TMalign.cc File Reference

A reimplementation of TM-align algorithm. More...

#include <protocols/hybridization/TMalign.hh>
#include <cmath>
#include <string>
#include <vector>
#include <iterator>
#include <algorithm>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyzMatrix.hh>
#include <core/id/AtomID.hh>
#include <core/id/AtomID_Map.hh>
#include <core/conformation/Residue.hh>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::hybridization

Macros
#define	getmax(a, b)   ((a)>(b)?(a):(b))
#define	getmin(a, b)   ((a)>(b)?(b):(a))

Variables
core::Real	protocols::hybridization::D0_MIN
core::Real	protocols::hybridization::Lnorm
core::Real	protocols::hybridization::score_d8
core::Real	protocols::hybridization::d0
core::Real	protocols::hybridization::d0_search
core::Real	protocols::hybridization::dcu0
std::vector< std::vector< core::Real > >	protocols::hybridization::score
std::vector< std::vector< bool > >	protocols::hybridization::path
std::vector< std::vector< core::Real > >	protocols::hybridization::val
int	protocols::hybridization::xlen
int	protocols::hybridization::ylen
int	protocols::hybridization::minlen
std::vector< numeric::xyzVector< core::Real > >	protocols::hybridization::xa
std::vector< numeric::xyzVector< core::Real > >	protocols::hybridization::ya
std::vector< int >	protocols::hybridization::xresno
std::vector< int >	protocols::hybridization::yresno
std::vector< numeric::xyzVector< core::Real > >	protocols::hybridization::xtm
std::vector< numeric::xyzVector< core::Real > >	protocols::hybridization::ytm
std::vector< numeric::xyzVector< core::Real > >	protocols::hybridization::xt
std::string	protocols::hybridization::seqx
std::string	protocols::hybridization::seqy
std::vector< int >	protocols::hybridization::secx
std::vector< int >	protocols::hybridization::secy
std::vector< numeric::xyzVector< core::Real > >	protocols::hybridization::r1
std::vector< numeric::xyzVector< core::Real > >	protocols::hybridization::r2
numeric::xyzVector< core::Real >	protocols::hybridization::t
numeric::xyzMatrix< core::Real >	protocols::hybridization::u
int	protocols::hybridization::n_ali8_
std::vector< int >	protocols::hybridization::m1_
std::vector< int >	protocols::hybridization::m2_
core::Real	protocols::hybridization::d0_out_
core::Real	protocols::hybridization::d0A
core::Real	protocols::hybridization::d0B

Detailed Description

A reimplementation of TM-align algorithm.

Author

Yifan Song

Macro Definition Documentation

getmax

#define getmax	(		a,
			b
	)		((a)>(b)?(a):(b))

getmin

#define getmin	(		a,
			b
	)		((a)>(b)?(b):(a))