protocols::scoring Namespace Reference

Namespaces
	methods

Classes
class	ImplicitFastClashCheck
class	InterchainPotential
	Singleton class to hold the interface-derived statistics for residue-pair scores at protein/protein interfaces. More...
class	Interface
class	InterfaceInfo
	Keep track of the interface information. More...
class	ResidualDipolarCouplingRigidSegments
	ResidualDipolarCouplingRigidSegmentss are mainly handled by this class @detail related classed: RDC — a single line in an RDC file - representing a single dipolar coupling ResidualDipolarCouplingRigidSegmentsEnergy – an energy method which triggers computations handled by this class. More...
class	VDW_CachedRepScreenInfo
class	VDW_GridEnergy
class	VDW_GridEnergyCreator

Typedefs
using	Vec = numeric::xyzVector< Real >
using	Mat = numeric::xyzMatrix< Real >
typedef utility::pointer::shared_ptr< ImplicitFastClashCheck >	ImplicitFastClashCheckOP
typedef utility::pointer::shared_ptr< ImplicitFastClashCheck const >	ImplicitFastClashCheckCOP
typedef utility::pointer::weak_ptr< ImplicitFastClashCheck >	ImplicitFastClashCheckAP
typedef utility::pointer::weak_ptr< ImplicitFastClashCheck const >	ImplicitFastClashCheckCAP
typedef utility::pointer::shared_ptr< InterfaceInfo >	InterfaceInfoOP
typedef utility::pointer::shared_ptr< Interface >	InterfaceOP
typedef utility::pointer::shared_ptr< Interface const >	InterfaceCOP
typedef utility::pointer::shared_ptr< InterfaceInfo const >	InterfaceInfoCOP
using	RDC_lines_collection = utility::vector1< core::scoring::ResidualDipolarCoupling::RDC_lines >
typedef utility::pointer::shared_ptr< ResidualDipolarCouplingRigidSegments >	ResidualDipolarCouplingRigidSegmentsOP
typedef utility::pointer::shared_ptr< ResidualDipolarCouplingRigidSegments const >	ResidualDipolarCouplingRigidSegmentsCOP
typedef utility::pointer::shared_ptr< VDW_CachedRepScreenInfo >	VDW_CachedRepScreenInfoOP
typedef utility::pointer::shared_ptr< VDW_CachedRepScreenInfo const >	VDW_CachedRepScreenInfoCOP

Functions
static core::Size	max_interchain_sites (2)
void	store_RDC_segments_in_pose (ResidualDipolarCouplingRigidSegmentsOP rdcrs_info, core::pose::Pose &pose)
ResidualDipolarCouplingRigidSegmentsCOP	retrieve_RDC_segments_from_pose (core::pose::Pose const &pose)
ResidualDipolarCouplingRigidSegmentsOP	retrieve_RDC_segments_from_pose (core::pose::Pose &pose)
std::ostream &	operator<< (std::ostream &out, ResidualDipolarCouplingRigidSegments const &rdcrs)
VDW_CachedRepScreenInfo const &	const_vdw_cached_rep_screen_info_from_pose (core::pose::Pose const &pose)
VDW_CachedRepScreenInfo &	nonconst_vdw_cached_rep_screen_info_from_pose (core::pose::Pose &pose)
VDW_CachedRepScreenInfo const &	make_sure_vdw_cached_rep_screen_info_is_setup (core::pose::Pose &pose)
bool	vdw_cached_rep_screen_info_is_setup (core::pose::Pose const &pose)
bool	option_vdw_rep_screen_info_user (utility::options::OptionCollection const &options)
void	set_vdw_cached_rep_screen_info (core::pose::Pose &pose, VDW_CachedRepScreenInfoOP &vdw_cached_rep_screen_info)
void	set_vdw_cached_rep_screen_info_from_pose (core::pose::Pose &new_pose, core::pose::Pose const &pose)
void	fill_vdw_cached_rep_screen_info_from_command_line (core::pose::Pose &pose)
void	fill_vdw_cached_rep_screen_info_from_options (core::pose::Pose &pose, utility::options::OptionCollection const &options)
void	fill_vdw_cached_rep_screen_info_from_command_line (utility::vector1< core::pose::Pose * > &pose_pointers)
void	fill_vdw_cached_rep_screen_info_from_options (utility::vector1< core::pose::Pose * > &pose_pointers, utility::options::OptionCollection const &options)

