Rosetta 3.4
Classes | Typedefs | Functions
protocols::rosetta_scripts Namespace Reference

Classes

class  ParsedProtocol
class  ParsedProtocolCreator
class  SavePoseMover
 mover that can be used to save or restore a pose at an arbitrary point during a rosetta scripts protocol. other movers or filters can be set up to access poses saved by this mover during their apply calls. More...
class  SavePoseMoverCreator

Typedefs

typedef core::Real Real
typedef core::pose::Pose Pose
typedef
utility::pointer::owning_ptr
< ParsedProtocol
ParsedProtocolOP
typedef
utility::pointer::owning_ptr
< ParsedProtocol const > 
ParsedProtocolCOP
typedef
utility::pointer::owning_ptr
< SavePoseMover
SavePoseMoverOP
typedef
utility::pointer::owning_ptr
< SavePoseMover const > 
SavePoseMoverCOP

Functions

static basic::Tracer TR ("protocols.rosetta_scripts.ParsedProtocol")
static basic::Tracer TR_report ("protocols.rosetta_scripts.ParsedProtocol.REPORT")
static
numeric::random::RandomGenerator 
RG (48569)
core::Size get_resnum (utility::tag::TagPtr const tag_ptr, core::pose::Pose const &pose, std::string const &prefix)
core::Size parse_resnum (std::string const &resnum, core::pose::Pose const &pose)
 Extracts a residue number from a string. Recognizes two forms of numbering:
vector1< Sizeget_resnum_list (utility::tag::TagPtr const tag_ptr, string const &tag, pose::Pose const &pose)
 Extracts a list of residue numbers from a tag.
set< Sizeget_resnum_list (std::string const str, core::pose::Pose const &pose)
 returns a resnum list directly from a string
utility::vector1< Sizeget_resnum_list_ordered (std::string const str, core::pose::Pose const &pose)
 returns a resnum list directly from a string, preserving order
core::pack::task::TaskFactoryOP parse_task_operations (utility::tag::TagPtr const tag, protocols::moves::DataMap const &data)
core::pack::task::TaskFactoryOP parse_task_operations (utility::tag::TagPtr const tag, protocols::moves::DataMap &data, core::pack::task::TaskFactoryOP &task_factory)
 option to add or refer to a Taskfactory through the datamap, similar to how to add/refer to movemap OPs (EMS)
utility::vector1
< core::pack::task::operation::TaskOperationOP
get_task_operations (utility::tag::TagPtr const tag, protocols::moves::DataMap const &data)
core::scoring::ScoreFunctionOP parse_score_function (utility::tag::TagPtr const tag, protocols::moves::DataMap const &data, std::string const dflt_key)
core::pose::PoseOP saved_reference_pose (utility::tag::TagPtr const in_tag, protocols::moves::DataMap &data_map)
 convenience function to access pointers to poses that will be stored in the data map at an arbitrary point during an RS protocol
void foreach_movemap_tag (utility::tag::TagPtr const in_tag, core::pose::Pose const &pose, core::kinematics::MoveMapOP mm)
 utility function for parse_movemap which goes over each of the tags in a movemap section
void parse_movemap (utility::tag::TagPtr const in_tag, core::pose::Pose const &pose, core::kinematics::MoveMapOP &mm, protocols::moves::DataMap &data, bool const reset_map)
 variant of parse_movemap that takes in a datamap and searches it for already existing movemaps
void parse_movemap (utility::tag::TagPtr const in_tag, core::pose::Pose const &pose, core::kinematics::MoveMapOP mm)
protocols::filters::FilterOP parse_filter (std::string const filter_name, protocols::filters::Filters_map const &filters)
protocols::moves::MoverOP parse_mover (std::string const mover_name, protocols::moves::Movers_map const &movers)
numeric::xyzVector< core::Realparse_xyz_vector (utility::tag::TagPtr const xyz_vector_tag)
 utility function for parsing xyzVector
core::Size find_nearest_res (core::pose::Pose const &source, core::pose::Pose const &target, core::Size const res)
 Return the number of the residue on source that is nearest to res on target. If the distance is greater than 2.0 returns 0 to indicate error.
utility::vector1< core::Sizeresidue_packer_states (core::pose::Pose const &pose, core::pack::task::TaskFactoryCOP tf, bool const designable, bool const packable)
 returns a vector containing all the residues with a given packer state according to the TF

Typedef Documentation


Function Documentation

core::Size protocols::rosetta_scripts::find_nearest_res ( core::pose::Pose const &  source,
core::pose::Pose const &  target,
core::Size const  res 
)

Return the number of the residue on source that is nearest to res on target. If the distance is greater than 2.0 returns 0 to indicate error.

find source residue that is nearest to res on source. If distance is greater than 2.0A, return 0

References core::conformation::Residue::is_ligand(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by protocols::protein_interface_design::filters::RelativeSegmentFilter::apply().

void protocols::rosetta_scripts::foreach_movemap_tag ( utility::tag::TagPtr const  in_tag,
core::pose::Pose const &  pose,
core::kinematics::MoveMapOP  mm 
)
core::Size protocols::rosetta_scripts::get_resnum ( utility::tag::TagPtr const  tag_ptr,
core::pose::Pose const &  pose,
std::string const &  prefix 
)

References core::pose::Pose::pdb_info(), and TR().

