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protocols::environment Namespace Reference

Namespaces

 claims
 

Classes

class  AutoCutData
 
class  AutoCutDataCreator
 
class  ClientMover
 
class  Comparator
 A brief comparator object initialized with the correct strength accessor for reuse of setup_passports. More...
 
class  CoMTrackerCM
 
class  CoMTrackerCMCreator
 
class  DofUnlock
 
class  EnvClaimBroker
 
class  Environment
 
class  EnvMover
 
class  EnvMoverCreator
 
class  EXCN_Env_Passport
 
class  EXCN_Env_Security_Exception
 
class  ProtectedConformation
 
class  ScriptCM
 
class  ScriptCMCreator
 

Typedefs

typedef
utility::pointer::shared_ptr
< AutoCutData
AutoCutDataOP
 
typedef
utility::pointer::shared_ptr
< AutoCutData const > 
AutoCutDataCOP
 
typedef
utility::pointer::shared_ptr
< ClientMover
ClientMoverOP
 
typedef
utility::pointer::shared_ptr
< ClientMover const > 
ClientMoverCOP
 
typedef
utility::pointer::weak_ptr
< ClientMover
ClientMoverAP
 
typedef
utility::pointer::weak_ptr
< ClientMover const > 
ClientMoverCAP
 
typedef
utility::pointer::shared_ptr
< CoMTrackerCM
CoMTrackerCMOP
 
typedef
utility::pointer::shared_ptr
< CoMTrackerCM const > 
CoMTrackerCMCOP
 
typedef
utility::pointer::shared_ptr
< DofUnlock
DofUnlockOP
 
typedef
utility::pointer::shared_ptr
< DofUnlock const > 
DofUnlockCOP
 
typedef
utility::pointer::shared_ptr
< EnvClaimBroker
EnvClaimBrokerOP
 
typedef
utility::pointer::shared_ptr
< EnvClaimBroker const > 
EnvClaimBrokerCOP
 
typedef
utility::pointer::weak_ptr
< EnvClaimBroker
EnvClaimBrokerAP
 
typedef
utility::pointer::weak_ptr
< EnvClaimBroker const > 
EnvClaimBrokerCAP
 
typedef
utility::pointer::shared_ptr
< Environment
EnvironmentOP
 
typedef
utility::pointer::shared_ptr
< Environment const > 
EnvironmentCOP
 
typedef
utility::pointer::weak_ptr
< Environment
EnvironmentAP
 
typedef
utility::pointer::weak_ptr
< Environment const > 
EnvironmentCAP
 
typedef
utility::pointer::shared_ptr
< EnvMover
EnvMoverOP
 
typedef
utility::pointer::shared_ptr
< EnvMover const > 
EnvMoverCOP
 
typedef
utility::pointer::shared_ptr
< ProtectedConformation
ProtectedConformationOP
 
typedef
utility::pointer::shared_ptr
< ProtectedConformation const > 
ProtectedConformationCOP
 
typedef
utility::pointer::weak_ptr
< ProtectedConformation
ProtectedConformationAP
 
typedef
utility::pointer::weak_ptr
< ProtectedConformation const > 
ProtectedConformationCAP
 
typedef
utility::pointer::shared_ptr
< ScriptCM
ScriptCMOP
 
typedef
utility::pointer::shared_ptr
< ScriptCM const > 
ScriptCMCOP
 

Functions

bool ang_delta (core::Real const &a, core::Real const &b)
 
static basic::Tracer tr ("protocols.rigid.CoMTrackerCM", basic::t_info)
 
numeric::xyzVector< core::Realcom_calc (core::pose::Pose const &pose, utility::vector1_bool const &rsds)
 
void update_pdb_info (core::pose::PDBInfoCOP input_pdb_info, core::pose::Pose &pose, EnvClaimBroker::BrokerResult const &result)
 
void safe_set_conf (core::pose::Pose &pose, core::conformation::ConformationOP conf)
 
core::Size find_implied_cut (utility::vector1< core::Size > const &cycle, core::conformation::Conformation const &conf)
 
utility::vector1< core::Sizeintroduce_datamap_cuts (FoldTreeSketch const &fts, basic::datacache::BasicDataCache &datacache)
 
core::Size inherit_cuts (utility::vector1< core::Size > const &cycle, core::kinematics::FoldTree const &input_ft)
 
ControlStrength const & init_str_selector (std::pair< claims::DOFElement, ClientMoverOP > const &d)
 
