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extra_pose_info_util.hh File Reference

Pose utilities. More...

#include <core/pose/Pose.fwd.hh>
#include <core/pose/MiniPose.fwd.hh>
#include <core/types.hh>
#include <core/id/AtomID.fwd.hh>
#include <core/id/AtomID_Map.fwd.hh>
#include <core/id/DOF_ID_Mask.fwd.hh>
#include <core/id/NamedAtomID.fwd.hh>
#include <core/id/NamedStubID.fwd.hh>
#include <core/id/TorsionID.fwd.hh>
#include <core/id/SequenceMapping.fwd.hh>
#include <core/io/StructFileRep.fwd.hh>
#include <core/kinematics/FoldTree.fwd.hh>
#include <core/kinematics/Jump.fwd.hh>
#include <core/kinematics/MoveMap.fwd.hh>
#include <core/kinematics/RT.fwd.hh>
#include <core/kinematics/tree/Atom.fwd.hh>
#include <core/scoring/ScoreType.hh>
#include <utility/vector1.fwd.hh>
#include <map>
#include <set>

Namespaces

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

Functions

void core::pose::set_ss_from_phipsi (pose::Pose &pose)
 Analyzes <pose> residue phi/psi sets and guesses the secondary structure, ideally dssp should be used for that. More...
 
utility::vector1< char > core::pose::read_psipred_ss2_file (pose::Pose const &pose, std::string const &filename)
 
utility::vector1< char > core::pose::read_psipred_ss2_file (pose::Pose const &pose)
 
bool core::pose::hasPoseExtraScore (core::pose::Pose const &pose, std::string const &name)
 does this ExtraScore exist? More...
 
bool core::pose::hasPoseExtraScore_str (core::pose::Pose const &pose, std::string const &name)
 does this (string) ExtraScore exist? More...
 
Real core::pose::getPoseExtraScore (core::pose::Pose const &pose, std::string const &name)
 return value is ExtraScore if exist, runtime_assert if it doesn't exist More...
 
bool core::pose::getPoseExtraScore (core::pose::Pose const &pose, std::string const &name, core::Real &value)
 return bool is T/F for whether the requested datum exists. "value" is the data, pass-by-ref. More...
 
bool core::pose::getPoseExtraScore (core::pose::Pose const &pose, std::string const &name, std::string &value)
 return bool is T/F for whether the requested datum exists. "value" is the data, pass-by-ref. More...
 
void core::pose::clearPoseExtraScore (core::pose::Pose &pose, std::string const &name)
 Clear a specific data type from the arbitrary data cache in the pose. More...
 
void core::pose::clearPoseExtraScores (core::pose::Pose &pose)
 Clear ALL PoseExtraScores. More...
 
void core::pose::setPoseExtraScore (core::pose::Pose &pose, std::string const &name, core::Real value)
 Set a core::Real in the pose datacache, that will be output as a score in the scorefile. More...
 
void core::pose::setPoseExtraScore (core::pose::Pose &pose, std::string const &name, std::string const &value)
 Set a string in the pose datacache, that will be output as a score in the scorefile. More...
 
std::map< std::string, float > core::pose::getPoseExtraFloatScores (core::pose::Pose const &pose)
 
std::map< std::string,
std::string > 
core::pose::getPoseExtraStringScores (core::pose::Pose const &pose)
 
void core::pose::add_comment (core::pose::Pose &pose, std::string const &key, std::string const &val)
 Adds a key-value pair to the STRING_MAP in the Pose DataCache. If there is no STRING_MAP in the DataCache, one is created. More...
 
bool core::pose::get_comment (core::pose::Pose const &pose, std::string const &key, std::string &val)
 Attempts to access the entry in the STRING_MAP associated with the given key. If an entry for the key exists, the value associated with the key is put into val, and this function returns true. Otherwise, this function returns false and val left unmodified. More...
 
void core::pose::delete_comment (core::pose::Pose &pose, std::string const &key)
 Deletes the entry in the STRING_MAP associated with the given key. More...
 
void core::pose::read_comment_pdb (std::string const &file_name, core::pose::Pose &pose)
 Reads the comments from the pdb file and adds it into comments. More...
 
void core::pose::dump_comment_pdb (std::string const &file_name, core::pose::Pose const &pose)
 dumps pose+ comments to pdb file More...
 
std::map< std::string,
std::string > 
core::pose::get_all_comments (core::pose::Pose const &pose)
 Gets a map< string, string > representing comments about the Pose in the form of key-value pairs. More...
 
void core::pose::add_score_line_string (core::pose::Pose &pose, std::string const &key, std::string const &val)
 Sets a PDB-style REMARK entry in the Pose. More...
 
bool core::pose::get_score_line_string (core::pose::Pose const &pose, std::string const &key, std::string &val)
 
std::map< std::string,
std::string > 
core::pose::get_all_score_line_strings (core::pose::Pose const &pose)
 Gets a map< string, string > representing score_line_strings about the Pose in the form of key-value pairs. More...
 
std::string core::pose::tag_from_pose (core::pose::Pose const &pose)
 
std::string core::pose::extract_tag_from_pose (core::pose::Pose &pose)
 Returns a string giving the pose's tag if there is such a thing or "UnknownTag" otherwise. More...
 
void core::pose::tag_into_pose (core::pose::Pose &pose, std::string const &tag)
 
void core::pose::set_output_res_and_chain (pose::Pose &extended_pose, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &output_resnum_and_chain)
 

Detailed Description

Pose utilities.

Author
Phil Bradley
Modified by Sergey Lyskov, Vikram K. Mulligan, Jared Adolf-Bryfogle