protocols::environment Namespace Reference

Namespaces
	claims

Classes
class	AutoCutData
class	AutoCutDataCreator
class	ClientMover
class	CoMTrackerCM
class	CoMTrackerCMCreator
class	DofUnlock
class	Comparator
	A brief comparator object initialized with the correct strength accessor for reuse of setup_passports. More...
class	EnvClaimBroker
class	EXCN_Env_Security_Exception
class	EXCN_Env_Passport
class	Environment
class	EnvMover
class	EnvMoverCreator
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::Real >	com_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::Size >	introduce_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

AutoCutDataCOP

typedef utility::pointer::shared_ptr< AutoCutData const > protocols::environment::AutoCutDataCOP

AutoCutDataOP

typedef utility::pointer::shared_ptr< AutoCutData > protocols::environment::AutoCutDataOP

ClientMoverAP

typedef utility::pointer::weak_ptr< ClientMover > protocols::environment::ClientMoverAP

ClientMoverCAP

typedef utility::pointer::weak_ptr< ClientMover const > protocols::environment::ClientMoverCAP

ClientMoverCOP

typedef utility::pointer::shared_ptr< ClientMover const > protocols::environment::ClientMoverCOP

ClientMoverOP

typedef utility::pointer::shared_ptr< ClientMover > protocols::environment::ClientMoverOP

CoMTrackerCMCOP

typedef utility::pointer::shared_ptr< CoMTrackerCM const > protocols::environment::CoMTrackerCMCOP

CoMTrackerCMOP

typedef utility::pointer::shared_ptr< CoMTrackerCM > protocols::environment::CoMTrackerCMOP

DofUnlockCOP

typedef utility::pointer::shared_ptr< DofUnlock const > protocols::environment::DofUnlockCOP

DofUnlockOP

typedef utility::pointer::shared_ptr< DofUnlock > protocols::environment::DofUnlockOP

EnvClaimBrokerAP

typedef utility::pointer::weak_ptr< EnvClaimBroker > protocols::environment::EnvClaimBrokerAP

EnvClaimBrokerCAP

typedef utility::pointer::weak_ptr< EnvClaimBroker const > protocols::environment::EnvClaimBrokerCAP

EnvClaimBrokerCOP

typedef utility::pointer::shared_ptr< EnvClaimBroker const > protocols::environment::EnvClaimBrokerCOP

EnvClaimBrokerOP

typedef utility::pointer::shared_ptr< EnvClaimBroker > protocols::environment::EnvClaimBrokerOP

EnvironmentAP

typedef utility::pointer::weak_ptr< Environment > protocols::environment::EnvironmentAP

EnvironmentCAP

typedef utility::pointer::weak_ptr< Environment const > protocols::environment::EnvironmentCAP

EnvironmentCOP

typedef utility::pointer::shared_ptr< Environment const > protocols::environment::EnvironmentCOP

EnvironmentOP

typedef utility::pointer::shared_ptr< Environment > protocols::environment::EnvironmentOP

EnvMoverCOP

typedef utility::pointer::shared_ptr< EnvMover const > protocols::environment::EnvMoverCOP

EnvMoverOP

typedef utility::pointer::shared_ptr< EnvMover > protocols::environment::EnvMoverOP

ProtectedConformationAP

typedef utility::pointer::weak_ptr< ProtectedConformation > protocols::environment::ProtectedConformationAP

ProtectedConformationCAP

typedef utility::pointer::weak_ptr< ProtectedConformation const > protocols::environment::ProtectedConformationCAP

ProtectedConformationCOP

typedef utility::pointer::shared_ptr< ProtectedConformation const > protocols::environment::ProtectedConformationCOP

ProtectedConformationOP

typedef utility::pointer::shared_ptr< ProtectedConformation > protocols::environment::ProtectedConformationOP

ScriptCMCOP

typedef utility::pointer::shared_ptr< ScriptCM const > protocols::environment::ScriptCMCOP

ScriptCMOP

typedef utility::pointer::shared_ptr< ScriptCM > protocols::environment::ScriptCMOP

Function Documentation

add_variant()

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
	)

References core::conformation::ResidueFactory::create_residue(), core::chemical::DISULFIDE, core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(), core::conformation::Residue::name3(), core::conformation::Residue::seqpos(), and tr().

