protocols::stepwise::sampling::protein::StepWisePoseSetup Member List

This is the complete list of members for protocols::stepwise::sampling::protein::StepWisePoseSetup, including all inherited members.

add_aa_virt_rsd_as_root(core::pose::Pose &pose)	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
add_peptide_plane_variants_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
add_terminal_res_repulsion(core::pose::Pose &pose) const	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
add_virt_res_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
align_file_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
align_pose(core::pose::Pose &pose) const	protocols::stepwise::sampling::protein::StepWisePoseSetup
align_poses(core::pose::Pose &pose)	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
alignment_atom_id_map_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
already_connected(std::pair< Size, Size > const &potential_chain_partner, utility::vector1< std::pair< Size, Size > > const &chain_partners) const	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
already_connected(Size const start_chain, Size const stop_chain, utility::vector1< std::pair< Size, Size > > const &chain_partners, utility::vector1< bool > already_checked) const	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
apply(core::pose::Pose &pose_to_visualize)	protocols::stepwise::sampling::protein::StepWisePoseSetup	virtual
protocols::moves::Mover::apply(core::io::serialization::PipeMap &pmap)	protocols::moves::Mover	virtual
apply_bulge_variants(core::pose::Pose &pose) const	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
apply_cutpoint_variants(core::pose::Pose &pose) const	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
apply_full_to_sub_mapping(utility::vector1< Size > &res_vector) const	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
apply_peptide_plane_variants(core::pose::Pose &pose) const	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
apply_peptide_plane_variants_OLD(core::pose::Pose &pose) const	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
apply_terminus_variants_at_protein_rna_boundaries(core::pose::Pose &pose) const	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
apply_virtual_phosphate_variants(core::pose::Pose &pose) const	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
apply_virtual_res_variant(core::pose::Pose &pose) const	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
BRIDGE_RES_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
bridge_res_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
bulge_res_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
calc_rms_res_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
check_close_chain_break(core::pose::Pose const &pose) const	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
check_moving_res_in_chain(Size const &start_chain, Size const &end_chain, Size const &num_chains, Size &which_chain_has_moving_res)	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
check_superimpose_res(core::pose::Pose const &pose)	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
clear_info()	protocols::moves::Mover	inlinevirtual
clone() const	protocols::moves::Mover	virtual
copy_rna_chi(core::pose::Pose &pose, core::pose::Pose const import_pose, utility::vector1< core::Size > const &input_res, utility::vector1< core::Size > const &slice_res)	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
create()	protocols::moves::Mover	virtual
cst_file_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
cst_set_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
cutpoint_closed_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
cutpoint_open_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
cuts_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
desired_sequence_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
disulfide_file_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
dump_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
extra_minimize_res_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
figure_out_cuts()	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
figure_out_gap_size_and_first_chain_break_res()	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
figure_out_jump_partners()	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
figure_out_partition_definition(core::pose::Pose const &pose)	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
figure_out_Prepend_Internal(core::pose::Pose const &pose)	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
figure_out_working_sequence_and_mapping()	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
Filters_map typedef	protocols::moves::Mover
fix_phi_psi_offsets(core::pose::Pose &pose) const	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
fixed_res_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
fresh_instance() const	protocols::moves::Mover	virtual
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	protocols::stepwise::sampling::protein::StepWisePoseSetup	virtual
get_native_pose() const	protocols::moves::Mover
get_stepwise_jump_atom(core::conformation::Residue const &rsd)	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
get_type() const	protocols::moves::Mover	inline
get_working_pose(core::pose::Pose const &pose, core::pose::Pose &working_pose)	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
Import_pose(core::pose::Pose &import_pose, InputStreamWithResidueInfoOP &stream)	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
info()	protocols::moves::Mover	inlinevirtual
info() const	protocols::moves::Mover	inlinevirtual
initialize_phi_psi_offsets(core::pose::Pose const &pose)	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
initialize_pose_from_streams(core::pose::Pose &pose)	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
input_streams_with_residue_info_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
is_cutpoint_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
is_working_cutpoint_closed(Size const res, std::map< Size, Size > &full_to_sub) const	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
job_parameters()	protocols::stepwise::sampling::protein::StepWisePoseSetup
job_parameters_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
jump_partners_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
jump_res_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
last_proposal_density_ratio()	protocols::moves::Mover	inlinevirtual
make_full_pose(core::pose::Pose &pose)	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
