protocols::sparta::ANN Class Reference

#include <ANN.hh>

Collaboration diagram for protocols::sparta::ANN:

Public Member Functions
	ANN ()
	ANN (const std::string &dPATH, const std::string &dNAME_PREFIX)
	ANN (int N1_nodeI, int N1_nodeH, int N1_nodeO, const std::string &dPATH, const std::string &dNAME_PREFIX)
	ANN (int N1_nodeI, int N1_nodeH, int N1_nodeO, int N2_nodeI, int N2_nodeH, int N2_nodeO, const std::string &dPATH, const std::string &dNAME_PREFIX)
void	init (int N1_nodeI, int N1_nodeH, int N1_nodeO, int N2_nodeI, int N2_nodeH, int N2_nodeO, const std::string &dPATH, const std::string &dNAME_PREFIX)
void	getSlashChar ()
void	set_input_code (int c)
void	loadWeights ()
void	loadWeightBias3 (const std::string &fName, boost::unordered_map< int, utility::vector0< float > > &W1, utility::vector0< float > &B1, boost::unordered_map< int, utility::vector0< float > > &W2, utility::vector0< float > &B2, boost::unordered_map< int, utility::vector0< float > > &W3, utility::vector0< float > &B3, int N_W_row, int N_W_col, int N_B)
void	calcLevel1 ()
void	calcLevel2 ()
void	runSpartaANN (boost::unordered_map< int, utility::vector0< float > > &inMatrix)
void	applyANNTransformation (utility::vector0< float > &inp, boost::unordered_map< int, utility::vector0< float > > &w, utility::vector0< float > &b, utility::vector0< float > &out, int code)
void	applyVecAverage (utility::vector0< float > &v1, utility::vector0< float > &v2, utility::vector0< float > &v3, utility::vector0< float > &vout)
void	applyVecNormalization (utility::vector0< float > &v)
float	getConfidence (utility::vector0< float > &v)
int	getNumberMissCS (utility::vector0< float > &v)
char *	ftoa (float n, char *buff, char f='g', int prec=6)
char *	itoa (int n, char *buff, int base=10)

Public Attributes
boost::unordered_map< int, utility::vector0< float > >	ANN_IN_MTX
boost::unordered_map< int, utility::vector0< float > >	ANN_IN_MTX_LEVEL1
boost::unordered_map< int, utility::vector0< float > >	ANN_IN_MTX_LEVEL2
boost::unordered_map< int, utility::vector0< float > >	ANN_OUT_MTX_LEVEL1
boost::unordered_map< int, boost::unordered_map < std::string, std::string > >::iterator	it
boost::unordered_map< int, utility::vector0< float > >	ANN_OUT_MTX_LEVEL2

Private Attributes
char	buf [30]
std::string	slash_char
int	input_code
std::string	DB_PATH
std::string	DB_NAME_PREFIX
std::string	DB_FNAME_LEVEL1_1
std::string	DB_FNAME_LEVEL1_2
std::string	DB_FNAME_LEVEL1_3
std::string	DB_FNAME_LEVEL2_1
std::string	DB_FNAME_LEVEL2_2
std::string	DB_FNAME_LEVEL2_3
int	N1_NODE_I
int	N1_NODE_H
int	N1_NODE_O
int	N2_NODE_I
int	N2_NODE_H
int	N2_NODE_O
boost::unordered_map< int, utility::vector0< float > >	WI_1
boost::unordered_map< int, utility::vector0< float > >	WI_2
boost::unordered_map< int, utility::vector0< float > >	WI_3
utility::vector0< float >	BI_1
utility::vector0< float >	BI_2
utility::vector0< float >	BI_3
boost::unordered_map< int, utility::vector0< float > >	WL1_1
boost::unordered_map< int, utility::vector0< float > >	WL1_2
boost::unordered_map< int, utility::vector0< float > >	WL1_3
utility::vector0< float >	BL1_1
utility::vector0< float >	BL1_2
utility::vector0< float >	BL1_3
boost::unordered_map< int, utility::vector0< float > >	WL2_1
boost::unordered_map< int, utility::vector0< float > >	WL2_2
boost::unordered_map< int, utility::vector0< float > >	WL2_3
utility::vector0< float >	BL2_1
utility::vector0< float >	BL2_2
utility::vector0< float >	BL2_3
boost::unordered_map< int, utility::vector0< float > >	W2I_1
boost::unordered_map< int, utility::vector0< float > >	W2I_2
boost::unordered_map< int, utility::vector0< float > >	W2I_3
utility::vector0< float >	B2I_1
utility::vector0< float >	B2I_2
utility::vector0< float >	B2I_3
boost::unordered_map< int, utility::vector0< float > >	W2L1_1
boost::unordered_map< int, utility::vector0< float > >	W2L1_2
boost::unordered_map< int, utility::vector0< float > >	W2L1_3
utility::vector0< float >	B2L1_1
utility::vector0< float >	B2L1_2
utility::vector0< float >	B2L1_3
boost::unordered_map< int, utility::vector0< float > >	W2L2_1
boost::unordered_map< int, utility::vector0< float > >	W2L2_2
boost::unordered_map< int, utility::vector0< float > >	W2L2_3
utility::vector0< float >	B2L2_1
utility::vector0< float >	B2L2_2
utility::vector0< float >	B2L2_3

