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import_pose.cc File Reference

various functions to construct Pose object(s) from PDB(s) More...

#include <core/import_pose/import_pose.hh>
#include <core/import_pose/import_pose_options.hh>
#include <core/types.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/VariantType.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/pack/pack_missing_sidechains.hh>
#include <core/pack/optimizeH.hh>
#include <core/pose/PDBInfo.hh>
#include <core/io/pdb/pdb_dynamic_reader.hh>
#include <core/io/pdb/pdb_dynamic_reader_options.hh>
#include <core/io/pdb/file_data.hh>
#include <core/io/pdb/file_data_options.hh>
#include <basic/Tracer.hh>
#include <ObjexxFCL/string.functions.hh>
#include <utility/exit.hh>
#include <utility/string_util.hh>
#include <utility/io/izstream.hh>
#include <utility/vector1.hh>
#include <boost/foreach.hpp>

Namespaces

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

Constant Groups

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

Macros

#define foreach   BOOST_FOREACH
 

Functions

basic::Tracer core::import_pose::TR ("core.import_pose.import_pose")
 
void core::import_pose::read_additional_pdb_data (std::string const &s, pose::Pose &pose, io::pdb::FileData const &, bool read_fold_tree)
 
void core::import_pose::read_additional_pdb_data (std::string const &s, pose::Pose &pose, ImportPoseOptions const &options, bool read_fold_tree)
 
pose::PoseOP core::import_pose::pose_from_pdb (std::string const &filename, bool read_fold_tree=false)
 Returns a PoseOP object from the Pose created from input PDB <filename> More...
 
pose::PoseOP core::import_pose::pose_from_pdb (chemical::ResidueTypeSet const &residue_set, std::string const &filename, bool read_fold_tree=false)
 Returns a PoseOP object from the Pose created by reading the input PDB <filename>, this constructor allows for a non-default ResidueTypeSet <residue_set> More...
 
void core::import_pose::pose_from_pdb (pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, std::string const &filename, bool read_fold_tree=false)
 Reads in data from input PDB <filename> and stores it in the Pose <pose>, this constructor allows for a non-default ResidueTypeSet <residue_set> More...
 
void core::import_pose::pose_from_pdb (pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, std::string const &filenames_string, ImportPoseOptions const &options, bool read_fold_tree)
 
void core::import_pose::pose_from_pdb (pose::Pose &pose, std::string const &filename, bool read_fold_tree=false)
 Reads in data from input PDB <filename> and stores it in the Pose <pose>, uses the FA_STANDARD ResidueTypeSet (fullatom) by default. More...
 
void core::import_pose::pose_from_pdb (pose::Pose &pose, std::string const &filename, ImportPoseOptions const &options, bool read_fold_tree)
 
utility::vector1
< core::pose::PoseOP
core::import_pose::poseOPs_from_pdbs (utility::vector1< std::string > const &filenames, bool read_fold_tree)
 
utility::vector1
< core::pose::PoseOP
core::import_pose::poseOPs_from_pdbs (utility::vector1< std::string > const &filenames, ImportPoseOptions const &options, bool read_fold_tree)
 
utility::vector1
< core::pose::Pose
core::import_pose::poses_from_pdbs (utility::vector1< std::string > const &filenames, bool read_fold_tree)
 
utility::vector1
< core::pose::Pose
core::import_pose::poses_from_pdbs (chemical::ResidueTypeSet const &residue_set, utility::vector1< std::string > const &filenames, bool read_fold_tree)
 
void core::import_pose::read_all_poses (const utility::vector1< std::string > &filenames, utility::vector1< core::pose::Pose > *poses)
 
utility::vector1
< core::pose::PoseOP
core::import_pose::poseOPs_from_pdbs (chemical::ResidueTypeSet const &residue_set, utility::vector1< std::string > const &filenames, ImportPoseOptions const &options, bool read_fold_tree)
 
void core::import_pose::pose_from_pdb (utility::vector1< pose::Pose > &poses, std::string const &filename, bool read_fold_tree=false)
 Reads data from an input PDB containing multiple models named <filename> and stores it in a vector of Pose objects named <poses> using the FA_STANDARD ResidueTypeSet (fullatom) More...
 
void core::import_pose::pose_from_pdb (utility::vector1< pose::Pose > &poses, chemical::ResidueTypeSet const &residue_set, std::string const &filename, bool read_fold_tree=false)
 Reads data from an input PDB containing multiple models named <filename> and stores it in a vector of Pose objects named <poses> using ResidueTypeSet <residue_set> More...
 
void core::import_pose::pose_from_pdb (utility::vector1< pose::Pose > &poses, chemical::ResidueTypeSet const &residue_set, std::string const &filename, ImportPoseOptions const &options, bool read_fold_tree)
 
void core::import_pose::pose_from_pdbstring (pose::Pose &pose, std::string const &pdbcontents, ImportPoseOptions const &options, std::string const &filename)
 
void core::import_pose::pose_from_pdbstring (pose::Pose &pose, std::string const &pdbcontents, std::string const &filename)
 
void core::import_pose::pose_from_pdbstring (pose::Pose &pose, std::string const &pdbcontents, chemical::ResidueTypeSet const &residue_set, std::string const &filename)
 
void core::import_pose::pose_from_pdbstring (pose::Pose &pose, std::string const &pdbcontents, chemical::ResidueTypeSet const &residue_set, ImportPoseOptions const &options, std::string const &filename)
 
void core::import_pose::pose_from_pdb_stream (pose::Pose &pose, std::istream &pdb_stream, std::string const &filename, ImportPoseOptions const &options)
 
void core::import_pose::centroid_pose_from_pdb (pose::Pose &pose, std::string const &filename, bool read_fold_tree=false)
 uses the CENTROID residue_set More...
 
void core::import_pose::build_pose (io::pdb::FileData &fd,pose::Pose &pose, chemical::ResidueTypeSet const &residue_set)
 Create pose object, using given FileData object. If PDB cleanin specified - it will be applied first. Constructs a ImportPoseOptions object from the command line. More...
 
void core::import_pose::build_pose (io::pdb::FileData &fd,pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, ImportPoseOptions const &options)
 Create pose object, using given FileData object. If PDB cleanin specified - it will be applied first. More...
 
void core::import_pose::build_pose_as_is2 (io::pdb::FileData &fd, pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, id::AtomID_Mask &missing, ImportPoseOptions const &options)
 
void core::import_pose::build_pose_as_is (io::pdb::FileData &fd,pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, ImportPoseOptions const &options)
 Create pose object, using given FileData object. No PDB cleanin will be appliend. More...
 
void core::import_pose::set_reasonable_fold_tree (pose::Pose &pose)
 

Detailed Description

various functions to construct Pose object(s) from PDB(s)

Author
Sergey Lyskov

Macro Definition Documentation

#define foreach   BOOST_FOREACH