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
basic::Tracer	TR ("core.import_pose.import_pose")
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)
	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	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	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)
	Create pose object, using given FileData object. No PDB cleanin will be appliend. More...
void	set_reasonable_fold_tree (pose::Pose &pose)
basic::Tracer	tr ("core.import_pose.import_pose_options")
static basic::Tracer	tr ("core.io.silent.PDBSilentStruct")

Variables
basic::Tracer	TR_dump_pdb_dummy
	special Tracer instance acting as special param for all traced_dump_pdb functions More...

Typedef Documentation

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

Definition at line 30 of file import_pose_options.fwd.hh.

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

Definition at line 27 of file import_pose_options.fwd.hh.

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

Definition at line 25 of file PoseFromPDBLoader.fwd.hh.

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

Definition at line 23 of file PoseFromPDBLoader.fwd.hh.

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

Definition at line 271 of file import_pose.hh.

Function Documentation

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.

Definition at line 547 of file import_pose.cc.

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
	)

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

Build Rosetta 3 Pose object from FileData.

Definition at line 560 of file import_pose.cc.

References build_pose_as_is().

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.

trying to Build pose object from pdb 'as-is'. PDB file must be really clean.

Definition at line 580 of file import_pose.cc.

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
	)

Definition at line 593 of file import_pose.cc.

References core::chemical::FA_STANDARD, core::chemical::ResidueTypeSet::name(), core::import_pose::ImportPoseOptions::no_optH(), core::pack::optimize_H_and_notify(), core::pack::pack_missing_sidechains(), core::import_pose::ImportPoseOptions::pack_missing_sidechains(), core::pose::Pose::pdb_info(), set_reasonable_fold_tree(), and core::import_pose::ImportPoseOptions::skip_set_reasonable_fold_tree().

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)

Definition at line 534 of file import_pose.cc.

References core::chemical::CENTROID, core::chemical::ChemicalManager::get_instance(), and pose_from_pdb().

Referenced by protocols::jd2::parser::FragmentReader::apply(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_mutation_data(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamer_energies_for_assigned_pdbs(), protocols::optimize_weights::IterativeOptEDriver::load_pose(), protocols::jobdist::main_plain_mover(), protocols::jobdist::main_plain_pdb_mover(), protocols::optimize_weights::IterativeOptEDriver::make_simple_ssd_from_pdb(), protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag(), protocols::loops::read_loop_fragments(), protocols::protein_interface_design::PatchdockReader::read_poses(), and protocols::jobdist::universal_main().

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

Definition at line 154 of file import_pose.cc.

