Classes
class	ChemistryBase

class	Reprotonate

Typedefs
typedef utility::pointer::shared_ptr< ChemistryBase >	ChemistryBaseOP

typedef utility::pointer::shared_ptr< ChemistryBase const >	ChemistryBaseCOP

typedef utility::pointer::shared_ptr< Reprotonate >	ReprotonateOP

Enumerations
enum	ChemistryStatus { SUCCESS = 0 , FAIL_RETRY , FAIL_DO_NOT_RETRY , FAIL_BAD_INPUT , FAIL_BAD_SETTINGS }
	What was the status of the last call to apply (or get_additional_output) More...

Functions
static basic::Tracer	TR ("core.chemical.modifications.Reprotonate")

std::string	get_new_hydrogen_name (MutableResidueType &res)
	Comes up with a new name for a hydrogen to add. (One that isn't used.) More...

core::Size	add_hydrogens_to_atom (MutableResidueType &res, VD atom_vd)
	Add hydrogens to the given Atom, based on existing geometry and Gasteiger atom type Returns the number of hydrogens added. More...

static basic::Tracer	TR ("core.chemical.modifications.ValenceHandler")

utility::vector1< numeric::xyzVector< core::Real > >	determine_coordinates (core::chemical::MutableResidueType const &res, core::chemical::VD const &atom)

numeric::xyzVector< core::Real >	linear_coordinates (numeric::xyzVector< core::Real > const &vector_a, numeric::xyzVector< core::Real > const &vector_b, core::Real const distance_xa)
	calculates point X in B->A->X where A, B and X are on the same line More...

numeric::xyzVector< core::Real >	angle_coordinates (const numeric::xyzVector< core::Real > &VECTOR_A, const numeric::xyzVector< core::Real > &VECTOR_B, const numeric::xyzVector< core::Real > &VECTOR_C, const core::Real DISTANCE_XA, const core::Real ANGLE_XAB, const core::Real ANGLE_XAC, const bool SIDE, const numeric::xyzVector< core::Real > &VECTOR_SIDE)
	calculates coordinates using angle information (point X in B,C->A->X) More...

numeric::xyzVector< core::Real >	triganol_coordinates (const numeric::xyzVector< core::Real > &VECTOR_A, const numeric::xyzVector< core::Real > &VECTOR_B, const numeric::xyzVector< core::Real > &VECTOR_C, const double DISTANCE_XA)
	calculates the unit vector starting from one linal::Vector3D to another More...

numeric::xyzVector< core::Real >	tetrahedral_coordinates (const numeric::xyzVector< core::Real > &VECTOR_A, const numeric::xyzVector< core::Real > &VECTOR_B, const numeric::xyzVector< core::Real > &VECTOR_C, const numeric::xyzVector< core::Real > &VECTOR_D, const double DISTANCE_XA)
	calculates point X in B,C,D->A->X More...

double	projection_angle (const numeric::xyzVector< core::Real > &VECTOR_A, const numeric::xyzVector< core::Real > &VECTOR_B)
	calculates projection angle between two linal::Vector3D More...

double	projection_angle_cosin (const numeric::xyzVector< core::Real > &VECTOR_A, const numeric::xyzVector< core::Real > &VECTOR_B)

double	dihedral_coordinates (const numeric::xyzVector< core::Real > &VECTOR_A, const numeric::xyzVector< core::Real > &VECTOR_B, const numeric::xyzVector< core::Real > &VECTOR_C, const numeric::xyzVector< core::Real > &VECTOR_D)
	dihedral angle between four points (A->B -x-> C->D) More...

Typedef Documentation

◆ ChemistryBaseCOP

typedef utility::pointer::shared_ptr<ChemistryBase const> core::chemical::modifications::ChemistryBaseCOP

◆ ChemistryBaseOP

typedef utility::pointer::shared_ptr<ChemistryBase> core::chemical::modifications::ChemistryBaseOP

◆ ReprotonateOP

typedef utility::pointer::shared_ptr< Reprotonate > core::chemical::modifications::ReprotonateOP

Enumeration Type Documentation

◆ ChemistryStatus

enum core::chemical::modifications::ChemistryStatus

What was the status of the last call to apply (or get_additional_output)

Enumerator
SUCCESS
FAIL_RETRY
FAIL_DO_NOT_RETRY
FAIL_BAD_INPUT
FAIL_BAD_SETTINGS

Function Documentation

◆ add_hydrogens_to_atom()

core::Size core::chemical::modifications::add_hydrogens_to_atom	(	MutableResidueType &	res,
		VD	atom_vd
	)

Add hydrogens to the given Atom, based on existing geometry and Gasteiger atom type Returns the number of hydrogens added.

