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

typedef utility::pointer::owning_ptr< ImportPoseOptions const > core::import_pose::ImportPoseOptionsCOP

typedef utility::pointer::owning_ptr< ImportPoseOptions > core::import_pose::ImportPoseOptionsOP

typedef utility::pointer::owning_ptr< PoseFromPDBLoader const > core::import_pose::PoseFromPDBLoaderCOP

typedef utility::pointer::owning_ptr< PoseFromPDBLoader > core::import_pose::PoseFromPDBLoaderOP

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

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::ResidueTypeSet::name(), options, core::chemical::RNA, 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
	)

Referenced by build_pose_as_is().

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::ResidueTypeSet::name(), options, pose_from_pdb(), core::chemical::RNA, 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
	)

References build_pose(), core::chemical::CENTROID, core::pose::Pose::conformation(), core::io::pdb::PDB_DReader::createFileData(), file, filename(), core::io::pdb::FileData::filename, utility::join(), core::chemical::ResidueTypeSet::name(), read_additional_pdb_data(), core::conformation::Conformation::same_type_as_me(), core::pose::Pose::set_new_conformation(), core::pose::set_ss_from_phipsi(), utility::slurp(), utility::split(), TR, and utility_exit_with_message.

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
	)

References core::chemical::CENTROID, core::import_pose::ImportPoseOptions::centroid(), chemical, core::chemical::FA_STANDARD, core::chemical::ChemicalManager::get_instance(), pose_from_pdb(), core::chemical::ChemicalManager::residue_type_set(), and core::import_pose::ImportPoseOptions::rna().

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::ResidueTypeSet::name(), options, pose_from_pdb(), core::chemical::RNA, 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
	)

References build_pose(), core::io::pdb::PDB_DReader::createFileData(), file, core::io::pdb::FileData::filename, read_additional_pdb_data(), utility::slurp(), TR, and utility_exit_with_message.

void core::import_pose::pose_from_pdb_stream	(	pose::Pose &	pose,
		std::istream &	pdb_stream,
		std::string const &	filename,
		ImportPoseOptions const &	options
	)

References core::chemical::ChemicalManager::get_instance(), pose_from_pdbstring(), read_additional_pdb_data(), core::import_pose::ImportPoseOptions::read_fold_tree(), residue_type_set, core::import_pose::ImportPoseOptions::residue_type_set(), and utility::slurp().

Referenced by core::import_pose::PoseFromPDBLoader::create_resource().

void core::import_pose::pose_from_pdbstring	(	pose::Pose &	pose,
		std::string const &	pdbcontents,
		ImportPoseOptions const &	options,
		std::string const &	filename
	)

References build_pose(), core::io::pdb::PDB_DReader::createFileData(), core::chemical::FA_STANDARD, core::io::pdb::FileData::filename, core::chemical::ChemicalManager::get_instance(), and residue_type_set.

Referenced by pose_from_pdb_stream(), and pose_from_pdbstring().

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
	)

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

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
	)

References build_pose(), core::io::pdb::PDB_DReader::createFileData(), and core::io::pdb::FileData::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
	)

References core::chemical::CENTROID, core::import_pose::ImportPoseOptions::centroid(), chemical, core::chemical::FA_STANDARD, and poseOPs_from_pdbs().

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
	)

References chemical, core::sequence::end, and pose_from_pdb().

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
	)

References chemical, core::sequence::end, core::chemical::ResidueTypeSet::name(), options, pose_from_pdb(), and core::chemical::RNA.

void core::import_pose::read_additional_pdb_data	(	std::string const &	s,
		pose::Pose &	pose,
		io::pdb::FileData const &	,
		bool	read_fold_tree
	)

References options.

Referenced by core::import_pose::PDBSilentStruct::fill_pose(), pose_from_pdb(), and pose_from_pdb_stream().

void core::import_pose::read_additional_pdb_data	(	std::string const &	s,
		pose::Pose &	pose,
		ImportPoseOptions const &	options,
		bool	read_fold_tree
	)

References core::pose::Pose::fold_tree(), core::import_pose::ImportPoseOptions::fold_tree_io(), j, l, core::pose::Pose::pdb_info(), core::io::serialization::size(), start, utility::string_split(), tag, core::pose::Pose::total_residue(), TR, and utility_exit.

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 )

All ligand residues and polymer branches have been appended by a jump. This method creates a new fold tree without jumps through ligands, using CHEMICAL edges instead.

References core::conformation::Residue::atom_name(), core::chemical::BRANCH_LOWER_TERMINUS, core::chemical::BRANCH_POINT, core::conformation::Residue::chain(), core::conformation::Residue::connect_atom(), core::conformation::Residue::connect_map(), core::conformation::Residue::connection_incomplete(), core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::kinematics::Edge::is_jump(), core::kinematics::Edge::label(), core::chemical::ResidueType::n_residue_connections(), core::chemical::ResidueType::name(), core::chemical::ResConnID::resid(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), runtime_assert, core::kinematics::Edge::stop(), core::pose::Pose::total_residue(), and TR.