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

ang_delta()

bool protocols::environment::ang_delta	(	core::Real const &	a,
		core::Real const &	b
	)

References core::pose::motif::a(), protocols::match::upstream::b, and TOLERANCE.

Referenced by protocols::environment::ClientMover::sandboxed_copy().

bond_angles()

void protocols::environment::bond_angles	(	std::map< core::id::DOF_ID, core::Real > &	dofs,
		core::conformation::ConformationOP	conf,
		core::Size	seqpos
	)

References core::kinematics::tree::Atom::child(), core::kinematics::tree::Atom::id(), core::kinematics::tree::Atom::is_jump(), core::kinematics::tree::Atom::n_children(), core::kinematics::tree::Atom::parent(), core::id::AtomID::rsd(), and core::chemical::rings::THETA.

Referenced by protocols::kinematic_closure::ClosureProblem::apply_internal_coordinates(), and protocols::kinematic_closure::ClosureProblem::extract_internal_coordinates().

bond_lengths()

void protocols::environment::bond_lengths	(	std::map< core::id::DOF_ID, core::Real > &	dofs,
		core::conformation::ConformationOP	conf,
		core::Size	seqpos
	)

References core::kinematics::tree::Atom::child(), core::kinematics::tree::Atom::id(), core::kinematics::tree::Atom::is_jump(), core::kinematics::tree::Atom::n_children(), core::kinematics::tree::Atom::parent(), core::id::AtomID::rsd(), and core::chemical::rings::THETA.

Referenced by protocols::kinematic_closure::ClosureProblem::apply_internal_coordinates(), and protocols::kinematic_closure::ClosureProblem::extract_internal_coordinates().

bond_torsions()

void protocols::environment::bond_torsions	(	std::map< core::id::DOF_ID, core::Real > &	dofs,
		core::conformation::ConformationOP	conf,
		core::Size	seqpos
	)

References core::id::BB, core::chemical::rna::CHI, core::id::omega_torsion(), and core::id::psi_torsion().

collect_dofs()

std::map< core::id::DOF_ID, core::Real > protocols::environment::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.

References core::kinematics::AtomTree::atom(), core::conformation::Conformation::atom_tree(), core::id::D, core::conformation::Conformation::dof(), core::kinematics::tree::Atom::is_jump(), protocols::mean_field::max(), protocols::mean_field::min(), core::conformation::Residue::natoms(), core::id::PHI, core::id::RB1, core::id::RB6, core::conformation::Conformation::residue(), core::conformation::Conformation::size(), and core::id::THETA.

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

com_calc()

numeric::xyzVector< core::Real > protocols::environment::com_calc	(	core::pose::Pose const &	pose,
		utility::vector1_bool const &	rsds
	)

References core::conformation::Residue::atom_begin(), core::pose::center_of_mass(), protocols::simple_filters::coords(), core::conformation::Residue::heavyAtoms_end(), and core::pose::Pose::residue().

Referenced by protocols::environment::CoMTrackerCM::update_com().

ctrl_str_selector()

ControlStrength const& protocols::environment::ctrl_str_selector

(

std::pair< claims::DOFElement, ClientMoverOP > const &

d

)

Referenced by protocols::environment::EnvClaimBroker::broker_dofs().

dof_id_to_string()

std::string protocols::environment::dof_id_to_string	(	core::id::DOF_ID const &	id,
		ProtectedConformation const &	conf
	)

References core::conformation::Residue::atom_name(), core::id::D, core::conformation::Residue::name3(), core::id::PHI, core::id::RB1, core::id::RB6, core::conformation::Conformation::residue(), and core::id::THETA.

Referenced by protocols::environment::EXCN_Env_Security_Exception::EXCN_Env_Security_Exception().

find_implied_cut()

core::Size protocols::environment::find_implied_cut	(	utility::vector1< core::Size > const &	cycle,
		core::conformation::Conformation const &	conf
	)

References core::conformation::Conformation::residue(), core::conformation::Conformation::size(), tr(), and core::conformation::Residue::xyz().

Referenced by protocols::environment::EnvClaimBroker::render_fold_tree().

find_mover()

moves::MoverOP protocols::environment::find_mover	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

References protocols::rosetta_scripts::parse_mover_or_null().