Detailed Description

Definition at line 32 of file ANN.hh.

Constructor & Destructor Documentation

protocols::sparta::ANN::ANN

(

)

Definition at line 47 of file ANN.cc.

protocols::sparta::ANN::ANN	(	const std::string &	dPATH,
		const std::string &	dNAME_PREFIX
	)

Definition at line 58 of file ANN.cc.

protocols::sparta::ANN::ANN	(	int	N1_nodeI,
		int	N1_nodeH,
		int	N1_nodeO,
		const std::string &	dPATH,
		const std::string &	dNAME_PREFIX
	)

Definition at line 74 of file ANN.cc.

protocols::sparta::ANN::ANN	(	int	N1_nodeI,
		int	N1_nodeH,
		int	N1_nodeO,
		int	N2_nodeI,
		int	N2_nodeH,
		int	N2_nodeO,
		const std::string &	dPATH,
		const std::string &	dNAME_PREFIX
	)

Definition at line 93 of file ANN.cc.

Member Function Documentation

void protocols::sparta::ANN::applyANNTransformation	(	utility::vector0< float > &	inp,
		boost::unordered_map< int, utility::vector0< float > > &	w,
		utility::vector0< float > &	b,
		utility::vector0< float > &	out,
		int	code
	)

Definition at line 290 of file ANN.cc.

References protocols::sparta::tr().

void protocols::sparta::ANN::applyVecAverage	(	utility::vector0< float > &	v1,
		utility::vector0< float > &	v2,
		utility::vector0< float > &	v3,
		utility::vector0< float > &	vout
	)

Definition at line 311 of file ANN.cc.

void protocols::sparta::ANN::applyVecNormalization

(

utility::vector0< float > &

v)

Definition at line 332 of file ANN.cc.

References protocols::match::upstream::b, and core::pack::dunbrack::c.

void protocols::sparta::ANN::calcLevel1

(

)

Definition at line 204 of file ANN.cc.

void protocols::sparta::ANN::calcLevel2

(

)

Definition at line 241 of file ANN.cc.

char * protocols::sparta::ANN::ftoa	(	float	n,
		char *	buff,
		char	f = 'g',
		int	prec = 6
	)

Definition at line 378 of file ANN.cc.

float protocols::sparta::ANN::getConfidence

(

utility::vector0< float > &

v)

Definition at line 347 of file ANN.cc.

References MAX, and MIN.

int protocols::sparta::ANN::getNumberMissCS

(

utility::vector0< float > &

v)

Definition at line 359 of file ANN.cc.

void protocols::sparta::ANN::getSlashChar

(

)

Definition at line 405 of file ANN.cc.

void protocols::sparta::ANN::init	(	int	N1_nodeI,
		int	N1_nodeH,
		int	N1_nodeO,
		int	N2_nodeI,
		int	N2_nodeH,
		int	N2_nodeO,
		const std::string &	dPATH,
		const std::string &	dNAME_PREFIX
	)

Definition at line 112 of file ANN.cc.

char * protocols::sparta::ANN::itoa	(	int	n,
		char *	buff,
		int	base = 10
	)

Definition at line 369 of file ANN.cc.

void protocols::sparta::ANN::loadWeightBias3	(	const std::string &	fName,
		boost::unordered_map< int, utility::vector0< float > > &	W1,
		utility::vector0< float > &	B1,
		boost::unordered_map< int, utility::vector0< float > > &	W2,
		utility::vector0< float > &	B2,
		boost::unordered_map< int, utility::vector0< float > > &	W3,
		utility::vector0< float > &	B3,
		int	N_W_row,
		int	N_W_col,
		int	N_B
	)

Definition at line 166 of file ANN.cc.

