Rosetta  2020.50
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Namespaces | Functions
annotated_sequence.hh File Reference
#include <core/pose/Pose.fwd.hh>
#include <core/types.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/chemical/ResidueType.fwd.hh>
#include <core/chemical/AA.hh>
#include <utility/vector1.hh>
#include <string>

Namespaces

 core
 A class for reading in the atom type properties.
 
 core::pose
 

Functions

void core::pose::parse_sequence (std::string const &sequence_in, utility::vector1< std::string > &fullname_list, std::vector< Size > &oneletter_to_fullname_index, std::string &one_letter_sequence)
 parse the annotated sequence. More...
 
Size core::pose::get_sequence_len (std::string const &sequence_in)
 Get the length of the annotated sequence. More...
 
chemical::ResidueTypeCOPs core::pose::residue_types_from_sequence (std::string const &sequence_in, chemical::ResidueTypeSet const &residue_set, bool const auto_termini=true, bool const metapatches=true)
 return a list of ResidueTypes corresponding to an annotated protein sequence More...
 
chemical::ResidueTypeCOPs core::pose::residue_types_from_saccharide_sequence (std::string const &sequence, chemical::ResidueTypeSet const &residue_set)
 Return a list of carbohydrate ResidueTypes corresponding to an annotated, linear, IUPAC polysaccharide sequence. More...
 
void core::pose::append_pose_with_glycan_residues (pose::Pose &pose, chemical::ResidueTypeCOPs residue_types, core::uint resnum_to_be_appended=0)
 Append an empty or current Pose with saccharide residues, building branches as necessary. More...
 
void core::pose::make_pose_from_sequence (pose::Pose &pose, chemical::ResidueTypeCOPs requested_types, bool const auto_termini=true)
 Creates a Pose from the annotated protein sequence <sequence> with ResidueTypeSet <residue_set> and stores it in <pose> More...
 
void core::pose::make_pose_from_sequence (pose::Pose &pose, std::string const &sequence_in, chemical::ResidueTypeSet const &residue_set, bool const auto_termini, bool const metapatches)
 
void core::pose::make_pose_from_sequence (pose::Pose &pose, std::string const &sequence_in, chemical::ResidueTypeSetCOP residue_set, bool const auto_termini, bool const metapatches)
 
void core::pose::make_pose_from_sequence (pose::Pose &pose, std::string const &sequence, std::string const &type_set_name, bool const auto_termini=true, bool const metapatches=true)
 Creates a Pose from the annotated protein sequence <sequence> with the desired <type_set_name> and stores it in <pose> More...
 
void core::pose::make_pose_from_saccharide_sequence (pose::Pose &pose, std::string const &sequence, chemical::ResidueTypeSet const &residue_set, bool const auto_termini=true, bool const idealize_linkages=true)
 Create a Pose from an annotated, linear, IUPAC polysaccharide sequence <sequence> with ResidueTypeSet <residue_set> and store it in <pose>. More...
 
void core::pose::make_pose_from_saccharide_sequence (pose::Pose &pose, std::string const &sequence, std::string const &type_set_name="fa_standard", bool const auto_termini=true, bool const idealize_linkages=true)
 Create a Pose from an annotated, linear, IUPAC polysaccharide sequence <sequence> with residue type set name <type_set_name> and store it in <pose>. More...
 
pose::PoseOP core::pose::pose_from_saccharide_sequence (std::string const &sequence, std::string const &type_set_name="fa_standard", bool const auto_termini=true, bool const idealize_linkages=true)
 Return a Pose from an annotated, linear, IUPAC polysaccharide sequence <sequence> with residue type set name <type_set_name>. More...
 
std::string core::pose::annotated_to_oneletter_sequence (std::string const &annotated_seq)
 Returns the oneletter_sequence that corresponds to the given annotated sequence. More...
 
chemical::ResidueTypeCOP core::pose::get_rsd_type_from_aa (chemical::ResidueTypeSet const &residue_set, core::chemical::AA const &my_aa, bool const &is_lower_terminus, bool const &is_upper_terminus, bool const metapatches=true)
 use efficient residue type finder to find simplest residue type with this AA & requested termini. More...