Referenced by protocols::simple_moves::DesignRepackMover::parse_my_tag(), protocols::simple_filters::ResidueDistanceFilter::parse_my_tag(), protocols::simple_filters::ResidueBurialFilter::parse_my_tag(), protocols::simple_filters::NeighborTypeFilter::parse_my_tag(), protocols::simple_filters::EnergyPerResidueFilter::parse_my_tag(), protocols::protein_interface_design::EnergyPerResidueFilter::parse_my_tag(), protocols::protein_interface_design::HbondsToResidueFilter::parse_my_tag(), protocols::protein_interface_design::ResidueDistanceFilter::parse_my_tag(), protocols::protein_interface_design::ResidueBurialFilter::parse_my_tag(), protocols::protein_interface_design::NeighborTypeFilter::parse_my_tag(), protocols::protein_interface_design::movers::TryRotamers::parse_my_tag(), protocols::protein_interface_design::movers::PeptideStapleDesignMover::parse_my_tag(), protocols::protein_interface_design::movers::LoopRemodel::parse_my_tag(), protocols::protein_interface_design::movers::LoopFinder::parse_my_tag(), protocols::protein_interface_design::movers::HotspotHasherMover::parse_my_tag(), protocols::protein_interface_design::movers::BackrubDDMover::parse_my_tag(), protocols::protein_interface_design::filters::RmsdFilter::parse_my_tag(), protocols::protein_interface_design::filters::HbondsToResidueFilter::parse_my_tag(), protocols::loophash::LoopHashMoverWrapper::parse_my_tag(), protocols::enzdes::EnzScoreFilter::parse_my_tag(), protocols::enzdes::DiffAtomSasaFilter::parse_my_tag(), and protocols::abinitio::DomainAssembly::parse_my_tag().

utility::vector1< core::Size > protocols::rosetta_scripts::get_resnum_list ( utility::tag::TagPtr const  tag_ptr,
string const &  tag,
pose::Pose const &  pose 
)
std::set< core::Size > protocols::rosetta_scripts::get_resnum_list ( std::string const  str,
core::pose::Pose const &  pose 
)

returns a resnum list directly from a string

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

utility::vector1< core::Size > protocols::rosetta_scripts::get_resnum_list_ordered ( std::string const  str,
core::pose::Pose const &  pose 
)
utility::vector1< core::pack::task::operation::TaskOperationOP > protocols::rosetta_scripts::get_task_operations ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap const &  data 
)
protocols::filters::FilterOP protocols::rosetta_scripts::parse_filter ( std::string const  filter_name,
protocols::filters::Filters_map const &  filters 
)
void protocols::rosetta_scripts::parse_movemap ( utility::tag::TagPtr const  in_tag,
core::pose::Pose const &  pose,
core::kinematics::MoveMapOP  mm 
)

modifies an existing movemap according to tag the movemap defaults to move all bb, chi, and jumps.

References foreach_movemap_tag(), and TR().

void protocols::rosetta_scripts::parse_movemap ( utility::tag::TagPtr const  in_tag,
core::pose::Pose const &  pose,
core::kinematics::MoveMapOP mm,
protocols::moves::DataMap data,
bool const  reset_map 
)
protocols::moves::MoverOP protocols::rosetta_scripts::parse_mover ( std::string const  mover_name,
protocols::moves::Movers_map const &  movers 
)
core::Size protocols::rosetta_scripts::parse_resnum ( std::string const &  resnum,
core::pose::Pose const &  pose 
)

Extracts a residue number from a string. Recognizes two forms of numbering:

  • Rosetta residue numbers (numbered sequentially from 1 to the last residue in the pose). These have the form [0-9]+
  • PDB numbers. These have the form [0-9]+[A-Z], where the trailing letter is the chain ID.
    Returns:
    the rosetta residue number for the string, or 0 upon an error

References core::pose::Pose::pdb_info(), and TR().

Referenced by protocols::canonical_sampling::MetricRecorder::add_torsion(), protocols::seeded_abinitio::adjust_des_residues(), protocols::seeded_abinitio::adjust_residues(), protocols::seeded_abinitio::adjust_single_residues(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::protein_interface_design::movers::AddChainBreak::apply(), get_resnum_list(), get_resnum_list_ordered(), protocols::loops::loops_from_string(), protocols::simple_moves::SetTorsion::parse_my_tag(), protocols::simple_moves::MutateResidue::parse_my_tag(), protocols::simple_filters::AtomicDistanceFilter::parse_my_tag(), protocols::simple_filters::AtomicContactFilter::parse_my_tag(), protocols::seeded_abinitio::SwapSegment::parse_my_tag(), protocols::seeded_abinitio::GrowPeptides::parse_my_tag(), protocols::seeded_abinitio::CAcstGenerator::parse_my_tag(), protocols::protein_interface_design::movers::VLB::parse_my_tag(), protocols::protein_interface_design::movers::TryRotamers::parse_my_tag(), protocols::protein_interface_design::movers::LoopLengthChange::parse_my_tag(), protocols::protein_interface_design::movers::BackrubDDMover::parse_my_tag(), protocols::protein_interface_design::filters::Torsion::parse_my_tag(), protocols::protein_interface_design::filters::RelativePoseFilter::parse_my_tag(), protocols::comparative_modeling::LoopRelaxMover::parse_my_tag(), protocols::seeded_abinitio::parse_seeds(), and protocols::seeded_abinitio::parse_spans().

