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protocols::hybridization::HybridizeProtocol Member List

This is the complete list of members for protocols::hybridization::HybridizeProtocol, including all inherited members.

add_big_fragments(core::fragment::FragSetOP newval)protocols::hybridization::HybridizeProtocolinline
add_fragment_csts(core::pose::Pose &pose)protocols::hybridization::HybridizeProtocol
add_hetatm_protocols::hybridization::HybridizeProtocolprivate
add_non_init_chunks_protocols::hybridization::HybridizeProtocolprivate
add_null_template(core::pose::PoseOP template_pose, std::string cst_fn, std::string symmdef_file="NULL", core::Real weight=1.)protocols::hybridization::HybridizeProtocol
add_small_fragments(core::fragment::FragSetOP newval)protocols::hybridization::HybridizeProtocolinline
add_template(std::string const &template_fn, std::string const &cst_fn, std::string const &symmdef_file="NULL", core::Real const weight=1., utility::vector1< char > const &rand_chains=utility::vector1< core::Size >(0), bool const align_pdb_info=true)protocols::hybridization::HybridizeProtocol
add_template(core::pose::PoseOP template_pose, std::string const &cst_fn, std::string const &symmdef_file="NULL", core::Real const weight=1., utility::vector1< char > const &rand_chains=utility::vector1< core::Size >(0), std::string const &filename="default", bool const align_pdb_info=true)protocols::hybridization::HybridizeProtocol
align_by_domain(core::pose::Pose &pose, core::pose::Pose const &ref_pose, utility::vector1< protocols::loops::Loops > domains)protocols::hybridization::HybridizeProtocol
align_templates_by_domain(core::pose::PoseOP &ref_pose, utility::vector1< protocols::loops::Loops > domains=utility::vector1< protocols::loops::Loops >())protocols::hybridization::HybridizeProtocol
aln_protocols::hybridization::HybridizeProtocolprivate
apply(Pose &) overrideprotocols::hybridization::HybridizeProtocolvirtual
auto_frag_insertion_weight_protocols::hybridization::HybridizeProtocolprivate
batch_relax_protocols::hybridization::HybridizeProtocolprivate
big_frag_insertion_weight_protocols::hybridization::HybridizeProtocolprivate
cartfrag_overlap_protocols::hybridization::HybridizeProtocolprivate
cen_cst_in_protocols::hybridization::HybridizeProtocolprivate
cenrot_protocols::hybridization::HybridizeProtocolprivate
check_and_create_fragments(Pose &)protocols::hybridization::HybridizeProtocol
chunk_insertion_weight_protocols::hybridization::HybridizeProtocolprivate
clear_info()protocols::moves::Moverinlinevirtual
clone() const overrideprotocols::hybridization::HybridizeProtocolvirtual
coord_cst_res_protocols::hybridization::HybridizeProtocolprivate
create()protocols::moves::Movervirtual
csts_from_frags_protocols::hybridization::HybridizeProtocolprivate
current_job_protocols::moves::Moverprivate
current_tag_protocols::moves::Moverprivate
detailed_controls_settings_protocols::hybridization::HybridizeProtocolprivate
disulf_file_protocols::hybridization::HybridizeProtocolprivate
do_intrastage_docking(core::pose::Pose &pose)protocols::hybridization::HybridizeProtocol
domain_parse_templates(core::Size nres)protocols::hybridization::HybridizeProtocol
domains_all_templ_protocols::hybridization::HybridizeProtocolprivate
fa_cst_fn_protocols::hybridization::HybridizeProtocolprivate
fa_cst_in_protocols::hybridization::HybridizeProtocolprivate
fa_scorefxn_protocols::hybridization::HybridizeProtocolprivate
filter_templates_protocols::hybridization::HybridizeProtocolprivate
frag_1mer_insertion_weight_protocols::hybridization::HybridizeProtocolprivate
frag_weight_aligned_protocols::hybridization::HybridizeProtocolprivate
fragments_big_protocols::hybridization::HybridizeProtocolprivate
fragments_small_protocols::hybridization::HybridizeProtocolprivate
fragprob_stage2_protocols::hybridization::HybridizeProtocolprivate
fresh_instance() const overrideprotocols::hybridization::HybridizeProtocolvirtual
get_additional_output()protocols::moves::Movervirtual
get_current_job() constprotocols::moves::Mover
get_current_tag() constprotocols::moves::Moverinline
get_disulf_file() constprotocols::hybridization::HybridizeProtocolinline
get_input_pose() constprotocols::moves::Mover
