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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 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 
)

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

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.

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.

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 
)
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 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>

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 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 
)
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 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 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>

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

Variable Documentation

basic::Tracer core::import_pose::TR_dump_pdb_dummy

special Tracer instance acting as special param for all traced_dump_pdb functions