core::scoring::ScoreFunctionOP protocols::rosetta_scripts::parse_score_function ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap const &  data,
std::string const  dflt_key 
)
core::pack::task::TaskFactoryOP protocols::rosetta_scripts::parse_task_operations ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap data,
core::pack::task::TaskFactoryOP task_factory 
)

option to add or refer to a Taskfactory through the datamap, similar to how to add/refer to movemap OPs (EMS)

allows the transfer of whole taskfactories on the datamap. This way a "base" taskfactory can be created, transferred on the datamap, and individual mover's specific taskoperations can be added on top

References protocols::moves::DataMap::add(), core::sequence::end, protocols::moves::DataMap::get(), protocols::moves::DataMap::has(), make_table_of_pilot_apps::name, and TR().

core::pack::task::TaskFactoryOP protocols::rosetta_scripts::parse_task_operations ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap const &  data 
)

This is essentially a shameless copy of Justin's PackRotamersMover::parse_task_operations. In truth DesignRepackMover should disappear into Justin's better organized class, but this will wait... (SJF)

References core::sequence::end, protocols::moves::DataMap::get(), protocols::moves::DataMap::has(), and TR().

Referenced by protocols::simple_moves::RotamerTrialsMover::parse_my_tag(), protocols::simple_moves::RotamerTrialsMinMover::parse_my_tag(), protocols::simple_moves::GreedyOptMutationMover::parse_my_tag(), protocols::simple_moves::DesignRepackMover::parse_my_tag(), protocols::simple_moves::ConsensusDesignMover::parse_my_tag(), protocols::simple_moves::AddConstraintsToCurrentConformationMover::parse_my_tag(), protocols::simple_filters::RotamerBoltzmannWeight::parse_my_tag(), protocols::simple_filters::ResidueBurialFilter::parse_my_tag(), protocols::relax::FastRelax::parse_my_tag(), protocols::protein_interface_design::movers::TaskAwareCsts::parse_my_tag(), protocols::protein_interface_design::movers::RandomMutation::parse_my_tag(), protocols::protein_interface_design::movers::PrepackMover::parse_my_tag(), protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::parse_my_tag(), protocols::protein_interface_design::movers::LoopRemodel::parse_my_tag(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::parse_my_tag(), protocols::protein_interface_design::movers::DockAndRetrieveSidechains::parse_my_tag(), protocols::protein_interface_design::movers::BuildAlaPose::parse_my_tag(), protocols::protein_interface_design::movers::BackrubDDMover::parse_my_tag(), protocols::protein_interface_design::filters::Torsion::parse_my_tag(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::parse_my_tag(), protocols::protein_interface_design::filters::FilterScanFilter::parse_my_tag(), protocols::protein_interface_design::filters::DesignableResiduesFilter::parse_my_tag(), protocols::protein_interface_design::filters::BindingStrainFilter::parse_my_tag(), protocols::protein_interface_design::filters::AverageDegreeFilter::parse_my_tag(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::parse_my_tag(), protocols::enzdes::EnzRepackMinimize::parse_my_tag(), protocols::docking::DockingProtocol::parse_my_tag(), protocols::simple_moves::TaskAwareMinMover::parse_task_operations(), protocols::simple_moves::PackRotamersMover::parse_task_operations(), protocols::simple_moves::MinPackMover::parse_task_operations(), protocols::simple_moves::AddConstraintsToCurrentConformationMover::parse_task_operations(), and protocols::moves::GenericMonteCarloMover::parse_task_operations().

numeric::xyzVector< core::Real > protocols::rosetta_scripts::parse_xyz_vector ( utility::tag::TagPtr const  xyz_vector_tag)

utility function for parsing xyzVector

Referenced by protocols::rigid::RollMover::parse_my_tag().

utility::vector1< core::Size > protocols::rosetta_scripts::residue_packer_states ( core::pose::Pose const &  pose,
core::pack::task::TaskFactoryCOP  tf,
bool const  designable,
bool const  packable 
)
static numeric::random::RandomGenerator protocols::rosetta_scripts::RG ( 48569  ) [static]
core::pose::PoseOP protocols::rosetta_scripts::saved_reference_pose ( utility::tag::TagPtr const  in_tag,
protocols::moves::DataMap data_map 
)
static basic::Tracer protocols::rosetta_scripts::TR ( "protocols.rosetta_scripts.ParsedProtocol"  ) [static]
static basic::Tracer protocols::rosetta_scripts::TR_report ( "protocols.rosetta_scripts.ParsedProtocol.REPORT"  ) [static]
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