get_last_move_status() constprotocols::moves::Mover
get_name() const overrideprotocols::hybridization::HybridizeProtocolvirtual
get_native_pose() constprotocols::moves::Mover
get_self_ptr() constprotocols::moves::Moverinline
get_self_ptr()protocols::moves::Moverinline
get_self_weak_ptr() constprotocols::moves::Moverinline
get_self_weak_ptr()protocols::moves::Moverinline
get_type() constprotocols::moves::Moverinline
hcut_protocols::hybridization::HybridizeProtocolprivate
hetatm_prot_cst_weight_protocols::hybridization::HybridizeProtocolprivate
hetatm_self_cst_weight_protocols::hybridization::HybridizeProtocolprivate
HybridizeProtocol()protocols::hybridization::HybridizeProtocol
HybridizeProtocol(utility::vector1< core::pose::PoseOP > templates_in, utility::vector1< core::Real > template_weights_in, core::scoring::ScoreFunctionOP stage1_scorefxn_in, core::scoring::ScoreFunctionOP stage2_scorefxn_in, core::scoring::ScoreFunctionOP fa_scorefxn_in, std::string const &frag3_fn, std::string const &frag9_fn, std::string const &cen_cst_in, std::string const &fa_cst_in)protocols::hybridization::HybridizeProtocol
include_loop_ss_chunks_protocols::hybridization::HybridizeProtocolprivate
info()protocols::moves::Moverinlinevirtual
info() constprotocols::moves::Moverinlinevirtual
info_protocols::moves::Moverprivate
init()protocols::hybridization::HybridizeProtocol
initialize_and_sample_loops(core::pose::Pose &pose, core::pose::PoseOP chosen_templ, protocols::loops::Loops template_contigs_icluster, core::scoring::ScoreFunctionOP scorefxn)protocols::hybridization::HybridizeProtocol
input_pose_protocols::moves::Moverprivate
jump_move_protocols::hybridization::HybridizeProtocolprivate
jump_move_repeat_protocols::hybridization::HybridizeProtocolprivate
keep_pose_constraint_protocols::hybridization::HybridizeProtocolprivate
last_proposal_density_ratio()protocols::moves::Moverinlinevirtual
last_status_protocols::moves::Moverprivate
length_protocols::hybridization::HybridizeProtocolprivate
linmin_only_protocols::hybridization::HybridizeProtocolprivate
max_contig_insertion_protocols::hybridization::HybridizeProtocolprivate
max_registry_shift_protocols::hybridization::HybridizeProtocolprivate
min_after_stage1_protocols::hybridization::HybridizeProtocolprivate
Mover()protocols::moves::Mover
Mover(std::string const &type_name)protocols::moves::Mover
mover_name()protocols::hybridization::HybridizeProtocolstatic
name()protocols::moves::Moverinlinestatic
native_protocols::hybridization::HybridizeProtocolprivate
native_needs_load_protocols::hybridization::HybridizeProtocolprivate
native_needs_load_from_align_rmsd_target_protocols::hybridization::HybridizeProtocolprivate
native_pose_protocols::moves::Moverprivate
no_global_frame_protocols::hybridization::HybridizeProtocolprivate
non_null_template_indices_protocols::hybridization::HybridizeProtocolprivate
pairings_file_protocols::hybridization::HybridizeProtocolprivate
parse_my_tag(TagCOP, basic::datacache::DataMap &) overrideprotocols::hybridization::HybridizeProtocolvirtual
pcut_protocols::hybridization::HybridizeProtocolprivate
pick_starting_template()protocols::hybridization::HybridizeProtocol
Pose typedefprotocols::moves::Mover
PoseCOP typedefprotocols::moves::Mover
provide_citation_info(basic::citation_manager::CitationCollectionList &) const overrideprotocols::hybridization::HybridizeProtocolvirtual
provide_xml_schema(utility::tag::XMLSchemaDefinition &xsd)protocols::hybridization::HybridizeProtocolstatic
randfragprob_stage2_protocols::hybridization::HybridizeProtocolprivate
random_sheets_protocols::hybridization::HybridizeProtocolprivate
randomize_chains_protocols::hybridization::HybridizeProtocolprivate
realign_domains_protocols::hybridization::HybridizeProtocolprivate
realign_domains_stage2_protocols::hybridization::HybridizeProtocolprivate
register_options()protocols::moves::Moverinlinestatic
reinitialize_for_each_job() constprotocols::moves::Movervirtual
reinitialize_for_new_input() constprotocols::moves::Movervirtual
relax_repeats_protocols::hybridization::HybridizeProtocolprivate
reset_status()protocols::moves::Mover
residue_max_registry_shift_protocols::hybridization::HybridizeProtocolprivate
