protocols::sparta::ANN Class Reference

#include <ANN.hh>

Public Types
typedef utility::vector0< float >	ANN_Vector
typedef std::map< int, ANN_Vector >	ANN_Matrix

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, ANN_Matrix &W1, ANN_Vector &B1, ANN_Matrix &W2, ANN_Vector &B2, ANN_Matrix &W3, ANN_Vector &B3, int N_W_row, int N_W_col, int N_B)
void	calcLevel1 ()
void	calcLevel2 ()
void	runSpartaANN (ANN_Matrix &inMatrix)
void	applyANNTransformation (ANN_Vector &inp, ANN_Matrix &w, ANN_Vector &b, ANN_Vector &out, int code)
void	applyVecAverage (ANN_Vector &v1, ANN_Vector &v2, ANN_Vector &v3, ANN_Vector &vout)
void	applyVecNormalization (ANN_Vector &v)
float	getConfidence (ANN_Vector &v)
int	getNumberMissCS (ANN_Vector &v)
char *	ftoa (float n, char *buff, char f='g', int prec=6)
char *	itoa (int n, char *buff, int base=10)

Public 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
ANN_Matrix	WI_1
ANN_Matrix	WI_2
ANN_Matrix	WI_3
ANN_Vector	BI_1
ANN_Vector	BI_2
ANN_Vector	BI_3
ANN_Matrix	WL1_1
ANN_Matrix	WL1_2
ANN_Matrix	WL1_3
ANN_Vector	BL1_1
ANN_Vector	BL1_2
ANN_Vector	BL1_3
ANN_Matrix	WL2_1
ANN_Matrix	WL2_2
ANN_Matrix	WL2_3
ANN_Vector	BL2_1
ANN_Vector	BL2_2
ANN_Vector	BL2_3
ANN_Matrix	W2I_1
ANN_Matrix	W2I_2
ANN_Matrix	W2I_3
ANN_Vector	B2I_1
ANN_Vector	B2I_2
ANN_Vector	B2I_3
ANN_Matrix	W2L1_1
ANN_Matrix	W2L1_2
ANN_Matrix	W2L1_3
ANN_Vector	B2L1_1
ANN_Vector	B2L1_2
ANN_Vector	B2L1_3
ANN_Matrix	W2L2_1
ANN_Matrix	W2L2_2
ANN_Matrix	W2L2_3
ANN_Vector	B2L2_1
ANN_Vector	B2L2_2
ANN_Vector	B2L2_3
ANN_Matrix	ANN_IN_MTX
ANN_Matrix	ANN_IN_MTX_LEVEL1
ANN_Matrix	ANN_IN_MTX_LEVEL2
ANN_Matrix	ANN_OUT_MTX_LEVEL1
ANN_Matrix	ANN_OUT_MTX_LEVEL2

Member Typedef Documentation

typedef std::map< int, ANN_Vector > protocols::sparta::ANN::ANN_Matrix

typedef utility::vector0<float> protocols::sparta::ANN::ANN_Vector

Constructor & Destructor Documentation

protocols::sparta::ANN::ANN

(

)

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

References DB_NAME_PREFIX, DB_PATH, getSlashChar(), input_code, loadWeights(), N1_NODE_H, N1_NODE_I, N1_NODE_O, N2_NODE_H, N2_NODE_I, and N2_NODE_O.

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

References DB_NAME_PREFIX, DB_PATH, getSlashChar(), input_code, loadWeights(), N1_NODE_H, N1_NODE_I, N1_NODE_O, N2_NODE_H, N2_NODE_I, and N2_NODE_O.

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
	)

References DB_NAME_PREFIX, DB_PATH, getSlashChar(), input_code, loadWeights(), N1_NODE_H, N1_NODE_I, N1_NODE_O, N2_NODE_H, N2_NODE_I, and N2_NODE_O.

Member Function Documentation

void protocols::sparta::ANN::applyANNTransformation	(	ANN_Vector &	inp,
		ANN_Matrix &	w,
		ANN_Vector &	b,
		ANN_Vector &	out,
		int	code
	)

References core::simple_metrics::metrics::sum, and protocols::sparta::tr().