References core::chemical::MutableResidueType::add_atom(), core::chemical::MutableResidueType::add_bond(), core::chemical::MutableResidueType::atom(), core::chemical::MutableResidueType::atom_name(), protocols::simple_filters::coords(), determine_coordinates(), core::chemical::ElementSet::element(), core::chemical::ResidueTypeBase::element_set(), core::chemical::Atom::element_type(), core::chemical::Atom::gasteiger_atom_type(), get_new_hydrogen_name(), core::chemical::element::H, core::chemical::Atom::ideal_xyz(), core::chemical::MutableResidueType::number_bonded_hydrogens(), core::chemical::SingleBond, and TR().

Referenced by core::chemical::modifications::Reprotonate::apply().

◆ angle_coordinates()

numeric::xyzVector<core::Real> core::chemical::modifications::angle_coordinates	(	const numeric::xyzVector< core::Real > &	VECTOR_A,
		const numeric::xyzVector< core::Real > &	VECTOR_B,
		const numeric::xyzVector< core::Real > &	VECTOR_C,
		const core::Real	DISTANCE_XA,
		const core::Real	ANGLE_XAB,
		const core::Real	ANGLE_XAC,
		const bool	SIDE,
		const numeric::xyzVector< core::Real > &	VECTOR_SIDE
	)

calculates coordinates using angle information (point X in B,C->A->X)

Parameters

VECTOR_A	first point
VECTOR_B	second point
VECTOR_C	third point
DISTANCE_XA	distance between X and VECTOR_A
ANGLE_XAB	angle between X, VECTOR_A, and VECTOR_B
ANGLE_XAC	angle between X, VECTOR_A, and VECTOR_C
SIDE	true if on a side
VECTOR_SIDE	vector of the side

Returns: point X in B,C->A->X

References core::pose::motif::a(), protocols::match::upstream::b, dihedral_coordinates(), protocols::mean_field::max(), and projection_angle().

Referenced by determine_coordinates().

◆ determine_coordinates()

utility::vector1< numeric::xyzVector< core::Real > > core::chemical::modifications::determine_coordinates	(	core::chemical::MutableResidueType const &	res,
		core::chemical::VD const &	atom
	)

References angle_coordinates(), core::chemical::MutableResidueType::atom(), core::chemical::MutableResidueType::atom_name(), core::chemical::MutableResidueType::bonded_neighbor_iterators(), core::chemical::Atom::gasteiger_atom_type(), core::chemical::Atom::ideal_xyz(), linear_coordinates(), core::chemical::Atom::name(), core::chemical::gasteiger::GasteigerAtomTypeData::SP, core::chemical::gasteiger::GasteigerAtomTypeData::SP2, tetrahedral_coordinates(), TR(), triganol_coordinates(), and core::chemical::gasteiger::GasteigerAtomTypeData::Unhybridized.

Referenced by add_hydrogens_to_atom(), and protocols::drug_design::RandomFragmentLigand::apply().

◆ dihedral_coordinates()

double core::chemical::modifications::dihedral_coordinates	(	const numeric::xyzVector< core::Real > &	VECTOR_A,
		const numeric::xyzVector< core::Real > &	VECTOR_B,
		const numeric::xyzVector< core::Real > &	VECTOR_C,
		const numeric::xyzVector< core::Real > &	VECTOR_D
	)

dihedral angle between four points (A->B -x-> C->D)

see http://en.wikipedia.org/wiki/Dihedral_angle for reference

Parameters

VECTOR_A	first vector (point)
VECTOR_B	second vector (point)
VECTOR_C	third vector (point)
VECTOR_D	fourth vector (point)

Returns: dihedral angle between four points

References core::kinematics::distance().

