Classes
class	LeGrandSasa
	LeGrand SASA approximation method Used by SasaCalc but can be used by itself. More...

class	SasaCalc
	Main interface to sasa calculations outside of pose metrics. More...

class	SasaMethod
	Abstract base class for SasaMethods. Feel free to edit as needed. More...

Enumerations
enum	SasaRadii { LJ = 1, legacy, naccess, reduce, chothia =naccess, SasaRadii_total = reduce }
	Type of Radii to use. More...

enum	SasaMethodEnum { LeGrand = 1, SasaMethodType_total = LeGrand }

Functions
SasaMethodOP	create_sasa_method (SasaMethodEnum method, core::Real probe_radius, SasaRadii radii_set)
	Very (very) basic implementation until I understand the regular implementation used by constraints/features/etc. Also used for me to debug everything else before creating the real factory. More...

std::pair< Real, Real >	get_sc_bb_sasa (const pose::Pose &pose, const id::AtomID_Map< Real > &atom_sasa)
	Calculate the sidechain and backbone sasa from atom sasa. More...

std::pair< utility::vector1 < Real >, utility::vector1 < Real > >	get_sc_bb_sasa_per_res (const pose::Pose &pose, const id::AtomID_Map< Real > &atom_sasa)

SasaMethodEnum	get_sasa_method_from_string (std::string method)
	Gets sasa enum from string passed by options system. More...

std::string	get_sasa_radii_parameter_name (SasaRadii radii_set)
	Get string name of SASA radii used to obtain extra parameter index from atom_type_set. More...

SasaRadii	get_sasa_radii_set_from_string (std::string radii_set)
	Gets sasa radii enum from string passed by options system. More...

ObjexxFCL::FArray2D_int	angles (num_phi, num_theta)

ObjexxFCL::FArray2D_ubyte	masks (num_bytes, num_overlaps *num_orientations)

ObjexxFCL::FArray2D_ubyte const &	get_legrand_sasa_masks ()
	Returns const access to the masks FArray, which contains the information in the SASA database file sampling/SASA-masks.dat. Adding this in so that the values in the SASA database files can be used in SASA-based scores. (ronj) More...

ObjexxFCL::FArray2D_int const &	get_legrand_sasa_angles ()
	Returns const access to the angles FArray, which contains the information in the SASA database file sampling/SASA-angles.dat. Adding this in so that the values in the SASA database files can be used in SASA-based scores. (ronj) More...

void	input_legrand_sasa_dats ()
	Reads in the SASA database files sampling/SASA-angles.dat and sampling/SASA-masks.dat into FArrays above. More...

void	get_legrand_atomic_overlap (Real const radius_a, Real const radius_b, Real const distance_ijxyz, int &degree_of_overlap)

void	get_legrand_orientation (Vector const &a_xyz, Vector const &b_xyz, int &phi_index, int &theta_index, Real distance_ijxyz)
	Gets the orientation of a to b (i to j, see below). Does this by calculating two angles, aphi and theta. (j) More...

void	get_legrand_2way_orientation (Vector const &a_xyz, Vector const &b_xyz, int &phi_a2b_index, int &theta_a2b_index, int &phi_b2a_index, int &theta_b2a_index, Real distance_ijxyz)
	Gets the orientation of a to b (i to j, see below). Does this by calculating two angles, aphi and theta. (j) More...

Variables
int const	num_bytes = 21

int const	num_phi = 64

int const	num_theta = 64

int const	num_overlaps = 100

int const	num_orientations = 162

Typedef Documentation

typedef utility::pointer::owning_ptr< LeGrandSasa const> core::scoring::sasa::LeGrandSasaCOP

typedef utility::pointer::owning_ptr< LeGrandSasa> core::scoring::sasa::LeGrandSasaOP

typedef utility::pointer::owning_ptr< SasaCalc const> core::scoring::sasa::SasaCalcCOP

typedef utility::pointer::owning_ptr< SasaCalc> core::scoring::sasa::SasaCalcOP

typedef utility::pointer::owning_ptr< SasaMethod const> core::scoring::sasa::SasaMethodCOP

typedef utility::pointer::owning_ptr< SasaMethod> core::scoring::sasa::SasaMethodOP

Enumeration Type Documentation

enum core::scoring::sasa::SasaMethodEnum

Enumerator
LeGrand
SasaMethodType_total

enum core::scoring::sasa::SasaRadii

Type of Radii to use.

LJ: Refers to Leonard Jones radii - Rosetta uses radii at the minimum of the potential (sigma2). Legacy: Refers to radii optimized for a no longer in use term, but some protocols have been optimized to use it. naccess: Refers to radii used in the program naccess. Originally derived from Chothia. Do not use for all-atom SASA as hydrogens are implicitly included. 'The Nature of the Accessible and Buried Surfaces in Proteins' J. Mol. Biol. (1976) 105, 1-14 reduce: Radii used by the program reduce. Hydrogens are explicitly included in the radii.

Enumerator
LJ
legacy
naccess
reduce
chothia
SasaRadii_total

Function Documentation

ObjexxFCL::FArray2D_int core::scoring::sasa::angles	(	num_phi	,
		num_theta
	)

Referenced by get_legrand_sasa_angles(), and input_legrand_sasa_dats().

