core::scoring::bin_transitions Namespace Reference

Classes
class	BinTransitionCalculator
class	BinTransitionCalculatorManager
	A static singleton that ensures that BinTransitionCalculators load data from disk once, lazily, and in a threadsafe manner. More...
class	BinTransitionData

Typedefs
typedef utility::pointer::shared_ptr< BinTransitionCalculator >	BinTransitionCalculatorOP
typedef utility::pointer::shared_ptr< BinTransitionCalculator const >	BinTransitionCalculatorCOP
typedef utility::vector1< BinTransitionCalculatorOP >	BinTransitionCalculatorOPs
typedef utility::vector1< BinTransitionCalculatorCOP >	BinTransitionCalculatorCOPs
using	BinTransitionCalculatorManagerOP = utility::pointer::shared_ptr< BinTransitionCalculatorManager >
using	BinTransitionCalculatorManagerCOP = utility::pointer::shared_ptr< BinTransitionCalculatorManager const >
typedef utility::pointer::shared_ptr< BinTransitionData >	BinTransitionDataOP
typedef utility::pointer::shared_ptr< BinTransitionData const >	BinTransitionDataCOP
typedef utility::vector1< BinTransitionDataOP >	BinTransitionDataOPs
typedef utility::vector1< BinTransitionDataCOP >	BinTransitionDataCOPs

Enumerations
enum	BT_PROPERTIES {   BT_PROTEIN =1 , BT_L_AA , BT_D_AA , BT_ALPHA_AA ,   BT_BETA_AA , BT_POLAR , BT_METALBINDING , BT_CHARGED ,   BT_AROMATIC , BT_DISULFIDE_BONDED , BT_SIDECHAIN_THIOL , BT_CYCLIC ,   BT_UNKNOWN_PROPERTY , BT_END_OF_LIST }
	Enum for the properties that can be required or prohibited at the i or i+1 position. More...
enum	BTSB_SUBBIN_TYPE {   BTSB_NONE =1 , BTSB_L_AA , BTSB_D_AA , BTSB_L_PRO ,   BTSB_D_PRO , BTSB_GLY , BTSB_UNKNOWN , BTSB_END_OF_LIST }
	Enum for the way in which bins will be divided into subbins. More...

Functions
static basic::Tracer	TR ("core.scoring.bin_transitions.BinTransitionCalculator")
BinTransitionCalculatorOP	deep_copy (BinTransitionCalculator const &src)
static basic::Tracer	TR ("core.scoring.bin_transitions.BinTransitionData")

Typedef Documentation

BinTransitionCalculatorCOP

typedef utility::pointer::shared_ptr< BinTransitionCalculator const > core::scoring::bin_transitions::BinTransitionCalculatorCOP

BinTransitionCalculatorCOPs

typedef utility::vector1<BinTransitionCalculatorCOP> core::scoring::bin_transitions::BinTransitionCalculatorCOPs

BinTransitionCalculatorManagerCOP

using core::scoring::bin_transitions::BinTransitionCalculatorManagerCOP = typedef utility::pointer::shared_ptr< BinTransitionCalculatorManager const >

BinTransitionCalculatorManagerOP

using core::scoring::bin_transitions::BinTransitionCalculatorManagerOP = typedef utility::pointer::shared_ptr< BinTransitionCalculatorManager >

BinTransitionCalculatorOP

typedef utility::pointer::shared_ptr< BinTransitionCalculator > core::scoring::bin_transitions::BinTransitionCalculatorOP

BinTransitionCalculatorOPs

typedef utility::vector1<BinTransitionCalculatorOP> core::scoring::bin_transitions::BinTransitionCalculatorOPs

BinTransitionDataCOP

typedef utility::pointer::shared_ptr< BinTransitionData const > core::scoring::bin_transitions::BinTransitionDataCOP

BinTransitionDataCOPs

typedef utility::vector1<BinTransitionDataCOP> core::scoring::bin_transitions::BinTransitionDataCOPs

BinTransitionDataOP

typedef utility::pointer::shared_ptr< BinTransitionData > core::scoring::bin_transitions::BinTransitionDataOP

BinTransitionDataOPs

typedef utility::vector1<BinTransitionDataOP> core::scoring::bin_transitions::BinTransitionDataOPs

Enumeration Type Documentation

BT_PROPERTIES

enum core::scoring::bin_transitions::BT_PROPERTIES

Enum for the properties that can be required or prohibited at the i or i+1 position.

These reflect properties that residues can have. Whenever a property is added, add it (1) here, (2) to the get_property_effect_name function, and (3) to the has_property function.

Enumerator
BT_PROTEIN
BT_L_AA
BT_D_AA
BT_ALPHA_AA
BT_BETA_AA
BT_POLAR
BT_METALBINDING
BT_CHARGED
BT_AROMATIC
BT_DISULFIDE_BONDED
BT_SIDECHAIN_THIOL
BT_CYCLIC
BT_UNKNOWN_PROPERTY
BT_END_OF_LIST

BTSB_SUBBIN_TYPE

enum core::scoring::bin_transitions::BTSB_SUBBIN_TYPE

Enum for the way in which bins will be divided into subbins.

Default is BTSB_NONE, which means that the bin has no subbins. As subbin types are added, add them (1) here, and (2) to the get_subbin_type_name function, and (3) to the setup_subbin_type function, then add a function called by the setup_subbin_type function.

Enumerator
BTSB_NONE
BTSB_L_AA
BTSB_D_AA
BTSB_L_PRO
BTSB_D_PRO
BTSB_GLY
BTSB_UNKNOWN
BTSB_END_OF_LIST

Function Documentation

deep_copy()

BinTransitionCalculatorOP core::scoring::bin_transitions::deep_copy

(

BinTransitionCalculator const &

src

)

References core::scoring::bin_transitions::BinTransitionCalculator::clone().

TR() [1/2]

static basic::Tracer core::scoring::bin_transitions::TR ( "core.scoring.bin_transitions.BinTransitionCalculator"  )

static

Referenced by core::scoring::bin_transitions::BinTransitionCalculator::has_another_matrix(), core::scoring::bin_transitions::BinTransitionCalculator::load_bin_params(), core::scoring::bin_transitions::BinTransitionCalculator::p_i_given_iplus1(), core::scoring::bin_transitions::BinTransitionCalculator::p_iplus1_given_i(), core::scoring::bin_transitions::BinTransitionCalculator::parse_lines(), core::scoring::bin_transitions::BinTransitionCalculator::populate_matrix(), core::scoring::bin_transitions::BinTransitionCalculator::random_bin_based_on_prev_and_next(), core::scoring::bin_transitions::BinTransitionData::set_n_bins(), core::scoring::bin_transitions::BinTransitionCalculator::set_up_bins(), and core::scoring::bin_transitions::BinTransitionData::which_bin_i().

TR() [2/2]

static basic::Tracer core::scoring::bin_transitions::TR ( "core.scoring.bin_transitions.BinTransitionData"  )

static