Referenced by protocols::abinitio::StructureStore::add(), protocols::topology_broker::add_cmdline_claims(), protocols::simple_filters::ChiWellRmsdEvaluatorCreator::add_evaluators(), protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator::add_evaluators(), protocols::simple_filters::ContactMapEvaluatorCreator::add_evaluators(), protocols::simple_filters::NativeEvaluatorCreator::add_evaluators(), protocols::simple_filters::RdcTargetEvaluatorCreator::add_evaluators(), protocols::simple_filters::RmsdEvaluatorCreator::add_evaluators(), protocols::simple_filters::RmsdTargetEvaluatorCreator::add_evaluators(), protocols::toolbox::task_operations::JointSequenceOperation::add_native_pdb(), protocols::pack_daemon::DaemonSet::add_pack_daemon(), protocols::toolbox::task_operations::JointSequenceOperation::add_pdb(), protocols::hybridization::HybridizeProtocol::add_template(), protocols::swa::StepWisePoseSetup::align_poses(), protocols::loop_build::LoopBuildMover::apply(), protocols::simple_moves::LoadPDBMover::apply(), protocols::simple_moves::SuperimposeMover::apply(), protocols::protein_interface_design::filters::RelativeSegmentFilter::apply(), protocols::medal::MedalMover::apply(), protocols::anchored_design::AnchoredDesignMover::apply(), protocols::swa::protein::StepWiseProteinPoseSetup::apply(), protocols::loophash::Mover_LoopHashRefine::apply(), protocols::antibody2::ModelCDRH3::apply(), protocols::flexpep_docking::FlexPepDockingProtocol::apply(), protocols::loophash::LoopHashLibrary::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::protein_interface_design::movers::Splice::apply(), protocols::antibody::CDRH3Modeler::build_centroid_loop(), centroid_pose_from_pdb(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_binding_data(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_mutation_data(), protocols::optimize_weights::IterativeOptEDriver::collect_ligand_discrimination_data(), protocols::forge::remodel::RemodelData::collectInsertionPose(), protocols::enzdes::DesignVsNativeComparison::compare_to_native(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamer_energies_for_assigned_pdbs(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamers_around_ligands(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::create_VDW_rep_screen_pose(), protocols::ddG_main(), protocols::nonlocal::StarTreeBuilder::do_compute_jump_rmsd(), protocols::enzdes::EnzdesBaseProtocol::EnzdesBaseProtocol(), core::import_pose::pose_stream::PDBPoseInputStream::fill_pose(), core::fragment::fill_template_frames_from_pdb(), protocols::docking::DockingProtocol::finalize_setup(), protocols::swa::protein::generate_beta_database_test(), protocols::inputter::PDBInputter::get_nth_pose(), protocols::motifs::get_targetconformers_user(), protocols::swa::rna::StepWiseRNA_PoseSetup::Import_pose(), protocols::hybridization::HybridizeProtocol::init(), protocols::rna::RNA_IdealCoord::init(), protocols::hybridization::FoldTreeHybridize::init(), protocols::antibody2::GraftCDRLoopsProtocol::init_from_options(), protocols::antibody2::AntibodyModelerProtocol::init_from_options(), protocols::docking::DockingProtocol::init_from_options(), protocols::antibody::AntibodyModeler::init_on_new_input(), protocols::anchored_design::AnchoredDesignMover::init_on_new_input(), protocols::coarse_rna::CoarseRNA_Fragments::initialize_frag_source_pose(), protocols::abinitio::IterativeBase::IterativeBase(), protocols::ligand_docking::LigandDockMain::LigandDockMain(), protocols::dna::load_checkpoint(), protocols::optimize_weights::IterativeOptEDriver::load_pose(), protocols::antibody2::Ab_TemplateInfo::load_templates_from_pdbs(), protocols::jobdist::main_atom_tree_diff_mover(), protocols::jobdist::main_plain_mover(), protocols::jobdist::main_plain_pdb_mover(), protocols::frag_picker::scores::MakeGunnCostScore::make(), protocols::frag_picker::scores::MakePhiPsiRmsd::make(), protocols::frag_picker::scores::MakePhiPsiSquareWell::make(), protocols::frag_picker::scores::MakeFragmentDME::make(), protocols::frag_picker::scores::MakeFragmentCrmsd::make(), protocols::frag_picker