make_pose(core::pose::Pose &pose)	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
Mover()	protocols::moves::Mover
Mover(std::string const &type_name)	protocols::moves::Mover
Mover(Mover const &other)	protocols::moves::Mover
MOVING_RES_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
moving_res_list_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
name()	protocols::moves::Mover	inlinestatic
operator=(Mover const &other)	protocols::moves::Mover
parin_favorite_output_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
parse_def(utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)	protocols::moves::Mover	virtual
parse_my_tag(TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)	protocols::moves::Mover	virtual
parse_state(SerializableState const &state)	protocols::moves::Mover	virtual
phi_offsets_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
Pose typedef	protocols::moves::Mover
PoseCOP typedef	protocols::moves::Mover
psi_offsets_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
ready_to_align() const	protocols::stepwise::sampling::protein::StepWisePoseSetup
ready_to_align_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
register_options()	protocols::moves::Mover	inlinestatic
reinitialize_for_each_job() const	protocols::moves::Mover	virtual
reinitialize_for_new_input() const	protocols::moves::Mover	virtual
remove_cterminus_variant_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
remove_nterminus_variant_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
reroot_fold_tree(core::pose::Pose &pose)	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
reset_status()	protocols::moves::Mover
rsd_set_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
save_phi_psi_offsets(core::pose::Pose const &start_pose, utility::vector1< core::Size > const &input_res, utility::vector1< core::Size > const &slice_res)	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
save_state(SerializableState &state)	protocols::moves::Mover	virtual
secstruct_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
set_add_peptide_plane_variants(bool const &setting)	protocols::stepwise::sampling::protein::StepWisePoseSetup
set_add_virt_res(bool const setting)	protocols::stepwise::sampling::protein::StepWisePoseSetup
set_align_file(std::string const align_file)	protocols::stepwise::sampling::protein::StepWisePoseSetup
set_bridge_res(utility::vector1< core::Size > const &bridge_res)	protocols::stepwise::sampling::protein::StepWisePoseSetup
set_bulge_res(utility::vector1< core::Size > const &bulge_res)	protocols::stepwise::sampling::protein::StepWisePoseSetup
set_calc_rms_res(utility::vector1< core::Size > const &calc_rms_res)	protocols::stepwise::sampling::protein::StepWisePoseSetup
set_cst_file(std::string const cst_file)	protocols::stepwise::sampling::protein::StepWisePoseSetup
set_current_job(protocols::jobdist::BasicJobCOP job)	protocols::moves::Mover
set_current_tag(std::string const &new_tag)	protocols::moves::Mover	inline
set_disulfide_file(std::string const disulfide_file)	protocols::stepwise::sampling::protein::StepWisePoseSetup
set_dump(bool const dump)	protocols::stepwise::sampling::protein::StepWisePoseSetup
set_extra_minimize_res(utility::vector1< core::Size > const &setting)	protocols::stepwise::sampling::protein::StepWisePoseSetup	inline
set_fixed_res(utility::vector1< core::Size > const &fixed_res)	protocols::stepwise::sampling::protein::StepWisePoseSetup
set_input_pose(PoseCOP pose)	protocols::moves::Mover	virtual
set_jump_res(utility::vector1< core::Size > const &jump_res)	protocols::stepwise::sampling::protein::StepWisePoseSetup
set_last_move_status(MoverStatus status)	protocols::moves::Mover	protected
set_native_pose(PoseCOP pose)	protocols::moves::Mover	virtual
set_parin_favorite_output(bool const &setting)	protocols::stepwise::sampling::protein::StepWisePoseSetup	inline
set_remove_cterminus_variant(bool const &setting)	protocols::stepwise::sampling::protein::StepWisePoseSetup	inline
set_remove_nterminus_variant(bool const &setting)	protocols::stepwise::sampling::protein::StepWisePoseSetup	inline
set_rsd_set(core::chemical::ResidueTypeSetCAP &rsd_set)	protocols::stepwise::sampling::protein::StepWisePoseSetup
set_secstruct(std::string const secstruct)	protocols::stepwise::sampling::protein::StepWisePoseSetup
set_superimpose_res(utility::vector1< core::Size > const &superimpose_res)	protocols::stepwise::sampling::protein::StepWisePoseSetup
set_terminal_res(utility::vector1< core::Size > const &terminal_res)	protocols::stepwise::sampling::protein::StepWisePoseSetup
set_virtual_res(utility::vector1< core::Size > const &set_virtual_res_list)	protocols::stepwise::sampling::protein::StepWisePoseSetup
setup_constraints(core::pose::Pose &pose)	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
setup_disulfides(core::pose::Pose &pose)	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
setup_full_model_info(core::pose::Pose &pose) const	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
setup_secstruct(core::pose::Pose &pose) const	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
setup_working_native_pose()	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
show(std::ostream &output=std::cout) const	protocols::moves::Mover	virtual
StepWisePoseSetup(utility::vector1< core::Size > const &moving_res_list, std::string const &desired_sequence, utility::vector1< InputStreamWithResidueInfoOP > &input_streams_with_residue_info, utility::vector1< core::Size > const &cutpoint_open, utility::vector1< core::Size > const &cutpoint_closed)	protocols::stepwise::sampling::protein::StepWisePoseSetup
Strings typedef	protocols::moves::Mover
superimpose_res_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
TagCOP typedef	protocols::moves::Mover
terminal_res_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
test_move(Pose &pose)	protocols::moves::Mover	inlinevirtual
type() const	protocols::moves::Mover	inline
type(const std::string &type_in)	protocols::moves::Mover	inline
virtual_res_list_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
virtualize_5prime_phosphates_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
which_chain(Size const &i)	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
working_align_pose_	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
working_native_pose	protocols::stepwise::sampling::protein::StepWisePoseSetup	private
~Mover()	protocols::moves::Mover	virtual
~StepWisePoseSetup()	protocols::stepwise::sampling::protein::StepWisePoseSetup