ControlStrength const & ctrl_str_selector (std::pair< claims::DOFElement, ClientMoverOP > const &d)
 
std::string dof_id_to_string (core::id::DOF_ID const &id, ProtectedConformation const &conf)
 
moves::MoverOP find_mover (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
 
std::string get_mover_name (std::stack< DofPassportCOP > const &unlocks)
 
void bond_lengths (std::map< core::id::DOF_ID, core::Real > &dofs, core::conformation::ConformationOP conf, core::Size seqpos)
 
void bond_angles (std::map< core::id::DOF_ID, core::Real > &dofs, core::conformation::ConformationOP conf, core::Size seqpos)
 
void bond_torsions (std::map< core::id::DOF_ID, core::Real > &dofs, core::conformation::ConformationOP conf, core::Size seqpos)
 
void jump_dofs (std::map< core::id::DOF_ID, core::Real > &dofs, core::conformation::ConformationOP conf, core::Size seqpos)
 
std::map< core::id::DOF_ID,
core::Real
collect_dofs (core::Size const seqpos, core::conformation::Conformation const *conf)
 The plan here is to collect all the DoFs in the residue at 'seqpos' and on either side. More...
 
ResidueOP rm_variant (ResidueOP new_rsd, Residue const &old_rsd, core::chemical::ResidueTypeSet const &rsd_set, core::chemical::VariantType variant, core::conformation::Conformation const &conf)
 
ResidueOP add_variant (ResidueOP new_rsd, Residue const &old_rsd, core::chemical::ResidueTypeSet const &rsd_set, core::chemical::VariantType variant, core::conformation::Conformation const &conf)
 
static basic::Tracer tr ("protocols.environment.ScriptCM", basic::t_info)
 

Variables

core::Real const TOLERANCE = 1e-6
 
std::string const GENERATE_STATIONARY_ATTACHMENT_POINT = "[NOT_SET]"
 
std::string const NOT_SET = "[NOT_SET]"
 

Typedef Documentation

typedef utility::pointer::shared_ptr< AutoCutData const > protocols::environment::AutoCutDataCOP
typedef utility::pointer::shared_ptr< AutoCutData > protocols::environment::AutoCutDataOP
typedef utility::pointer::weak_ptr< ClientMover > protocols::environment::ClientMoverAP
typedef utility::pointer::weak_ptr< ClientMover const > protocols::environment::ClientMoverCAP
typedef utility::pointer::shared_ptr< ClientMover const > protocols::environment::ClientMoverCOP
typedef utility::pointer::shared_ptr< ClientMover > protocols::environment::ClientMoverOP
typedef utility::pointer::shared_ptr< CoMTrackerCM const > protocols::environment::CoMTrackerCMCOP
typedef utility::pointer::shared_ptr< CoMTrackerCM > protocols::environment::CoMTrackerCMOP
typedef utility::pointer::shared_ptr< DofUnlock const > protocols::environment::DofUnlockCOP
typedef utility::pointer::shared_ptr< DofUnlock > protocols::environment::DofUnlockOP
typedef utility::pointer::weak_ptr< EnvClaimBroker > protocols::environment::EnvClaimBrokerAP
typedef utility::pointer::weak_ptr< EnvClaimBroker const > protocols::environment::EnvClaimBrokerCAP
typedef utility::pointer::shared_ptr< EnvClaimBroker const > protocols::environment::EnvClaimBrokerCOP
typedef utility::pointer::shared_ptr< EnvClaimBroker > protocols::environment::EnvClaimBrokerOP
typedef utility::pointer::weak_ptr< Environment > protocols::environment::EnvironmentAP
typedef utility::pointer::weak_ptr< Environment const > protocols::environment::EnvironmentCAP
typedef utility::pointer::shared_ptr< Environment const > protocols::environment::EnvironmentCOP
typedef utility::pointer::shared_ptr< Environment > protocols::environment::EnvironmentOP
typedef utility::pointer::shared_ptr< EnvMover const > protocols::environment::EnvMoverCOP
typedef utility::pointer::shared_ptr< EnvMover > protocols::environment::EnvMoverOP
typedef utility::pointer::weak_ptr< ProtectedConformation const > protocols::environment::ProtectedConformationCAP
typedef utility::pointer::shared_ptr< ProtectedConformation const > protocols::environment::ProtectedConformationCOP
typedef utility::pointer::shared_ptr< ScriptCM const > protocols::environment::ScriptCMCOP
typedef utility::pointer::shared_ptr< ScriptCM > protocols::environment::ScriptCMOP