::scores::MakeFragmentAllAtomCrmsd::make(), protocols::frag_picker::scores::MakeFragmentCrmsdResDepth::make(), protocols::optimize_weights::IterativeOptEDriver::make_simple_ssd_from_pdb(), protocols::fibril::make_symmetric_fibril(), protocols::loophash::LoopHashRelaxProtocol::manual_call(), protocols::optimize_weights::IterativeOptEDriver::measure_sequence_recovery(), protocols::frag_picker::FragmentPicker::nonlocal_pairs(), protocols::jobdist::not_universal_main(), protocols::simple_moves::FavorSequenceProfile::parse_def(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::parse_def(), protocols::seeded_abinitio::DefineMovableLoops::parse_my_tag(), protocols::seeded_abinitio::SwapSegment::parse_my_tag(), protocols::simple_filters::SidechainRmsdFilter::parse_my_tag(), protocols::seeded_abinitio::GrowPeptides::parse_my_tag(), protocols::seeded_abinitio::CAcstGenerator::parse_my_tag(), protocols::simple_filters::DeltaFilter::parse_my_tag(), protocols::simple_moves::SuperimposeMover::parse_my_tag(), protocols::seeded_abinitio::CloseFold::parse_my_tag(), protocols::protein_interface_design::movers::VLB::parse_my_tag(), protocols::simple_filters::RelativePoseFilter::parse_my_tag(), protocols::rosetta_scripts::SavePoseMover::parse_my_tag(), protocols::protein_interface_design::filters::RmsdFilter::parse_my_tag(), protocols::simple_moves::FavorSequenceProfile::parse_my_tag(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::parse_my_tag(), protocols::ligand_docking::InterfaceScoreCalculator::parse_my_tag(), protocols::seeded_abinitio::SeedFoldTree::parse_my_tag(), protocols::comparative_modeling::PartialThreadingMover::parse_my_tag(), protocols::fldsgn::MatchResidues::parse_my_tag(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::parse_my_tag(), protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag(), protocols::features::ProteinRMSDFeatures::parse_my_tag(), protocols::simple_filters::SymmetricMotifFilter::parse_my_tag(), protocols::protein_interface_design::movers::Splice::parse_my_tag(), protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation::parse_tag(), protocols::toolbox::task_operations::RestrictNativeResiduesOperation::parse_tag(), protocols::simple_filters::RelativePoseFilter::pdb_name(), protocols::scoring::methods::saxs::PDDFEnergy::PDDFEnergy(), protocols::jd2::PDBJobInputter::pose_from_job(), protocols::jd2::AtomTreeDiffJobInputter::pose_from_job(), pose_from_pdb(), poseOPs_from_pdbs(), protocols::comparative_modeling::AlignmentClustering::poses_from_cmd_line(), protocols::comparative_modeling::poses_from_cmd_line(), poses_from_pdbs(), protocols::rna::RNA_ChunkLibrary::process_input_file(), protocols::RBSegmentRelaxImpl::RBSegmentRelaxImpl(), read_all_poses(), protocols::topology_broker::CoordConstraintClaimer::read_cst_pose(), protocols::hotspot_hashing::HotspotStubSet::read_data(), protocols::pmut_scan::PointMutScanDriver::read_in_structures(), protocols::ddG::ddGData::read_mut_data(), protocols::enzdes::enzutil::read_pose_from_pdb(), protocols::protein_interface_design::PatchdockReader::read_poses(), core::fragment::read_std_frags_from_cmd(), protocols::topology_broker::FibrilModelingClaimer::read_tag(), protocols::topology_broker::StartStructClaimer::read_tag(), protocols::topology_broker::RigidChunkClaimer::read_tag(), protocols::hybridization::HybridizeProtocol::read_template_structures(), protocols::ddG::ddGData::read_wt_data(), protocols::forge::remodel::RemodelAccumulator::recover_checkpoint(), protocols::symmetric_docking::SymDockProtocol::register_options(), protocols::relax::Relax_main(), protocols::antibody::GraftOneMover::set_default(), protocols::relax::WorkUnit_BatchRelax_and_PostRescore::set_defaults(), protocols::fldsgn::BluePrintBDR::set_instruction_blueprint(), protocols::jd2::set_native_in_mover(), protocols::abinitio::AbrelaxApplication::setup(), protocols::abinitio::AbrelaxApplication::setup_fold(), protocols::motifs::single_motif_from_filename(), protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::source_pose(), and protocols::jobdist::universal_main().

