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/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/kinematics/FoldTree.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/carbohydrates/util.hh>
#include <core/util/metalloproteins_util.hh>
#include <core/pack/pack_missing_sidechains.hh>
#include <core/pack/optimizeH.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 <utility/exit.hh>
#include <utility/string_util.hh>
#include <utility/io/izstream.hh>
#include <utility/vector1.hh>
#include <ObjexxFCL/string.functions.hh>
#include <boost/foreach.hpp>

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

Functions
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)
	Look for peptide bonds connected by >3A and replace them with a jump. More...
void	core::import_pose::build_pose (io::pdb::FileData &fd, pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, ImportPoseOptions const &options)
	Build Rosetta 3 Pose object from FileData. 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)
	Try to Build pose object from pdb 'as-is'. PDB file must be really clean. More...
void	core::import_pose::set_reasonable_fold_tree (pose::Pose &pose)

Variables
basic::Tracer	core::import_pose::TR ("core.import_pose.import_pose")

Detailed Description

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

A temporary copy of the pose_from_pdb code from the demo directory. Will be phased out in favor of file_data routines soon.

Author

Sergey Lyskov