Rosetta Protocols  2014.35
Namespaces | Classes | Typedefs | Functions | Variables
protocols::environment Namespace Reference

Namespaces

 claims
 

Classes

class  AutoCutData
 
class  AutoCutDataCreator
 
class  ClaimingMover
 
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::owning_ptr
< AutoCutData
AutoCutDataOP
 
typedef
utility::pointer::owning_ptr
< AutoCutData const > 
AutoCutDataCOP
 
typedef
utility::pointer::owning_ptr
< ClaimingMover
ClaimingMoverOP
 
typedef
utility::pointer::owning_ptr
< ClaimingMover const > 
ClaimingMoverCOP
 
typedef
utility::pointer::access_ptr
< ClaimingMover
ClaimingMoverAP
 
typedef
utility::pointer::access_ptr
< ClaimingMover const > 
ClaimingMoverCAP
 
typedef
utility::pointer::owning_ptr
< CoMTrackerCM
CoMTrackerCMOP
 
typedef
utility::pointer::owning_ptr
< CoMTrackerCM const > 
CoMTrackerCMCOP
 
typedef
utility::pointer::owning_ptr
< DofUnlock
DofUnlockOP
 
typedef
utility::pointer::owning_ptr
< DofUnlock const > 
DofUnlockCOP
 
typedef
utility::pointer::owning_ptr
< EnvClaimBroker
EnvClaimBrokerOP
 
typedef
utility::pointer::owning_ptr
< EnvClaimBroker const > 
EnvClaimBrokerCOP
 
typedef
utility::pointer::access_ptr
< EnvClaimBroker
EnvClaimBrokerAP
 
typedef
utility::pointer::access_ptr
< EnvClaimBroker const > 
EnvClaimBrokerCAP
 
typedef
utility::pointer::owning_ptr
< Environment
EnvironmentOP
 
typedef
utility::pointer::owning_ptr
< Environment const > 
EnvironmentCOP
 
typedef
utility::pointer::access_ptr
< Environment
EnvironmentAP
 
typedef
utility::pointer::access_ptr
< Environment const > 
EnvironmentCAP
 
typedef
utility::pointer::owning_ptr
< EnvMover
EnvMoverOP
 
typedef
utility::pointer::owning_ptr
< EnvMover const > 
EnvMoverCOP
 
typedef
utility::pointer::owning_ptr
< ProtectedConformation
ProtectedConformationOP
 
typedef
utility::pointer::owning_ptr
< ProtectedConformation const > 
ProtectedConformationCOP
 
typedef
utility::pointer::access_ptr
< ProtectedConformation
ProtectedConformationAP
 
typedef
utility::pointer::access_ptr
< ProtectedConformation const > 
ProtectedConformationCAP
 
typedef
utility::pointer::owning_ptr
< ScriptCM
ScriptCMOP
 
typedef
utility::pointer::owning_ptr
< ScriptCM const > 
ScriptCMCOP
 

Functions

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)
 
void safe_set_conf (core::pose::Pose &pose, core::conformation::ConformationOP conf)
 
ControlStrength const & init_str_selector (std::pair< claims::DOFElement, ClaimingMoverOP > const &d)
 
ControlStrength const & ctrl_str_selector (std::pair< claims::DOFElement, ClaimingMoverOP > const &d)
 
moves::MoverOP find_mover (utility::tag::TagCOP tag, moves::Movers_map movers)
 
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::ConformationCOP conf)
 The plan here is to collect all the DoFs in the residue at 'seqpos' and on either side. More...
 
std::string dof_id_to_string (core::id::DOF_ID const &id, ProtectedConformation const &conf)
 

Variables

std::string const GENERATE_STATIONARY_ATTACHMENT_POINT = "[NOT_SET]"
 
static basic::Tracer tr ("protocols.rigid.CoMTrackerCM", basic::t_info)
 
static
numeric::random::RandomGenerator 
RG (122485235)
 
std::string const NOT_SET = "[NOT_SET]"
 
static basic::Tracer tr ("protocols.environment.ScriptCM", basic::t_info)
 
static
numeric::random::RandomGenerator 
RG (9143235)
 

Typedef Documentation

Function Documentation

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 
)

References BB, and CHI.

std::map< core::id::DOF_ID, core::Real > protocols::environment::collect_dofs ( core::Size const  seqpos,
core::conformation::ConformationCOP  conf 
)

The plan here is to collect all the DoFs in the residue at 'seqpos' and on either side.

References core::id::D, core::id::PHI, core::id::RB1, core::id::RB6, and core::id::THETA.

Referenced by protocols::environment::ProtectedConformation::replace_residue_sandbox().

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, ClaimingMoverOP > const &  d)
std::string protocols::environment::dof_id_to_string ( core::id::DOF_ID const &  id,
ProtectedConformation const &  conf 
)
moves::MoverOP protocols::environment::find_mover ( utility::tag::TagCOP  tag,
moves::Movers_map  movers 
)
std::string protocols::environment::get_mover_name ( std::stack< DofPassportCOP > const &  unlocks)
ControlStrength const& protocols::environment::init_str_selector ( std::pair< claims::DOFElement, ClaimingMoverOP > const &  d)
void protocols::environment::jump_dofs ( std::map< core::id::DOF_ID, core::Real > &  dofs,
core::conformation::ConformationOP  conf,
core::Size  seqpos 
)
void protocols::environment::safe_set_conf ( core::pose::Pose pose,
core::conformation::ConformationOP  conf 
)
void protocols::environment::update_pdb_info ( core::pose::PDBInfoCOP  input_pdb_info,
core::pose::Pose pose 
)

Variable Documentation

std::string const protocols::environment::GENERATE_STATIONARY_ATTACHMENT_POINT = "[NOT_SET]"
std::string const protocols::environment::NOT_SET = "[NOT_SET]"
numeric::random::RandomGenerator protocols::environment::RG(9143235)
static
numeric::random::RandomGenerator protocols::environment::RG(122485235)
static
basic::Tracer protocols::environment::tr("protocols.environment.ScriptCM", basic::t_info)
static
basic::Tracer protocols::environment::tr("protocols.rigid.CoMTrackerCM", basic::t_info)
static