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src/core/import_pose/import_pose.hh File Reference

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

#include <iosfwd>
#include <basic/Tracer.fwd.hh>
#include <core/types.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/io/pdb/file_data.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <utility/vector1.hh>

Namespaces

namespace  core
 

A class for defining atom parameters, known as atom_types.


namespace  core::import_pose

Typedefs

typedef std::string core::import_pose::String

Functions

void core::import_pose::read_all_poses (const utility::vector1< std::string > &filenames, utility::vector1< core::pose::Pose > *poses)
void core::import_pose::read_additional_pdb_data (std::string const &s, pose::Pose &pose, io::pdb::FileData const &, 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>
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>
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>
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.
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>
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::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)
utility::vector1
< core::pose::PoseOP
core::import_pose::poseOPs_from_pdbs (chemical::ResidueTypeSet const &residue_set, utility::vector1< std::string > const &filenames, 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)
void core::import_pose::pose_from_pdbstring (pose::Pose &pose, std::string const &pdbcontents, std::string const &filename)
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
void core::import_pose::set_reasonable_fold_tree (pose::Pose &pose)
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.
void core::import_pose::build_pose_as_is (io::pdb::FileData &fd,pose::Pose &pose, chemical::ResidueTypeSet const &residue_set)
 Create pose object, using given FileData object. No PDB cleanin will be appliend.

Variables

basic::Tracer core::import_pose::TR_dump_pdb_dummy
 special Tracer instance acting as special param for all traced_dump_pdb functions

Detailed Description

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

Author:
Sergey Lyskov
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