Referenced by angle_coordinates().

◆ get_new_hydrogen_name()

std::string core::chemical::modifications::get_new_hydrogen_name ( MutableResidueType & res )

Comes up with a new name for a hydrogen to add. (One that isn't used.)

References core::chemical::MutableResidueType::has(), and core::id::to_string().

Referenced by add_hydrogens_to_atom().

◆ linear_coordinates()

numeric::xyzVector<core::Real> core::chemical::modifications::linear_coordinates	(	numeric::xyzVector< core::Real > const &	vector_a,
		numeric::xyzVector< core::Real > const &	vector_b,
		core::Real const	distance_xa
	)

calculates point X in B->A->X where A, B and X are on the same line

point X in B->A->X where A, B and X are on the same line

Parameters

VECTOR_A	first point
VECTOR_B	second point
DISTANCE_XA	distance between X and VECTOR_A

Returns: point X in B->A->X where A, B and X are on the same line

Referenced by determine_coordinates().

◆ projection_angle()

double core::chemical::modifications::projection_angle	(	const numeric::xyzVector< core::Real > &	VECTOR_A,
		const numeric::xyzVector< core::Real > &	VECTOR_B
	)

calculates projection angle between two linal::Vector3D

Parameters

VECTOR_A	first vector (point)
VECTOR_B	second vector (point)

Returns: projection angle between two linal::Vector3D

References projection_angle_cosin().

Referenced by angle_coordinates().

◆ projection_angle_cosin()

double core::chemical::modifications::projection_angle_cosin	(	const numeric::xyzVector< core::Real > &	VECTOR_A,
		const numeric::xyzVector< core::Real > &	VECTOR_B
	)

Referenced by projection_angle().

◆ tetrahedral_coordinates()

numeric::xyzVector<core::Real> core::chemical::modifications::tetrahedral_coordinates	(	const numeric::xyzVector< core::Real > &	VECTOR_A,
		const numeric::xyzVector< core::Real > &	VECTOR_B,
		const numeric::xyzVector< core::Real > &	VECTOR_C,
		const numeric::xyzVector< core::Real > &	VECTOR_D,
		const double	DISTANCE_XA
	)

calculates point X in B,C,D->A->X

point X in B,C,D->A->X

Parameters

VECTOR_A	first point
VECTOR_B	second point
VECTOR_C	third point
VECTOR_D	fourth point
DISTANCE_XA	distance between X and VECTOR_A

Returns: point X in B,C,D->A->X

Referenced by determine_coordinates().

◆ TR() [1/2]

static basic::Tracer core::chemical::modifications::TR ( "core.chemical.modifications.Reprotonate" )

static

Referenced by add_hydrogens_to_atom(), core::chemical::modifications::Reprotonate::apply(), and determine_coordinates().

◆ TR() [2/2]

static basic::Tracer core::chemical::modifications::TR ( "core.chemical.modifications.ValenceHandler" )

static

◆ triganol_coordinates()

numeric::xyzVector<core::Real> core::chemical::modifications::triganol_coordinates	(	const numeric::xyzVector< core::Real > &	VECTOR_A,
		const numeric::xyzVector< core::Real > &	VECTOR_B,
		const numeric::xyzVector< core::Real > &	VECTOR_C,
		const double	DISTANCE_XA
	)

calculates the unit vector starting from one linal::Vector3D to another

Parameters

ORIGIN	vector of origin
TARGET	target vector

Returns: the unit vector between ORIGIN and TARGET

Referenced by determine_coordinates().

Classes

Typedefs

Enumerations

Functions

Typedef Documentation

◆ ChemistryBaseCOP

◆ ChemistryBaseOP

◆ ReprotonateOP

Enumeration Type Documentation

◆ ChemistryStatus

Function Documentation

◆ add_hydrogens_to_atom()

◆ angle_coordinates()

◆ determine_coordinates()

◆ dihedral_coordinates()

◆ get_new_hydrogen_name()

◆ linear_coordinates()

◆ projection_angle()

◆ projection_angle_cosin()

◆ tetrahedral_coordinates()

◆ TR() [1/2]

◆ TR() [2/2]

◆ triganol_coordinates()