residue_sample_abinitio_protocols::hybridization::HybridizeProtocolprivate
residue_sample_template_protocols::hybridization::HybridizeProtocolprivate
seqfrags_only_protocols::hybridization::HybridizeProtocolprivate
set_add_hetatm(bool add_hetatm)protocols::hybridization::HybridizeProtocolinline
set_batch_relax(core::Size newval)protocols::hybridization::HybridizeProtocolinline
set_current_job(protocols::jobdist::BasicJobCOP job)protocols::moves::Mover
set_current_tag(std::string const &new_tag)protocols::moves::Moverinlinevirtual
set_disulf_file(std::string const &dsf)protocols::hybridization::HybridizeProtocolinline
set_fullatom_scorefxn(core::scoring::ScoreFunctionOP newval)protocols::hybridization::HybridizeProtocolinline
set_input_pose(PoseCOP pose)protocols::moves::Movervirtual
set_last_move_status(MoverStatus status)protocols::moves::Moverprotected
set_native_pose(PoseCOP pose)protocols::moves::Movervirtual
set_stage1_increase_cycles(core::Real newval)protocols::hybridization::HybridizeProtocolinline
set_stage1_scorefxn(core::scoring::ScoreFunctionOP newval)protocols::hybridization::HybridizeProtocolinline
set_stage2_increase_cycles(core::Real newval)protocols::hybridization::HybridizeProtocolinline
set_stage2_scorefxn(core::scoring::ScoreFunctionOP newval)protocols::hybridization::HybridizeProtocolinline
set_stage2min_scorefxn(core::scoring::ScoreFunctionOP newval)protocols::hybridization::HybridizeProtocolinline
set_stage2pack_scorefxn(core::scoring::ScoreFunctionOP newval)protocols::hybridization::HybridizeProtocolinline
set_type(std::string const &setting)protocols::moves::Moverinline
setup_templates_and_sampling_options(core::pose::Pose const &pose)protocols::hybridization::HybridizeProtocol
sheets_protocols::hybridization::HybridizeProtocolprivate
should_align_pdb_infos_protocols::hybridization::HybridizeProtocolprivate
show(std::ostream &output=std::cout) constprotocols::moves::Movervirtual
skip_long_min_protocols::hybridization::HybridizeProtocolprivate
small_frag_insertion_weight_protocols::hybridization::HybridizeProtocolprivate
stage1_1_cycles_protocols::hybridization::HybridizeProtocolprivate
stage1_2_cycles_protocols::hybridization::HybridizeProtocolprivate
stage1_3_cycles_protocols::hybridization::HybridizeProtocolprivate
stage1_4_cycles_protocols::hybridization::HybridizeProtocolprivate
stage1_increase_cycles_protocols::hybridization::HybridizeProtocolprivate
stage1_probability_protocols::hybridization::HybridizeProtocolprivate
stage1_scorefxn_protocols::hybridization::HybridizeProtocolprivate
stage25_increase_cycles_protocols::hybridization::HybridizeProtocolprivate
stage2_increase_cycles_protocols::hybridization::HybridizeProtocolprivate
stage2_scorefxn_protocols::hybridization::HybridizeProtocolprivate
stage2_temperature_protocols::hybridization::HybridizeProtocolprivate
stage2min_scorefxn_protocols::hybridization::HybridizeProtocolprivate
stage2pack_scorefxn_protocols::hybridization::HybridizeProtocolprivate
strand_pairs_protocols::hybridization::HybridizeProtocolprivate
Strings typedefprotocols::moves::Mover
symmdef_files_protocols::hybridization::HybridizeProtocolprivate
TagCOP typedefprotocols::moves::Mover
template_chunks_protocols::hybridization::HybridizeProtocolprivate
template_contigs_protocols::hybridization::HybridizeProtocolprivate
template_cst_fn_protocols::hybridization::HybridizeProtocolprivate
template_fns_protocols::hybridization::HybridizeProtocolprivate
template_weights_protocols::hybridization::HybridizeProtocolprivate
templates_protocols::hybridization::HybridizeProtocolprivate
templates_aln_protocols::hybridization::HybridizeProtocolprivate
test_move(Pose &pose)protocols::moves::Moverinlinevirtual
type(const std::string &type_in)protocols::moves::Moverinline
type() constprotocols::moves::Moverinline
type_protocols::moves::Moverprivate
update_template(core::Size const template_idx)protocols::hybridization::HybridizeProtocol
user_csts_protocols::hybridization::HybridizeProtocolprivate
validate_template(std::string const &filename, std::string const &fasta, core::pose::PoseOP template_pose, bool &align_pdb_info)protocols::hybridization::HybridizeProtocol