References protocols::sparta::GDB::Entries, protocols::sparta::itoa(), protocols::kinmatch::str(), and protocols::sparta::tr().

void protocols::sparta::ANN::loadWeights

(

)

Definition at line 136 of file ANN.cc.

void protocols::sparta::ANN::runSpartaANN

(

boost::unordered_map< int, utility::vector0< float > > &

inMatrix)

Definition at line 277 of file ANN.cc.

void protocols::sparta::ANN::set_input_code

(

int

c)

Definition at line 130 of file ANN.cc.

References core::pack::dunbrack::c.

Member Data Documentation

boost::unordered_map<int, utility::vector0<float> > protocols::sparta::ANN::ANN_IN_MTX

Definition at line 64 of file ANN.hh.

boost::unordered_map<int, utility::vector0<float> > protocols::sparta::ANN::ANN_IN_MTX_LEVEL1

Definition at line 66 of file ANN.hh.

boost::unordered_map<int, utility::vector0<float> > protocols::sparta::ANN::ANN_IN_MTX_LEVEL2

Definition at line 67 of file ANN.hh.

boost::unordered_map<int, utility::vector0<float> > protocols::sparta::ANN::ANN_OUT_MTX_LEVEL1

Definition at line 69 of file ANN.hh.

boost::unordered_map<int, utility::vector0<float> > protocols::sparta::ANN::ANN_OUT_MTX_LEVEL2

Definition at line 73 of file ANN.hh.

utility::vector0<float> protocols::sparta::ANN::B2I_1

private

Definition at line 57 of file ANN.hh.

utility::vector0<float> protocols::sparta::ANN::B2I_2

private

Definition at line 57 of file ANN.hh.

utility::vector0<float> protocols::sparta::ANN::B2I_3

private

Definition at line 57 of file ANN.hh.

utility::vector0<float> protocols::sparta::ANN::B2L1_1

private

Definition at line 59 of file ANN.hh.

utility::vector0<float> protocols::sparta::ANN::B2L1_2

private

Definition at line 59 of file ANN.hh.

utility::vector0<float> protocols::sparta::ANN::B2L1_3

private

Definition at line 59 of file ANN.hh.

utility::vector0<float> protocols::sparta::ANN::B2L2_1

private

Definition at line 61 of file ANN.hh.

utility::vector0<float> protocols::sparta::ANN::B2L2_2

private

Definition at line 61 of file ANN.hh.

utility::vector0<float> protocols::sparta::ANN::B2L2_3

private

Definition at line 61 of file ANN.hh.

utility::vector0<float> protocols::sparta::ANN::BI_1

private

Definition at line 49 of file ANN.hh.

utility::vector0<float> protocols::sparta::ANN::BI_2

private

Definition at line 49 of file ANN.hh.

utility::vector0<float> protocols::sparta::ANN::BI_3

private

Definition at line 49 of file ANN.hh.

utility::vector0<float> protocols::sparta::ANN::BL1_1

private

Definition at line 51 of file ANN.hh.

utility::vector0<float> protocols::sparta::ANN::BL1_2

private

Definition at line 51 of file ANN.hh.

utility::vector0<float> protocols::sparta::ANN::BL1_3

private

Definition at line 51 of file ANN.hh.

utility::vector0<float> protocols::sparta::ANN::BL2_1

private

Definition at line 53 of file ANN.hh.

utility::vector0<float> protocols::sparta::ANN::BL2_2

private

Definition at line 53 of file ANN.hh.

utility::vector0<float> protocols::sparta::ANN::BL2_3

private

Definition at line 53 of file ANN.hh.

char protocols::sparta::ANN::buf[30]

private

Definition at line 34 of file ANN.hh.

std::string protocols::sparta::ANN::DB_FNAME_LEVEL1_1

private

Definition at line 43 of file ANN.hh.

std::string protocols::sparta::ANN::DB_FNAME_LEVEL1_2

private

Definition at line 43 of file ANN.hh.

std::string protocols::sparta::ANN::DB_FNAME_LEVEL1_3

private

Definition at line 43 of file ANN.hh.

