower	inline
set_input_pose(PoseCOP pose)	protocols::moves::Mover	virtual
set_last_move_status(MoverStatus status)	protocols::moves::Mover	protected
set_loopnumber(core::Size loopnumber)	protocols::loop_grower::LoopGrower	inline
set_master_beam_cutoff(core::Real master_beam_cutoff)	protocols::loop_grower::LoopGrower	inline
set_master_beam_width(core::Size master_beam_width)	protocols::loop_grower::LoopGrower	inline
set_minimize(bool minimize)	protocols::loop_grower::LoopGrower	inline
set_minmelt(core::Size minmelt)	protocols::loop_grower::LoopGrower	inline
set_native(core::pose::PoseOP native)	protocols::loop_grower::LoopGrower	inline
set_native_pose(PoseCOP pose)	protocols::moves::Mover	virtual
set_nativegrow(bool nativegrow)	protocols::loop_grower::LoopGrower	inline
set_pack_min_cycles(core::Size pack_min_cycles)	protocols::loop_grower::LoopGrower	inline
set_parametercheck(bool parametercheck)	protocols::loop_grower::LoopGrower	inline
set_pcount(core::Size parallelcount)	protocols::loop_grower::LoopGrower	inline
set_readbeams(bool readbeams)	protocols::loop_grower::LoopGrower	inline
set_rephasemap(bool rephasemap)	protocols::loop_grower::LoopGrower	inline
set_rescorebeams(bool rescorebeams)	protocols::loop_grower::LoopGrower	inline
set_rmscutoff(core::Real rmscutoff)	protocols::loop_grower::LoopGrower	inline
set_rmswindow(core::Size rmswindow)	protocols::loop_grower::LoopGrower	inline
set_samplesheets(bool samplesheets)	protocols::loop_grower::LoopGrower	inline
set_sc_scale(core::Real sc_scale)	protocols::loop_grower::LoopGrower	inline
set_scorefunction(core::scoring::ScoreFunctionOP sf)	protocols::loop_grower::LoopGrower	inline
set_sheet_tolerance(core::Real sheet_tolerance)	protocols::loop_grower::LoopGrower	inline
set_sheetbonus(core::Real sheetbonus)	protocols::loop_grower::LoopGrower	inline
set_sheetcriteria(core::Size sheetcriteria)	protocols::loop_grower::LoopGrower	inline
set_skeletonfile(std::string skeletonfile)	protocols::loop_grower::LoopGrower	inline
set_steps(core::Size steps)	protocols::loop_grower::LoopGrower	inline
set_storedbeams(std::string storedbeams)	protocols::loop_grower::LoopGrower	inline
set_trackfragments(bool trackfragments)	protocols::loop_grower::LoopGrower	inline
set_type(std::string const &setting)	protocols::moves::Mover	inline
set_windowdensweight(core::Real windowdensweight)	protocols::loop_grower::LoopGrower	inline
set_writebeams(bool writebeams)	protocols::loop_grower::LoopGrower	inline
set_writelps(bool writelps)	protocols::loop_grower::LoopGrower	inline
sf_	protocols::loop_grower::LoopGrower	private
sheet_tolerance_	protocols::loop_grower::LoopGrower	private
sheetbonus_	protocols::loop_grower::LoopGrower	private
sheetcriteria_	protocols::loop_grower::LoopGrower	private
sheetscore(core::pose::Pose &fapose, core::pose::Pose &cen_pose, core::Size rangelo, core::Size rangehi)	protocols::loop_grower::LoopGrower
sheetsize_	protocols::loop_grower::LoopGrower	private
show(std::ostream &output=std::cout) const	protocols::moves::Mover	virtual
single_grow(core::pose::Pose &pose, core::pose::Pose &pose_cen, LoopPartialSolutionStore &solutionset, const core::chemical::ResidueTypeCOPs &restypes_pose, const core::chemical::ResidueTypeCOPs &restypes_pos_cen, core::Size lower_pose, core::Size upper_pose, core::Size upper_term, int lower_fasta, int upper_fasta, core::Size torsionrangelo, core::Size torsionrangehi, bool insert_lower, core::Size initial_melt_left, bool is_cterm, bool is_nterm, core::Size cycle, int n_to_insert)	protocols::loop_grower::LoopGrower
skeleton_	protocols::loop_grower::LoopGrower	private
skeleton_file_	protocols::loop_grower::LoopGrower	private
solutionset_	protocols::loop_grower::LoopGrower	private
startingscore_	protocols::loop_grower::LoopGrower	private
steps_	protocols::loop_grower::LoopGrower	private
store_sheets(core::pose::Pose &pose, LoopPartialSolution &lps)	protocols::loop_grower::LoopGrower
storedbeams_	protocols::loop_grower::LoopGrower	private
storehi_	protocols::loop_grower::LoopGrower	private
storelow_	protocols::loop_grower::LoopGrower	private
Strings typedef	protocols::moves::Mover
TagCOP typedef	protocols::moves::Mover
test_move(Pose &pose)	protocols::moves::Mover	inlinevirtual
total_residues_	protocols::loop_grower::LoopGrower	private
trackfragments_	protocols::loop_grower::LoopGrower	private
type(const std::string &type_in)	protocols::moves::Mover	inline
type() const	protocols::moves::Mover	inline
update_and_writelps(LoopPartialSolutionStore &solutionset, core::pose::Pose &fa_pose, core::pose::Pose &pose_cen, core::chemical::ResidueTypeCOPs &restypes_pose, core::chemical::ResidueTypeCOPs &restypes_pose_cen, int lower_pose, int upper_pose, bool is_nterm, bool is_cterm, core::Size fasta_range_low, core::Size fasta_range_hi, core::Size pose_range_low, core::Size pose_range_hi, int torsionrangelo, int torsionrangehi, int tgt_jump, bool update_pose)	protocols::loop_grower::LoopGrower
update_fragment_library_pointers()	protocols::loop_grower::LoopGrower
update_to_stored(core::pose::Pose &growpose, core::pose::Pose &growpose_cen, const core::chemical::ResidueTypeCOPs &restypes_pose, const core::chemical::ResidueTypeCOPs &restypes_pose_cen, int &lower_pose, int &upper_pose, int &lower_fasta, int &upper_fasta, core::Size newreslow, core::Size newreshi, bool is_cterm, bool is_nterm)	protocols::loop_grower::LoopGrower
upper_fasta_	protocols::loop_grower::LoopGrower	private
windowdensweight_	protocols::loop_grower::LoopGrower	private
write_to_disk(LoopPartialSolutionStore solutionset, core::Size step, core::Size added_lower, core::Size added_upper, bool filteronly, bool lower)	protocols::loop_grower::LoopGrower
writebeams_	protocols::loop_grower::LoopGrower	private
writelps_	protocols::loop_grower::LoopGrower	private