Typedef Documentation

ImplicitFastClashCheckAP

typedef utility::pointer::weak_ptr< ImplicitFastClashCheck > protocols::scoring::ImplicitFastClashCheckAP

ImplicitFastClashCheckCAP

typedef utility::pointer::weak_ptr< ImplicitFastClashCheck const > protocols::scoring::ImplicitFastClashCheckCAP

ImplicitFastClashCheckCOP

typedef utility::pointer::shared_ptr< ImplicitFastClashCheck const > protocols::scoring::ImplicitFastClashCheckCOP

ImplicitFastClashCheckOP

typedef utility::pointer::shared_ptr< ImplicitFastClashCheck > protocols::scoring::ImplicitFastClashCheckOP

InterfaceCOP

typedef utility::pointer::shared_ptr< Interface const > protocols::scoring::InterfaceCOP

InterfaceInfoCOP

typedef utility::pointer::shared_ptr< InterfaceInfo const > protocols::scoring::InterfaceInfoCOP

InterfaceInfoOP

typedef utility::pointer::shared_ptr< InterfaceInfo > protocols::scoring::InterfaceInfoOP

InterfaceOP

typedef utility::pointer::shared_ptr< Interface > protocols::scoring::InterfaceOP

Mat

using protocols::scoring::Mat = typedef numeric::xyzMatrix<Real>

RDC_lines_collection

using protocols::scoring::RDC_lines_collection = typedef utility::vector1<core::scoring::ResidualDipolarCoupling::RDC_lines>

ResidualDipolarCouplingRigidSegmentsCOP

typedef utility::pointer::shared_ptr< ResidualDipolarCouplingRigidSegments const > protocols::scoring::ResidualDipolarCouplingRigidSegmentsCOP

ResidualDipolarCouplingRigidSegmentsOP

typedef utility::pointer::shared_ptr< ResidualDipolarCouplingRigidSegments > protocols::scoring::ResidualDipolarCouplingRigidSegmentsOP

VDW_CachedRepScreenInfoCOP

typedef utility::pointer::shared_ptr< VDW_CachedRepScreenInfo const > protocols::scoring::VDW_CachedRepScreenInfoCOP

VDW_CachedRepScreenInfoOP

typedef utility::pointer::shared_ptr< VDW_CachedRepScreenInfo > protocols::scoring::VDW_CachedRepScreenInfoOP

Vec

using protocols::scoring::Vec = typedef numeric::xyzVector<Real>

Function Documentation

const_vdw_cached_rep_screen_info_from_pose()

VDW_CachedRepScreenInfo const & protocols::scoring::const_vdw_cached_rep_screen_info_from_pose

(

core::pose::Pose const &

pose

)

Pose must already contain a vdw_cached_rep_screen_info object or this method will fail.

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

Referenced by protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::FARFAR_setup_using_user_input_VDW_pose(), protocols::scoring::VDW_GridEnergy::finalize_total_energy(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::RNA_VDW_BinChecker(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::setup_using_user_input_VDW_pose(), and protocols::scoring::VDW_CachedRepScreenInfo::VDW_CachedRepScreenInfo().

fill_vdw_cached_rep_screen_info_from_command_line() [1/2]

void protocols::scoring::fill_vdw_cached_rep_screen_info_from_command_line

(

core::pose::Pose &

pose

)

References fill_vdw_cached_rep_screen_info_from_options().

Referenced by protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::apply(), protocols::rna::denovo::RNA_DeNovoProtocol::apply(), protocols::scoring::VDW_GridEnergy::setup_for_scoring(), and protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::setup_vdw_cached_rep_screen_info().

fill_vdw_cached_rep_screen_info_from_command_line() [2/2]

void protocols::scoring::fill_vdw_cached_rep_screen_info_from_command_line

(

utility::vector1< core::pose::Pose * > &

pose_pointers

)

References fill_vdw_cached_rep_screen_info_from_options().

fill_vdw_cached_rep_screen_info_from_options() [1/2]

void protocols::scoring::fill_vdw_cached_rep_screen_info_from_options	(	core::pose::Pose &	pose,
		utility::options::OptionCollection const &	options
	)

References make_sure_vdw_cached_rep_screen_info_is_setup(), and option_vdw_rep_screen_info_user().

