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protocols::sic_dock::Rose Class Reference

#include <Rose.hh>

Public Types

typedef platform::Size Size
 
typedef platform::Real Real
 
typedef core::id::AtomID AID
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
core::pose::xyzStripeHashPose 		Hash
 
typedef
core::pose::xyzStripeHashPoseOP 		HashOP
 
typedef
core::pose::xyzStripeHashPoseCOP 		HashCOP
 
typedef numeric::xyzTransform
< Real > 		X
 
typedef numeric::xyzMatrix< Real > M
 
typedef numeric::xyzVector< Real > V
 
typedef X const XC
 
typedef M const MC
 
typedef V const VC
 
typedef X const & XCR
 
typedef M const & MCR
 
typedef V const & VCR
 
typedef Rose const & RCR
 

Public Member Functions

 Rose (PoseCOP p)
 
 Rose (PoseCOP p, core::pose::PoseCoordPickMode const &coord_picker)
 
 Rose (PoseCOP p, core::id::AtomID_Map< Real > const &clash_atoms)
 
 Rose (RCR r, XCR x_in)
 
virtual ~Rose ()=default
 
bool clashes (VCR point) const
 
bool clashes (RCR other) const
 
Size contacts (RCR other) const
 
Rose operator+ (VCR b)
 
Rose operator- (VCR b)
 
Rose operator* (XCR b)
 
Rose operator* (MCR b)
 
XC res_anchor (Size const &ir) const
 
XC n_anchor () const
 
XC c_anchor () const
 
void align_n (XCR a)
 
void align_c (XCR a)
 
void dump_pdb (std::ostream &out) const
 
void dump_pdb (std::string const &fname) const
 
void dump_minimal_pdb (std::ostream &out, char chain='R')
 
PoseCOP pose () const
 
bool clashes_naive (RCR other) const
 
Size contacts_naive (RCR other) const
 

Public Attributes

PoseCOP p
 
HashCOP h
 
X x
 

Friends

bool operator== (RCR a, RCR b)
 
bool operator!= (RCR a, RCR b)
 
Rose operator* (XCR a, RCR b)
 
Rose operator* (MCR a, RCR b)
 

Member Typedef Documentation

typedef core::id::AtomID protocols::sic_dock::Rose::AID
typedef core::pose::xyzStripeHashPose protocols::sic_dock::Rose::Hash
typedef core::pose::xyzStripeHashPoseCOP protocols::sic_dock::Rose::HashCOP
typedef core::pose::xyzStripeHashPoseOP protocols::sic_dock::Rose::HashOP
typedef numeric::xyzMatrix<Real> protocols::sic_dock::Rose::M
typedef M const protocols::sic_dock::Rose::MC
typedef M const& protocols::sic_dock::Rose::MCR
typedef core::pose::Pose protocols::sic_dock::Rose::Pose
typedef core::pose::PoseCOP protocols::sic_dock::Rose::PoseCOP
typedef Rose const& protocols::sic_dock::Rose::RCR
typedef platform::Real protocols::sic_dock::Rose::Real
typedef platform::Size protocols::sic_dock::Rose::Size
typedef numeric::xyzVector<Real> protocols::sic_dock::Rose::V
typedef V const protocols::sic_dock::Rose::VC
typedef V const& protocols::sic_dock::Rose::VCR
typedef numeric::xyzTransform<Real> protocols::sic_dock::Rose::X
typedef X const protocols::sic_dock::Rose::XC
typedef X const& protocols::sic_dock::Rose::XCR

Constructor & Destructor Documentation

protocols::sic_dock::Rose::Rose ( PoseCOP  p)

Referenced by operator*(), operator+(), and operator-().

protocols::sic_dock::Rose::Rose ( PoseCOP  p,
core::pose::PoseCoordPickMode const &  coord_picker 
)
protocols::sic_dock::Rose::Rose ( PoseCOP  p,
core::id::AtomID_Map< Real > const &  clash_atoms 
)
protocols::sic_dock::Rose::Rose ( RCR  r,
XCR  x_in 
)
inline
virtual protocols::sic_dock::Rose::~Rose ( )
virtualdefault

Member Function Documentation

void protocols::sic_dock::Rose::align_c ( XCR  a)
inline

References p, and x.

void protocols::sic_dock::Rose::align_n ( XCR  a)
inline

References p, and x.

XC protocols::sic_dock::Rose::c_anchor ( ) const
inline

References p, and res_anchor().

bool protocols::sic_dock::Rose::clashes ( VCR  point) const
inline

References h, and x.

bool protocols::sic_dock::Rose::clashes ( RCR  other) const

References protocols::match::upstream::b, and h.

bool protocols::sic_dock::Rose::clashes_naive ( RCR  other) const

References h, protocols::hybridization::u, and x.

Size protocols::sic_dock::Rose::contacts ( RCR  other) const

References protocols::match::upstream::b, and h.

Size protocols::sic_dock::Rose::contacts_naive ( RCR  other) const

References h, protocols::hybridization::u, and x.

void protocols::sic_dock::Rose::dump_minimal_pdb ( std::ostream &  out,
char  chain = 'R' 
)

References core::chemical::element::F, core::chemical::element::I, p, and x.

void protocols::sic_dock::Rose::dump_pdb ( std::ostream &  out) const

References pose().

void protocols::sic_dock::Rose::dump_pdb ( std::string const &  fname) const

References pose().

XC protocols::sic_dock::Rose::n_anchor ( ) const
inline

References res_anchor().

Rose protocols::sic_dock::Rose::operator* ( XCR  b)
inline

References Rose(), and x.

Rose protocols::sic_dock::Rose::operator* ( MCR  b)
inline

References Rose(), and x.

Rose protocols::sic_dock::Rose::operator+ ( VCR  b)
inline

References Rose(), and x.

Rose protocols::sic_dock::Rose::operator- ( VCR  b)
inline

References Rose(), and x.

core::pose::PoseCOP protocols::sic_dock::Rose::pose ( ) const

References p, and x.

Referenced by dump_pdb().

XC protocols::sic_dock::Rose::res_anchor ( Size const &  ir) const
inline

References p, and x.

Referenced by c_anchor(), and n_anchor().

Friends And Related Function Documentation

bool operator!= ( RCR  a,
RCR  b 
)
friend
Rose operator* ( XCR  a,
RCR  b 
)
friend
Rose operator* ( MCR  a,
RCR  b 
)
friend
bool operator== ( RCR  a,
RCR  b 
)
friend

Member Data Documentation

HashCOP protocols::sic_dock::Rose::h

Referenced by clashes(), clashes_naive(), contacts(), and contacts_naive().

PoseCOP protocols::sic_dock::Rose::p

Referenced by align_c(), align_n(), c_anchor(), dump_minimal_pdb(), pose(), and res_anchor().

X protocols::sic_dock::Rose::x

Referenced by align_c(), align_n(), clashes(), clashes_naive(), contacts_naive(), dump_minimal_pdb(), operator*(), operator+(), operator-(), pose(), and res_anchor().

The documentation for this class was generated from the following files:
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