Function Documentation

ResidueOP protocols::environment::add_variant ( ResidueOP  new_rsd,
Residue const &  old_rsd,
core::chemical::ResidueTypeSet const &  rsd_set,
core::chemical::VariantType  variant,
core::conformation::Conformation const &  conf 
)
bool protocols::environment::ang_delta ( core::Real const &  a,
core::Real const &  b 
)
void protocols::environment::bond_angles ( std::map< core::id::DOF_ID, core::Real > &  dofs,
core::conformation::ConformationOP  conf,
core::Size  seqpos 
)
void protocols::environment::bond_lengths ( std::map< core::id::DOF_ID, core::Real > &  dofs,
core::conformation::ConformationOP  conf,
core::Size  seqpos 
)
void protocols::environment::bond_torsions ( std::map< core::id::DOF_ID, core::Real > &  dofs,
core::conformation::ConformationOP  conf,
core::Size  seqpos 
)
std::map< core::id::DOF_ID, core::Real > protocols::environment::collect_dofs ( core::Size const  seqpos,
core::conformation::Conformation const *  conf 
)
numeric::xyzVector< core::Real > protocols::environment::com_calc ( core::pose::Pose const &  pose,
utility::vector1_bool const &  rsds 
)
ControlStrength const& protocols::environment::ctrl_str_selector ( std::pair< claims::DOFElement, ClientMoverOP > const &  d)
std::string protocols::environment::dof_id_to_string ( core::id::DOF_ID const &  id,
ProtectedConformation const &  conf 
)
core::Size protocols::environment::find_implied_cut ( utility::vector1< core::Size > const &  cycle,
core::conformation::Conformation const &  conf 
)
moves::MoverOP protocols::environment::find_mover ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
std::string protocols::environment::get_mover_name ( std::stack< DofPassportCOP > const &  unlocks)
core::Size protocols::environment::inherit_cuts ( utility::vector1< core::Size > const &  cycle,
core::kinematics::FoldTree const &  input_ft 
)
ControlStrength const& protocols::environment::init_str_selector ( std::pair< claims::DOFElement, ClientMoverOP > const &  d)
utility::vector1< core::Size > protocols::environment::introduce_datamap_cuts ( FoldTreeSketch const &  fts,
basic::datacache::BasicDataCache &  datacache 
)
void protocols::environment::jump_dofs ( std::map< core::id::DOF_ID, core::Real > &  dofs,
core::conformation::ConformationOP  conf,
core::Size  seqpos 
)
ResidueOP protocols::environment::rm_variant ( ResidueOP  new_rsd,
Residue const &  old_rsd,
core::chemical::ResidueTypeSet const &  rsd_set,
core::chemical::VariantType  variant,
core::conformation::Conformation const &  conf 
)
void protocols::environment::safe_set_conf ( core::pose::Pose pose,
core::conformation::ConformationOP  conf 
)
static basic::Tracer protocols::environment::tr ( "protocols.environment.ScriptCM"  ,
basic::t_info   
)
static
static basic::Tracer protocols::environment::tr ( "protocols.rigid.CoMTrackerCM"  ,
basic::t_info   
)
static

Referenced by protocols::environment::ScriptCM::add_claim(), add_variant(), protocols::environment::EnvMover::apply(), protocols::environment::Environment::broker(), protocols::environment::EnvClaimBroker::broker_dofs(), protocols::environment::EnvClaimBroker::broker_fold_tree(), protocols::environment::EnvClaimBroker::BrokeredJumpData::BrokeredJumpData(), protocols::environment::Environment::cancel_passports(), protocols::environment::EnvClaimBroker::collect_claims(), protocols::environment::EnvClaimBroker::collect_elements(), protocols::environment::Environment::end(), protocols::environment::EnvClaimBroker::EnvClaimBroker(), find_implied_cut(), inherit_cuts(), protocols::environment::claims::TorsionClaim::insert_dof_element(), introduce_datamap_cuts(), protocols::environment::claims::EnvClaim::make_claim(), protocols::environment::ProtectedConformation::match_variants(), protocols::environment::ScriptCM::parse_my_tag(), protocols::environment::EnvMover::parse_subtag(), protocols::environment::EnvClaimBroker::process_elements(), protocols::environment::Environment::register_mover(), protocols::environment::Environment::remove_nonpermenant_features(), protocols::environment::EnvClaimBroker::render_fold_tree(), protocols::environment::ProtectedConformation::replace_residue_sandbox(), rm_variant(), protocols::environment::ClientMover::sandboxed_copy(), protocols::environment::ProtectedConformation::set_stub_transform(), protocols::environment::EnvClaimBroker::setup_passports(), protocols::environment::Environment::start(), protocols::environment::claims::TorsionClaim::TorsionClaim(), update_pdb_info(), protocols::environment::claims::XYZClaim::XYZClaim(), protocols::environment::ScriptCM::yield_claims(), protocols::environment::claims::XYZClaim::yield_elements(), protocols::environment::claims::TorsionClaim::yield_elements(), and protocols::environment::DofUnlock::~DofUnlock().

void protocols::environment::update_pdb_info ( core::pose::PDBInfoCOP  input_pdb_info,
core::pose::Pose pose,
EnvClaimBroker::BrokerResult const &  result 
)

Variable Documentation

std::string const protocols::environment::GENERATE_STATIONARY_ATTACHMENT_POINT = "[NOT_SET]"
std::string const protocols::environment::NOT_SET = "[NOT_SET]"
core::Real const protocols::environment::TOLERANCE = 1e-6