Referenced by protocols::environment::EnvMover::parse_subtag().

get_mover_name()

std::string protocols::environment::get_mover_name

(

std::stack< DofPassportCOP > const &

unlocks

)

Referenced by protocols::environment::ProtectedConformation::fail_verification(), and protocols::environment::ProtectedConformation::replace_residue_sandbox().

inherit_cuts()

core::Size protocols::environment::inherit_cuts	(	utility::vector1< core::Size > const &	cycle,
		core::kinematics::FoldTree const &	input_ft
	)

References core::kinematics::FoldTree::cutpoint(), core::kinematics::FoldTree::num_cutpoint(), and tr().

Referenced by protocols::environment::EnvClaimBroker::render_fold_tree().

init_str_selector()

ControlStrength const& protocols::environment::init_str_selector

(

std::pair< claims::DOFElement, ClientMoverOP > const &

d

)

Referenced by protocols::environment::EnvClaimBroker::broker_dofs(), and protocols::environment::EnvClaimBroker::setup_passports().

introduce_datamap_cuts()

utility::vector1< core::Size > protocols::environment::introduce_datamap_cuts	(	FoldTreeSketch const &	fts,
		basic::datacache::BasicDataCache &	datacache
	)

References core::environment::FoldTreeSketch::has_jump(), boost::tuples::hash_value(), core::environment::FoldTreeSketch::nres(), core::id::to_string(), and tr().

Referenced by protocols::environment::EnvClaimBroker::render_fold_tree().

jump_dofs()

void protocols::environment::jump_dofs	(	std::map< core::id::DOF_ID, core::Real > &	dofs,
		core::conformation::ConformationOP	conf,
		core::Size	seqpos
	)

References core::kinematics::tree::Atom::child(), core::kinematics::tree::Atom::dof(), core::kinematics::tree::Atom::id(), core::kinematics::tree::Atom::is_jump(), core::kinematics::tree::Atom::n_children(), core::id::RB1, core::id::RB2, core::id::RB3, core::id::RB4, core::id::RB5, and core::id::RB6.

rm_variant()

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
	)

References core::conformation::ResidueFactory::create_residue(), core::chemical::DISULFIDE, core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed(), core::conformation::Residue::name3(), core::conformation::Residue::seqpos(), and tr().

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

safe_set_conf()

void protocols::environment::safe_set_conf	(	core::pose::Pose &	pose,
		core::conformation::ConformationOP	conf
	)

References core::pose::Pose::data(), core::pose::Pose::set_new_conformation(), and core::pose::datacache::CacheableDataType::WRITEABLE_DATA.

Referenced by protocols::environment::EnvClaimBroker::EnvClaimBroker().

tr() [1/2]

static basic::Tracer protocols::environment::tr ( "protocols.environment.ScriptCM"  , basic::t_info    )

static

tr() [2/2]

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::TorsionClaim::yield_elements(), protocols::environment::claims::XYZClaim::yield_elements(), and protocols::environment::DofUnlock::~DofUnlock().

update_pdb_info()

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

References protocols::environment::EnvClaimBroker::BrokerResult::auto_cuts, core::conformation::Residue::natoms(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::size(), and tr().

Referenced by protocols::environment::EnvClaimBroker::EnvClaimBroker().

Variable Documentation

GENERATE_STATIONARY_ATTACHMENT_POINT

std::string const protocols::environment::GENERATE_STATIONARY_ATTACHMENT_POINT = "[NOT_SET]"

Referenced by protocols::environment::CoMTrackerCM::parse_my_tag(), protocols::environment::CoMTrackerCM::provide_xml_schema(), and protocols::environment::CoMTrackerCM::yield_claims().

NOT_SET

std::string const protocols::environment::NOT_SET = "[NOT_SET]"

Referenced by protocols::denovo_design::components::find_orientations_and_lengths().

TOLERANCE

core::Real const protocols::environment::TOLERANCE = 1e-6

Referenced by ang_delta(), protocols::loops::loop_mover::ang_delta(), protocols::abinitio::abscript::angle_cpy(), protocols::optimize_weights::PNatRotOptEPositionData::count_rotamer_as_native(), and protocols::environment::ClientMover::sandboxed_copy().