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protocols::rna::RNA_ChunkLibrary Member List

This is the complete list of members for protocols::rna::RNA_ChunkLibrary, including all inherited members.

add_chunk_set(std::string const &silent_file, core::pose::ResMap const &res_map, core::pose::Pose const &big_pose)protocols::rna::RNA_ChunkLibrary
align_to_chunk(core::pose::Pose &pose, ChunkSet const &chunk_set, core::Size const chunk_index) const protocols::rna::RNA_ChunkLibraryprivate
allow_insert()protocols::rna::RNA_ChunkLibraryinline
allow_insert_protocols::rna::RNA_ChunkLibraryprivate
check_connections(Size const &num_chain, core::pose::ResMap &res_map, utility::vector1< Size > const &chain_id, utility::vector1< Size > const &scratch_sequence_start, utility::vector1< std::string > const &scratch_sequences, utility::vector1< utility::vector1< Size > > const &matches_to_each_scratch_sequence, core::pose::Pose const &scratch_pose, std::map< Size, Size > const &connections_in_big_pose, utility::vector1< core::pose::ResMap > &res_maps) const protocols::rna::RNA_ChunkLibraryprivate
check_fold_tree_OK(core::pose::Pose const &pose)protocols::rna::RNA_ChunkLibrary
check_fold_tree_OK(core::pose::ResMap const &res_map, core::pose::Pose const &pose, core::pose::Pose const &scratch_pose)protocols::rna::RNA_ChunkLibraryprivate
check_jump_match(core::pose::Pose const &scratch_pose, std::map< core::Size, core::Size > const &connections_in_big_pose, core::pose::ResMap const &res_map, utility::vector1< Size > const &chain_id) const protocols::rna::RNA_ChunkLibraryprivate
check_res_map(core::pose::ResMap const &res_map, core::pose::Pose const &scratch_pose, std::string const &sequence) const protocols::rna::RNA_ChunkLibraryprivate
check_res_map_recursively(core::pose::ResMap const &res_map_old, utility::vector1< std::string > const &scratch_sequences, utility::vector1< utility::vector1< Size > > const &matches_to_each_scratch_sequence, core::pose::Pose const &scratch_pose, std::map< Size, Size > const &connections_in_big_pose, utility::vector1< core::Size > const &chain_id, core::Size const &num_sequence, core::Size const &num_match, utility::vector1< core::pose::ResMap > &res_maps) const protocols::rna::RNA_ChunkLibraryprivate
chunk_coverage() const protocols::rna::RNA_ChunkLibraryinline
chunk_coverage_protocols::rna::RNA_ChunkLibraryprivate
chunk_set(Size const n) const protocols::rna::RNA_ChunkLibraryinline
chunk_sets_protocols::rna::RNA_ChunkLibraryprivate
coarse_rna_protocols::rna::RNA_ChunkLibraryprivate
covered_by_chunk_protocols::rna::RNA_ChunkLibraryprivate
figure_out_chunk_coverage()protocols::rna::RNA_ChunkLibraryprivate
figure_out_possible_res_maps(utility::vector1< core::pose::ResMap > &res_maps, core::pose::Pose const &scratch_pose, std::string const &sequence_of_big_pose, std::map< Size, Size > const &connections_in_big_pose) const protocols::rna::RNA_ChunkLibraryprivate
fill_res_map(core::pose::ResMap &res_map, Size const &match_pos, Size const &scratch_start_pos, Size const &scratch_sequence_length) const protocols::rna::RNA_ChunkLibraryprivate
find_res_maps(utility::vector1< Size > const &chain_id, utility::vector1< Size > const &scratch_sequence_start, utility::vector1< std::string > const &scratch_sequences, utility::vector1< utility::vector1< Size > > const &matches_to_each_scratch_sequence, core::pose::Pose const &scratch_pose, std::map< Size, Size > const &connections_in_big_pose, utility::vector1< core::pose::ResMap > &res_maps) const protocols::rna::RNA_ChunkLibraryprivate
get_component_sequences(core::pose::Pose const &pose, utility::vector1< std::string > &sequences, utility::vector1< core::Size > &chain_id, utility::vector1< core::Size > &sequence_start) const protocols::rna::RNA_ChunkLibraryprivate
get_sequence_matches(utility::vector1< utility::vector1< Size > > &matches_to_each_scratch_sequence, utility::vector1< std::string > const &scratch_sequences, std::string const &sequence_of_big_pose) const protocols::rna::RNA_ChunkLibraryprivate
initialize_random_chunks(core::pose::Pose &pose, bool const dump_pdb=false) const protocols::rna::RNA_ChunkLibrary
initialize_rna_chunk_library(utility::vector1< std::string > const &pdb_files, utility::vector1< std::string > const &silent_files, core::pose::Pose const &pose, utility::vector1< core::Size > const &input_res)protocols::rna::RNA_ChunkLibrary
insert_chunk_into_pose(core::pose::Pose &pose, Size const &chunk_list_index, Size const &chunk_pose_index) const protocols::rna::RNA_ChunkLibrary
num_chunk_sets() const protocols::rna::RNA_ChunkLibraryinline
num_chunks(Size const n) const protocols::rna::RNA_ChunkLibraryinline
process_input_file(std::string const &silent_file, utility::vector1< core::pose::PoseOP > &pose_list, bool is_pdb=false) const protocols::rna::RNA_ChunkLibraryprivate
random_chunk_insertion(core::pose::Pose &pose) const protocols::rna::RNA_ChunkLibrary
RNA_ChunkLibrary()protocols::rna::RNA_ChunkLibrary
RNA_ChunkLibrary(utility::vector1< std::string > const &silent_files, core::pose::Pose const &pose, std::map< Size, Size > const &connections_in_big_pose)protocols::rna::RNA_ChunkLibrary
RNA_ChunkLibrary(utility::vector1< std::string > const &pdb_files, utility::vector1< std::string > const &silent_files, core::pose::Pose const &pose, utility::vector1< core::Size > const &input_res)protocols::rna::RNA_ChunkLibrary
RNA_ChunkLibrary(utility::vector1< std::string > const &silent_files, core::pose::Pose const &pose, utility::vector1< core::Size > const &input_res)protocols::rna::RNA_ChunkLibrary
set_allow_insert(toolbox::AllowInsertOP allow_insert)protocols::rna::RNA_ChunkLibrary
superimpose_to_first_chunk(core::pose::Pose &pose) const protocols::rna::RNA_ChunkLibrary
test_matches(Size const &res1, Size const &res2, core::pose::ResMap &res_map, utility::vector1< Size > const &chain_id, utility::vector1< Size > const &scratch_sequence_start, utility::vector1< std::string > const &scratch_sequences, utility::vector1< utility::vector1< Size > > const &matches_to_each_scratch_sequence, core::pose::Pose const &scratch_pose, std::map< Size, Size > const &connections_in_big_pose, utility::vector1< core::pose::ResMap > &res_maps) const protocols::rna::RNA_ChunkLibraryprivate
zero_out_allow_insert(core::pose::ResMap const &res_map, core::pose::Pose const &pose, core::pose::Pose const &scratch_pose, Size const domain_num)protocols::rna::RNA_ChunkLibraryprivate
~RNA_ChunkLibrary()protocols::rna::RNA_ChunkLibraryinline
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