Rosetta Core  2014.35
Namespaces | Classes | Typedefs | Functions | Variables
core::import_pose Namespace Reference

Namespaces

 atom_tree_diffs
 
 pose_stream
 

Classes

class  ImportPoseOptions
 This class contains all of the data which is used in the process of reading a PDB into a Pose. There is actually a substantial amount of data! More...
 
class  ImportPoseOptionsCreator
 
class  PDBSilentStruct
 
class  PDBSilentStructCreator
 creator for the PDBSilentStruct class More...
 
class  PoseFromPDBLoader
 
class  PoseFromPDBLoaderCreator
 

Typedefs

typedef std::string String
 
typedef
utility::pointer::owning_ptr
< ImportPoseOptions
ImportPoseOptionsOP
 
typedef
utility::pointer::owning_ptr
< ImportPoseOptions const > 
ImportPoseOptionsCOP
 
typedef
utility::pointer::owning_ptr
< PoseFromPDBLoader
PoseFromPDBLoaderOP
 
typedef
utility::pointer::owning_ptr
< PoseFromPDBLoader const > 
PoseFromPDBLoaderCOP
 

Functions

void read_additional_pdb_data (std::string const &s, pose::Pose &pose, io::pdb::FileData const &, bool read_fold_tree)
 
void read_additional_pdb_data (std::string const &s, pose::Pose &pose, ImportPoseOptions const &options, bool read_fold_tree)
 
pose::PoseOP 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 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 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 pose_from_pdb (pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, std::string const &filenames_string, ImportPoseOptions const &options, bool read_fold_tree)
 
void 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 pose_from_pdb (pose::Pose &pose, std::string const &filename, ImportPoseOptions const &options, bool read_fold_tree)
 
utility::vector1
< core::pose::PoseOP
poseOPs_from_pdbs (utility::vector1< std::string > const &filenames, bool read_fold_tree)
 
utility::vector1
< core::pose::PoseOP
poseOPs_from_pdbs (utility::vector1< std::string > const &filenames, ImportPoseOptions const &options, bool read_fold_tree)
 
utility::vector1
< core::pose::Pose
poses_from_pdbs (utility::vector1< std::string > const &filenames, bool read_fold_tree)
 
utility::vector1
< core::pose::Pose
poses_from_pdbs (chemical::ResidueTypeSet const &residue_set, utility::vector1< std::string > const &filenames, bool read_fold_tree)
 
void read_all_poses (const utility::vector1< std::string > &filenames, utility::vector1< core::pose::Pose > *poses)
 
utility::vector1
< core::pose::PoseOP
poseOPs_from_pdbs (chemical::ResidueTypeSet const &residue_set, utility::vector1< std::string > const &filenames, ImportPoseOptions const &options, bool read_fold_tree)
 
void 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 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 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 pose_from_pdbstring (pose::Pose &pose, std::string const &pdbcontents, ImportPoseOptions const &options, std::string const &filename)
 
void pose_from_pdbstring (pose::Pose &pose, std::string const &pdbcontents, std::string const &filename)
 
void pose_from_pdbstring (pose::Pose &pose, std::string const &pdbcontents, chemical::ResidueTypeSet const &residue_set, std::string const &filename)
 
void pose_from_pdbstring (pose::Pose &pose, std::string const &pdbcontents, chemical::ResidueTypeSet const &residue_set, ImportPoseOptions const &options, std::string const &filename)
 
void pose_from_pdb_stream (pose::Pose &pose, std::istream &pdb_stream, std::string const &filename, ImportPoseOptions const &options)
 
void centroid_pose_from_pdb (pose::Pose &pose, std::string const &filename, bool read_fold_tree=false)
 uses the CENTROID residue_set More...
 
void 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 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 build_pose_as_is2 (io::pdb::FileData &fd, pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, id::AtomID_Mask &missing, ImportPoseOptions const &options)
 
void 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 set_reasonable_fold_tree (pose::Pose &pose)
 
static basic::Tracer tr ("core.io.silent.PDBSilentStruct")
 

Variables

basic::Tracer TR ("core.import_pose.import_pose")
 
basic::Tracer TR_dump_pdb_dummy
 special Tracer instance acting as special param for all traced_dump_pdb functions More...
 
basic::Tracer tr ("core.import_pose.import_pose_options")
 

Typedef Documentation

Function Documentation

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.

Create pose object, using given FileData object. If PDB cleanin specified - it will be applied first. Constructs a ImportPoseOptions object from the command line

References core::chemical::FA_RNA, core::chemical::ResidueTypeSet::name(), options, and core::import_pose::ImportPoseOptions::set_rna().

