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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 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_CachedRepScreenInfononconst_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

typedef utility::pointer::weak_ptr< ImplicitFastClashCheck const > protocols::scoring::ImplicitFastClashCheckCAP
typedef utility::pointer::shared_ptr< ImplicitFastClashCheck const > protocols::scoring::ImplicitFastClashCheckCOP
typedef utility::pointer::shared_ptr< Interface const > protocols::scoring::InterfaceCOP
typedef utility::pointer::shared_ptr< InterfaceInfo const > protocols::scoring::InterfaceInfoCOP
typedef utility::pointer::shared_ptr< InterfaceInfo > protocols::scoring::InterfaceInfoOP
typedef utility::pointer::shared_ptr< Interface > protocols::scoring::InterfaceOP
using protocols::scoring::Mat = typedef numeric::xyzMatrix<Real>
typedef utility::pointer::shared_ptr< VDW_CachedRepScreenInfo const > protocols::scoring::VDW_CachedRepScreenInfoCOP
using protocols::scoring::Vec = typedef numeric::xyzVector<Real>

Function Documentation

VDW_CachedRepScreenInfo const & protocols::scoring::const_vdw_cached_rep_screen_info_from_pose ( core::pose::Pose const &  pose)
void protocols::scoring::fill_vdw_cached_rep_screen_info_from_command_line ( core::pose::Pose pose)
void protocols::scoring::fill_vdw_cached_rep_screen_info_from_command_line ( utility::vector1< core::pose::Pose * > &  pose_pointers)
void protocols::scoring::fill_vdw_cached_rep_screen_info_from_options ( core::pose::Pose pose,
utility::options::OptionCollection const &  options 
)
void protocols::scoring::fill_vdw_cached_rep_screen_info_from_options ( utility::vector1< core::pose::Pose * > &  pose_pointers,
utility::options::OptionCollection const &  options 
)
VDW_CachedRepScreenInfo const & protocols::scoring::make_sure_vdw_cached_rep_screen_info_is_setup ( core::pose::Pose pose)
static core::Size protocols::scoring::max_interchain_sites ( )
static
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().

std::ostream & protocols::scoring::operator<< ( std::ostream &  out,
ResidualDipolarCouplingRigidSegments const &  rdcrs 
)
bool protocols::scoring::option_vdw_rep_screen_info_user ( utility::options::OptionCollection const &  options)
ResidualDipolarCouplingRigidSegmentsCOP protocols::scoring::retrieve_RDC_segments_from_pose ( core::pose::Pose const &  pose)
ResidualDipolarCouplingRigidSegmentsOP protocols::scoring::retrieve_RDC_segments_from_pose ( core::pose::Pose pose)
void protocols::scoring::set_vdw_cached_rep_screen_info ( core::pose::Pose pose,
VDW_CachedRepScreenInfoOP &  vdw_cached_rep_screen_info 
)
void protocols::scoring::set_vdw_cached_rep_screen_info_from_pose ( core::pose::Pose new_pose,
core::pose::Pose const &  pose 
)
void protocols::scoring::store_RDC_segments_in_pose ( ResidualDipolarCouplingRigidSegmentsOP  rdcrs_info,
core::pose::Pose pose 
)
bool protocols::scoring::vdw_cached_rep_screen_info_is_setup ( core::pose::Pose const &  pose)