Referenced by calcLevel1(), and calcLevel2().

void protocols::sparta::ANN::applyVecAverage	(	ANN_Vector &	v1,
		ANN_Vector &	v2,
		ANN_Vector &	v3,
		ANN_Vector &	vout
	)

Referenced by calcLevel1(), and calcLevel2().

void protocols::sparta::ANN::applyVecNormalization

(

ANN_Vector &

v

)

References core::pose::motif::a(), protocols::match::upstream::b, core::pack::dunbrack::c, and core::simple_metrics::metrics::sum.

void protocols::sparta::ANN::calcLevel1

(

)

References ANN_IN_MTX_LEVEL1, ANN_OUT_MTX_LEVEL1, applyANNTransformation(), applyVecAverage(), BI_1, BI_2, BI_3, BL1_1, BL1_2, BL1_3, BL2_1, BL2_2, BL2_3, core::sequence::end, WI_1, WI_2, WI_3, WL1_1, WL1_2, WL1_3, WL2_1, WL2_2, and WL2_3.

Referenced by runSpartaANN().

void protocols::sparta::ANN::calcLevel2

(

)

References ANN_IN_MTX_LEVEL2, ANN_OUT_MTX_LEVEL2, applyANNTransformation(), applyVecAverage(), B2I_1, B2I_2, B2I_3, B2L1_1, B2L1_2, B2L1_3, B2L2_1, B2L2_2, B2L2_3, core::sequence::end, W2I_1, W2I_2, W2I_3, W2L1_1, W2L1_2, W2L1_3, W2L2_1, W2L2_2, and W2L2_3.

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

float protocols::sparta::ANN::getConfidence

(

ANN_Vector &

v

)

References MAX, and MIN.

int protocols::sparta::ANN::getNumberMissCS

(

ANN_Vector &

v

)

void protocols::sparta::ANN::getSlashChar

(

)

References slash_char.

Referenced by ANN(), and init().

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
	)

References DB_NAME_PREFIX, DB_PATH, getSlashChar(), input_code, loadWeights(), N1_NODE_H, N1_NODE_I, N1_NODE_O, N2_NODE_H, N2_NODE_I, and N2_NODE_O.

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

Referenced by loadWeightBias3().

void protocols::sparta::ANN::loadWeightBias3	(	const std::string &	fName,
		ANN_Matrix &	W1,
		ANN_Vector &	B1,
		ANN_Matrix &	W2,
		ANN_Vector &	B2,
		ANN_Matrix &	W3,
		ANN_Vector &	B3,
		int	N_W_row,
		int	N_W_col,
		int	N_B
	)

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

Referenced by loadWeights().

void protocols::sparta::ANN::loadWeights

(

)

References BI_1, BI_2, BI_3, BL1_1, BL1_2, BL1_3, BL2_1, BL2_2, BL2_3, DB_NAME_PREFIX, DB_PATH, loadWeightBias3(), N1_NODE_H, N1_NODE_I, N1_NODE_O, slash_char, WI_1, WI_2, WI_3, WL1_1, WL1_2, WL1_3, WL2_1, WL2_2, and WL2_3.

Referenced by ANN(), and init().

void protocols::sparta::ANN::runSpartaANN

(

ANN_Matrix &

inMatrix

)

References ANN_IN_MTX_LEVEL1, and calcLevel1().

void protocols::sparta::ANN::set_input_code

(

int

c

)

References core::pack::dunbrack::c, and input_code.

Member Data Documentation

ANN_Matrix protocols::sparta::ANN::ANN_IN_MTX

ANN_Matrix protocols::sparta::ANN::ANN_IN_MTX_LEVEL1

Referenced by calcLevel1(), and runSpartaANN().

ANN_Matrix protocols::sparta::ANN::ANN_IN_MTX_LEVEL2

Referenced by calcLevel2().

ANN_Matrix protocols::sparta::ANN::ANN_OUT_MTX_LEVEL1

Referenced by calcLevel1().

ANN_Matrix protocols::sparta::ANN::ANN_OUT_MTX_LEVEL2

Referenced by calcLevel2().

ANN_Vector protocols::sparta::ANN::B2I_1

Referenced by calcLevel2().

ANN_Vector protocols::sparta::ANN::B2I_2

Referenced by calcLevel2().

ANN_Vector protocols::sparta::ANN::B2I_3

Referenced by calcLevel2().

ANN_Vector protocols::sparta::ANN::B2L1_1

Referenced by calcLevel2().

ANN_Vector protocols::sparta::ANN::B2L1_2

Referenced by calcLevel2().