Referenced by core::import_pose::PDBSilentStruct::fill_pose(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), pose_from_pdb(), and pose_from_pdbstring().

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.

Create pose object, using given FileData object. If PDB cleanin specified - it will be applied first.

References build_pose_as_is(), and TR.

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.

Create pose object, using given FileData object. No PDB cleanin will be appliend.

References core::io::pdb::build_pose_as_is1(), and build_pose_as_is2().

Referenced by build_pose().

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::centroid_pose_from_pdb ( pose::Pose &  pose,
std::string const &  filename,
bool  read_fold_tree = false 
)

uses the CENTROID residue_set

Reads in data from input PDB <filename> and stores it in the Pose <pose> using the CENTROID ResidueTypeSet (centroid)

References core::chemical::CENTROID, chemical, pose_from_pdb(), and residue_type_set.

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>

Note
: in PyRosetta, this will return a Pose object

example(s): pose = pose_from_pdb("YFP.pdb") See also: Pose PDBInfo make_pose_from_sequence pose_from_rcsb pose_from_sequence

Referenced by centroid_pose_from_pdb(), core::import_pose::pose_stream::PDBPoseInputStream::fill_pose(), core::fragment::fill_template_frames_from_pdb(), pose_from_pdb(), poseOPs_from_pdbs(), poses_from_pdbs(), read_all_poses(), and core::fragment::read_std_frags_from_cmd().

pose::PoseOP core::import_pose::pose_from_pdb ( chemical::ResidueTypeSet const &  residue_set,
std::string const &  filename,
bool  read_fold_tree 
)

Returns a PoseOP object from the Pose created by reading the input PDB <filename>, this constructor allows for a non-default ResidueTypeSet <residue_set>

References pose_from_pdb().

void core::import_pose::pose_from_pdb ( pose::Pose &  pose,
chemical::ResidueTypeSet const &  residue_set,
std::string const &  filenames_string,
bool  read_fold_tree 
)

Reads in data from input PDB <filename> and stores it in the Pose <pose>, this constructor allows for a non-default ResidueTypeSet <residue_set>

References core::chemical::FA_RNA, core::chemical::ResidueTypeSet::name(), options, pose_from_pdb(), and core::import_pose::ImportPoseOptions::set_rna().

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.

Note
: will use centroid if in::file::centroid_input is true

example(s): pose_from_pdb(pose,"YFP.pdb") See also: Pose PDBInfo

References options, and pose_from_pdb().

void core::import_pose::pose_from_pdb ( pose::Pose &  pose,
std::string const &  filename,
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 
)

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)

References chemical, core::chemical::FA_STANDARD, pose_from_pdb(), and residue_type_set.

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 
)

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>

References core::chemical::FA_RNA, core::chemical::ResidueTypeSet::name(), options, pose_from_pdb(), and core::import_pose::ImportPoseOptions::set_rna().

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_pdb_stream ( pose::Pose &  pose,
std::istream &  pdb_stream,
std::string const &  filename,
ImportPoseOptions const &  options 
)
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 
)

References options, and pose_from_pdbstring().

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 
)
utility::vector1< core::pose::PoseOP > core::import_pose::poseOPs_from_pdbs ( utility::vector1< std::string > const &  filenames,
bool  read_fold_tree 
)

References options.

Referenced by poseOPs_from_pdbs().

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::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 
)
utility::vector1< core::pose::Pose > core::import_pose::poses_from_pdbs ( utility::vector1< std::string > const &  filenames,
bool  read_fold_tree 
)

Only returns full-atom poses

References chemical, core::chemical::FA_STANDARD, and residue_type_set.

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_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 
)
void core::import_pose::read_all_poses ( const utility::vector1< std::string > &  filenames,
utility::vector1< core::pose::Pose > *  poses 
)

References pose_from_pdb().

void core::import_pose::set_reasonable_fold_tree ( pose::Pose &  pose)
static basic::Tracer core::import_pose::tr ( "core.io.silent.PDBSilentStruct"  )
static

Variable Documentation

basic::Tracer core::import_pose::tr("core.io.silent.PDBSilentStruct") ( "core.import_pose.import_pose_options"  )
basic::Tracer core::import_pose::TR("core.import_pose.import_pose")
basic::Tracer core::import_pose::TR_dump_pdb_dummy

special Tracer instance acting as special param for all traced_dump_pdb functions

Referenced by core::io::pdb::traced_dump_pdb().