annotated_sequence.cc File Reference

utility functions for making poses from sequences More...

#include <core/pose/annotated_sequence.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/carbohydrates/CarbohydrateInfo.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/types.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <basic/Tracer.hh>
#include <utility/vector1.hh>
#include <ObjexxFCL/string.functions.hh>

Namespaces
	core
	A class for defining atom parameters, known as atom_types.
	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)
	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 polysaccharide sequence. 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)
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)
	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)
	Create a Pose from an annotated polysaccharide sequence <sequence> with ResidueTypeSet <residue_set> and stores 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)
	Create a Pose from an annotated polysaccharide sequence <sequence> with residue type set name <type_set_name> and stores 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)
	Return a Pose from an annotated 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...

Variables
static basic::Tracer	core::pose::tr ("core.pose")

Detailed Description

utility functions for making poses from sequences

Author

P. Douglas Renfrew

Sam Deluca

Labonte (carbohydrate versions)