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>

Definition at line 162 of file import_pose.cc.

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>

Definition at line 170 of file import_pose.cc.

References pose_from_pdb().

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
	)

Definition at line 182 of file import_pose.cc.

References build_pose(), core::chemical::CENTROID, core::pose::Pose::conformation(), core::io::pdb::PDB_DReader::createFileData(), protocols::abinitio::filename(), core::io::pdb::FileData::filename, 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(), and core::io::pdb::split().

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

Definition at line 226 of file import_pose.cc.

References pose_from_pdb().

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

Definition at line 236 of file import_pose.cc.

References core::chemical::CENTROID, core::import_pose::ImportPoseOptions::centroid(), 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)

Definition at line 361 of file import_pose.cc.

References core::chemical::FA_STANDARD, core::chemical::ChemicalManager::get_instance(), and pose_from_pdb().

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>

Definition at line 376 of file import_pose.cc.

References pose_from_pdb().

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
	)

Definition at line 388 of file import_pose.cc.

References build_pose(), core::io::pdb::PDB_DReader::createFileData(), protocols::abinitio::filename(), core::io::pdb::FileData::filename, and read_additional_pdb_data().

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

Definition at line 519 of file import_pose.cc.

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

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
	)

Definition at line 468 of file import_pose.cc.

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

Referenced by protocols::simple_moves::PDBReloadMover::apply(), protocols::pack_daemon::DynamicAggregateFunction::assign_jobs_to_local_daemon_set(), pose_from_pdb_stream(), pose_from_pdbstring(), protocols::pack_daemon::DaemonSet::process_add_daemon_message(), protocols::pack_daemon::DynamicAggregateFunction::process_POSE_ENERGY_line(), protocols::pack_daemon::DynamicAggregateFunction::process_POSE_ENERGY_VECTOR_line(), and protocols::pack_daemon::MPIMultistateFitnessFunction::recover_poses_from_states().

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

Definition at line 484 of file import_pose.cc.

References 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
	)

Definition at line 496 of file import_pose.cc.

References pose_from_pdbstring().

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
	)

Definition at line 507 of file import_pose.cc.

References build_pose(), core::io::pdb::PDB_DReader::createFileData(), protocols::abinitio::filename(), 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
	)

Definition at line 255 of file import_pose.cc.

Referenced by poseOPs_from_pdbs(), and protocols::comparative_modeling::ThreadingJobInputter::ThreadingJobInputter().

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

Definition at line 264 of file import_pose.cc.

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

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
	)

Definition at line 336 of file import_pose.cc.

References 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 fullatom poses

Definition at line 281 of file import_pose.cc.

References core::chemical::FA_STANDARD, and core::chemical::ChemicalManager::get_instance().

Referenced by protocols::docking::DockingEnsemble::load_ensemble(), and protocols::comparative_modeling::templates_from_cmd_line().

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
	)

Definition at line 293 of file import_pose.cc.

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

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

Definition at line 93 of file import_pose.cc.

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
	)

Definition at line 105 of file import_pose.cc.

References core::pose::Pose::fold_tree(), core::import_pose::ImportPoseOptions::fold_tree_io(), protocols::loops::start, and core::pose::Pose::total_residue().

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

Definition at line 318 of file import_pose.cc.

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.

Definition at line 634 of file import_pose.cc.

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::chemical::ResidueType::n_residue_connections(), core::chemical::ResidueType::name(), core::chemical::ResConnID::resid(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by build_pose_as_is2().

basic::Tracer core::import_pose::tr

(

"core.import_pose.import_pose_options"

)

Referenced by core::import_pose::PDBSilentStruct::get_CA_xyz(), core::import_pose::PDBSilentStruct::get_debug_rmsd(), core::import_pose::PDBSilentStruct::init_from_lines(), and core::import_pose::ImportPoseOptions::init_from_options().

static basic::Tracer core::import_pose::tr ( "core.io.silent.PDBSilentStruct"  )

static

basic::Tracer core::import_pose::TR

(

"core.import_pose.import_pose"

)

Referenced by core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff().

Variable Documentation

basic::Tracer core::import_pose::TR_dump_pdb_dummy

special Tracer instance acting as special param for all traced_dump_pdb functions