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>

Go to the source code of this file.

Namespaces
	core
	A class for defining atom parameters, known as atom_types.
	core::pose

Constant Groups
	core
	A class for defining atom parameters, known as atom_types.
	core::pose

Functions
static basic::Tracer	core::pose::tr ("core.pose")
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, std::string const &sequence, chemical::ResidueTypeSet const &residue_set, 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, 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...

Detailed Description

utility functions for making poses from sequences

Author

P. Douglas Renfrew

Sam Deluca

Labonte (carbohydrate versions)

Definition in file annotated_sequence.cc.