std::string protocols::sparta::ANN::DB_FNAME_LEVEL2_1

private

Definition at line 43 of file ANN.hh.

std::string protocols::sparta::ANN::DB_FNAME_LEVEL2_2

private

Definition at line 43 of file ANN.hh.

std::string protocols::sparta::ANN::DB_FNAME_LEVEL2_3

private

Definition at line 43 of file ANN.hh.

std::string protocols::sparta::ANN::DB_NAME_PREFIX

private

Definition at line 42 of file ANN.hh.

std::string protocols::sparta::ANN::DB_PATH

private

Definition at line 42 of file ANN.hh.

int protocols::sparta::ANN::input_code

private

Definition at line 36 of file ANN.hh.

boost::unordered_map< int, boost::unordered_map< std::string, std::string> >::iterator protocols::sparta::ANN::it

Definition at line 71 of file ANN.hh.

int protocols::sparta::ANN::N1_NODE_H

private

Definition at line 44 of file ANN.hh.

int protocols::sparta::ANN::N1_NODE_I

private

Definition at line 44 of file ANN.hh.

int protocols::sparta::ANN::N1_NODE_O

private

Definition at line 44 of file ANN.hh.

int protocols::sparta::ANN::N2_NODE_H

private

Definition at line 45 of file ANN.hh.

int protocols::sparta::ANN::N2_NODE_I

private

Definition at line 45 of file ANN.hh.

int protocols::sparta::ANN::N2_NODE_O

private

Definition at line 45 of file ANN.hh.

std::string protocols::sparta::ANN::slash_char

private

Definition at line 35 of file ANN.hh.

boost::unordered_map<int, utility::vector0<float> > protocols::sparta::ANN::W2I_1

private

Definition at line 56 of file ANN.hh.

boost::unordered_map<int, utility::vector0<float> > protocols::sparta::ANN::W2I_2

private

Definition at line 56 of file ANN.hh.

boost::unordered_map<int, utility::vector0<float> > protocols::sparta::ANN::W2I_3

private

Definition at line 56 of file ANN.hh.

boost::unordered_map<int, utility::vector0<float> > protocols::sparta::ANN::W2L1_1

private

Definition at line 58 of file ANN.hh.

boost::unordered_map<int, utility::vector0<float> > protocols::sparta::ANN::W2L1_2

private

Definition at line 58 of file ANN.hh.

boost::unordered_map<int, utility::vector0<float> > protocols::sparta::ANN::W2L1_3

private

Definition at line 58 of file ANN.hh.

boost::unordered_map<int, utility::vector0<float> > protocols::sparta::ANN::W2L2_1

private

Definition at line 60 of file ANN.hh.

boost::unordered_map<int, utility::vector0<float> > protocols::sparta::ANN::W2L2_2

private

Definition at line 60 of file ANN.hh.

boost::unordered_map<int, utility::vector0<float> > protocols::sparta::ANN::W2L2_3

private

Definition at line 60 of file ANN.hh.

boost::unordered_map<int, utility::vector0<float> > protocols::sparta::ANN::WI_1

private

Definition at line 48 of file ANN.hh.

boost::unordered_map<int, utility::vector0<float> > protocols::sparta::ANN::WI_2

private

Definition at line 48 of file ANN.hh.

boost::unordered_map<int, utility::vector0<float> > protocols::sparta::ANN::WI_3

private

Definition at line 48 of file ANN.hh.

boost::unordered_map<int, utility::vector0<float> > protocols::sparta::ANN::WL1_1

private

Definition at line 50 of file ANN.hh.

boost::unordered_map<int, utility::vector0<float> > protocols::sparta::ANN::WL1_2

private

Definition at line 50 of file ANN.hh.

boost::unordered_map<int, utility::vector0<float> > protocols::sparta::ANN::WL1_3

private

Definition at line 50 of file ANN.hh.

boost::unordered_map<int, utility::vector0<float> > protocols::sparta::ANN::WL2_1

private

Definition at line 52 of file ANN.hh.

boost::unordered_map<int, utility::vector0<float> > protocols::sparta::ANN::WL2_2

private

Definition at line 52 of file ANN.hh.

boost::unordered_map<int, utility::vector0<float> > protocols::sparta::ANN::WL2_3

private

Definition at line 52 of file ANN.hh.

---

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

• src/protocols/sparta/ANN.hh
• src/protocols/sparta/ANN.cc