ANN_Vector protocols::sparta::ANN::B2L1_3

Referenced by calcLevel2().

ANN_Vector protocols::sparta::ANN::B2L2_1

Referenced by calcLevel2().

ANN_Vector protocols::sparta::ANN::B2L2_2

Referenced by calcLevel2().

ANN_Vector protocols::sparta::ANN::B2L2_3

Referenced by calcLevel2().

ANN_Vector protocols::sparta::ANN::BI_1

Referenced by calcLevel1(), and loadWeights().

ANN_Vector protocols::sparta::ANN::BI_2

Referenced by calcLevel1(), and loadWeights().

ANN_Vector protocols::sparta::ANN::BI_3

Referenced by calcLevel1(), and loadWeights().

ANN_Vector protocols::sparta::ANN::BL1_1

Referenced by calcLevel1(), and loadWeights().

ANN_Vector protocols::sparta::ANN::BL1_2

Referenced by calcLevel1(), and loadWeights().

ANN_Vector protocols::sparta::ANN::BL1_3

Referenced by calcLevel1(), and loadWeights().

ANN_Vector protocols::sparta::ANN::BL2_1

Referenced by calcLevel1(), and loadWeights().

ANN_Vector protocols::sparta::ANN::BL2_2

Referenced by calcLevel1(), and loadWeights().

ANN_Vector protocols::sparta::ANN::BL2_3

Referenced by calcLevel1(), and loadWeights().

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

Referenced by loadWeightBias3().

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

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

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

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

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

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

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

Referenced by ANN(), init(), and loadWeights().

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

Referenced by ANN(), init(), and loadWeights().

int protocols::sparta::ANN::input_code

Referenced by ANN(), init(), and set_input_code().

int protocols::sparta::ANN::N1_NODE_H

Referenced by ANN(), init(), and loadWeights().

int protocols::sparta::ANN::N1_NODE_I

Referenced by ANN(), init(), and loadWeights().

int protocols::sparta::ANN::N1_NODE_O

Referenced by ANN(), init(), and loadWeights().

int protocols::sparta::ANN::N2_NODE_H

Referenced by ANN(), and init().

int protocols::sparta::ANN::N2_NODE_I

Referenced by ANN(), and init().

int protocols::sparta::ANN::N2_NODE_O

Referenced by ANN(), and init().

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

Referenced by getSlashChar(), and loadWeights().

ANN_Matrix protocols::sparta::ANN::W2I_1

Referenced by calcLevel2().

ANN_Matrix protocols::sparta::ANN::W2I_2

Referenced by calcLevel2().

ANN_Matrix protocols::sparta::ANN::W2I_3

Referenced by calcLevel2().

ANN_Matrix protocols::sparta::ANN::W2L1_1

Referenced by calcLevel2().

ANN_Matrix protocols::sparta::ANN::W2L1_2

Referenced by calcLevel2().

ANN_Matrix protocols::sparta::ANN::W2L1_3

Referenced by calcLevel2().

ANN_Matrix protocols::sparta::ANN::W2L2_1

Referenced by calcLevel2().

ANN_Matrix protocols::sparta::ANN::W2L2_2

Referenced by calcLevel2().

ANN_Matrix protocols::sparta::ANN::W2L2_3

Referenced by calcLevel2().

ANN_Matrix protocols::sparta::ANN::WI_1

Referenced by calcLevel1(), and loadWeights().

ANN_Matrix protocols::sparta::ANN::WI_2

Referenced by calcLevel1(), and loadWeights().

ANN_Matrix protocols::sparta::ANN::WI_3

Referenced by calcLevel1(), and loadWeights().

ANN_Matrix protocols::sparta::ANN::WL1_1

Referenced by calcLevel1(), and loadWeights().

ANN_Matrix protocols::sparta::ANN::WL1_2

Referenced by calcLevel1(), and loadWeights().

ANN_Matrix protocols::sparta::ANN::WL1_3

Referenced by calcLevel1(), and loadWeights().

ANN_Matrix protocols::sparta::ANN::WL2_1

Referenced by calcLevel1(), and loadWeights().

ANN_Matrix protocols::sparta::ANN::WL2_2

Referenced by calcLevel1(), and loadWeights().

ANN_Matrix protocols::sparta::ANN::WL2_3

Referenced by calcLevel1(), and loadWeights().

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

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