Referenced by fill_vdw_cached_rep_screen_info_from_command_line(), and fill_vdw_cached_rep_screen_info_from_options().

fill_vdw_cached_rep_screen_info_from_options() [2/2]

void protocols::scoring::fill_vdw_cached_rep_screen_info_from_options	(	utility::vector1< core::pose::Pose * > &	pose_pointers,
		utility::options::OptionCollection const &	options
	)

References fill_vdw_cached_rep_screen_info_from_options(), and option_vdw_rep_screen_info_user().

make_sure_vdw_cached_rep_screen_info_is_setup()

VDW_CachedRepScreenInfo const & protocols::scoring::make_sure_vdw_cached_rep_screen_info_is_setup

(

core::pose::Pose &

pose

)

References nonconst_vdw_cached_rep_screen_info_from_pose().

Referenced by fill_vdw_cached_rep_screen_info_from_options().

max_interchain_sites()

static core::Size protocols::scoring::max_interchain_sites ( 2  )

static

Referenced by protocols::scoring::Interface::calculate(), and protocols::scoring::Interface::show().

nonconst_vdw_cached_rep_screen_info_from_pose()

VDW_CachedRepScreenInfo & protocols::scoring::nonconst_vdw_cached_rep_screen_info_from_pose

(

core::pose::Pose &

pose

)

Either returns a non-const reference to the vdw_cached_rep_screen_info object already stored in the pose, or creates a new vdw_cached_rep_screen_info object, places it in the pose, and returns a non-const reference to it.

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

Referenced by make_sure_vdw_cached_rep_screen_info_is_setup().

operator<<()

std::ostream & protocols::scoring::operator<<	(	std::ostream &	out,
		ResidualDipolarCouplingRigidSegments const &	rdcrs
	)

References core::conformation::membrane::out, and protocols::scoring::ResidualDipolarCouplingRigidSegments::show().

option_vdw_rep_screen_info_user()

bool protocols::scoring::option_vdw_rep_screen_info_user

(

utility::options::OptionCollection const &

options

)

Referenced by fill_vdw_cached_rep_screen_info_from_options(), and set_vdw_cached_rep_screen_info_from_pose().

retrieve_RDC_segments_from_pose() [1/2]

ResidualDipolarCouplingRigidSegmentsOP protocols::scoring::retrieve_RDC_segments_from_pose

(

core::pose::Pose &

pose

)

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

retrieve_RDC_segments_from_pose() [2/2]

ResidualDipolarCouplingRigidSegmentsCOP protocols::scoring::retrieve_RDC_segments_from_pose

(

core::pose::Pose const &

pose

)

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

Referenced by protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments::rdc_segments_from_pose().

set_vdw_cached_rep_screen_info()

void protocols::scoring::set_vdw_cached_rep_screen_info	(	core::pose::Pose &	pose,
		VDW_CachedRepScreenInfoOP &	vdw_cached_rep_screen_info
	)

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

Referenced by set_vdw_cached_rep_screen_info_from_pose().

set_vdw_cached_rep_screen_info_from_pose()

void protocols::scoring::set_vdw_cached_rep_screen_info_from_pose	(	core::pose::Pose &	new_pose,
		core::pose::Pose const &	pose
	)

References option_vdw_rep_screen_info_user(), set_vdw_cached_rep_screen_info(), and protocols::scoring::VDW_CachedRepScreenInfo::VDW_CachedRepScreenInfo().

Referenced by protocols::stepwise::monte_carlo::mover::DeleteMover::remove_singletons_and_update_pose_focus(), protocols::stepwise::modeler::slice_out_pose(), protocols::stepwise::modeler::switch_focus_to_other_pose(), and protocols::stepwise::monte_carlo::mover::FromScratchMover::update_full_model_info_and_switch_focus_to_new_pose().

store_RDC_segments_in_pose()

void protocols::scoring::store_RDC_segments_in_pose	(	ResidualDipolarCouplingRigidSegmentsOP	rdcrs_info,
		core::pose::Pose &	pose
	)

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

Referenced by protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments::rdc_segments_from_pose().

vdw_cached_rep_screen_info_is_setup()

bool protocols::scoring::vdw_cached_rep_screen_info_is_setup

(

core::pose::Pose const &

pose

)

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