SasaMethodOP core::scoring::sasa::create_sasa_method	(	SasaMethodEnum	,
		core::Real	probe_radius,
		SasaRadii	radii_set
	)

Very (very) basic implementation until I understand the regular implementation used by constraints/features/etc. Also used for me to debug everything else before creating the real factory.

Referenced by core::scoring::sasa::SasaCalc::setup_sasa_method().

void core::scoring::sasa::get_legrand_2way_orientation	(	Vector const &	a_xyz,
		Vector const &	b_xyz,
		int &	phi_a2b_index,
		int &	theta_a2b_index,
		int &	phi_b2a_index,
		int &	theta_b2a_index,
		Real	distance_ijxyz
	)

Gets the orientation of a to b (i to j, see below). Does this by calculating two angles, aphi and theta. (j)

sasa.cc::get_2way_orientation

Detailed:: ronj This function is the same as the function above but get the orientation of a to b simultaneously with the ronj orientation of b to a. The same result could be achieved by making two separate get_legrand_2way_orientation() calls ronj but this method does it more efficiently by avoiding an atan2 and acos call. Instead, once you compute the ronj phi and theta for a on b, you can add/subtrate pi factors to get the phi and theta for b on a. ronj Still not sure how this method returns the correct values, though.

Detailed:: This function is the same as the function above but get the orientation of a to b simultaneously with the orientation of b to a. The same result could be achieved by making two separate get_2way_orientation() calls but this method does it more efficiently by avoiding an atan2 and acos call. Instead, once you compute the phi and theta for a on b, you can add/subtrate pi factors to get the phi and theta for b on a. Still not sure how this method returns the correct values, though. (ronj)

References num_phi, num_theta, pi_2, numeric::sin_cos_range(), and sin_cos_range().

Referenced by core::pack::interaction_graph::RotamerDots::get_atom_atom_coverage(), core::pack::interaction_graph::InvRotamerDots::overlap_exposed(), and core::pack::interaction_graph::InvRotamerDots::write_circle_intersection_mask_to_kinemage().

void core::scoring::sasa::get_legrand_atomic_overlap	(	Real const	radius_a,
		Real const	radius_b,
		Real const	distance_ijxyz,
		int &	degree_of_overlap
	)

sasa.cc::get_overlap

Detailed:: getting overlap from a to b (or i to j, as the atoms are referred to in calc_per_atom_sasa below). this returns the degree of overlap between two atoms adapted from erics code in area.c GetD2 and returns value from 1 to 100. This calculation is based on the law of cosines. See LeGrand and Merz, Journal of Computational Chemistry 14(3):349-52 (1993). Note that equation (4) is wrong, the denominator should be 2*ri*riq instead of 2*ri*rq (j)

The function gets passed in the sasa radius of atom i (plus the probe radius), the sasa radius of atom j (plus the probe radius), the distance between the atom centers, and a reference to the degree of overlap (represented as an int). The degree of overlap that's returned can be thought of as how much of atom a is covered by atom b. A value of 100 means that atom a is completely covered up by atom b. A value of 1 means that not much of the surface of 'a' is covered up by 'b'. The law of cosines relates the cosine of one angle of a triangle to the lengths of its sides. More specifically, c^2 = a^2 + b^2 - 2*a*b*cos theta, where theta is the angle between sides a and b. For the function we want to compute the angle of the cone of intersection between spheres 'a' and 'b'. Let the radius of atom a be ri, and the radius of atom b be rq, and the distance between atom centers be riq. Let the angle between ri and riq be theta_iq. The cosine of theta_iq will be equivalent to ( ri^2 + riq^2 - rq^2 ) / 2 * ri * riq

getting overlap from a to b (or i to j, as the atoms are referred to in calc_per_atom_sasa below). this returns the degree of overlap between two atoms adapted from erics code in area.c GetD2 and returns value from 1 to 100. This calculation is based on the law of cosines. See LeGrand and Merz, Journal of Computational Chemistry 14(3):349-52 (1993). Note that equation (4) is wrong, the denominator should be 2*ri*riq instead of 2*ri*rq (j)

The function gets passed in the sasa radius of atom i (plus the probe radius), the sasa radius of atom j (plus the probe radius), the distance between the atom centers, and a reference to the degree of overlap (represented as an int). The degree of overlap that's returned can be thought of as how much of atom a is covered by atom b. A value of 100 means that atom a is completely covered up by atom b. A value of 1 means that not much of the surface of 'a' is covered up by 'b'. The law of cosines relates the cosine of one angle of a triangle to the lengths of its sides. More specifically, c^2 = a^2 + b^2 - 2*a*b*cos theta, where theta is the angle between sides a and b. For the function we want to compute the angle of the cone of intersection between spheres 'a' and 'b'. Let the radius of atom a be ri, and the radius of atom b be rq, and the distance between atom centers be riq. Let the angle between ri and riq be theta_iq. The cosine of theta_iq will be equivalent to ( ri^2 + riq^2 - rq^2 ) / 2 * ri * riq

References epsilon, and utility::exit().

Referenced by core::pack::interaction_graph::RotamerDots::get_atom_atom_coverage(), core::pack::interaction_graph::HPatchNode< V, E, G >::initialize_atom_atom_overlap_cache(), core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::initialize_atom_atom_overlaps(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::initialize_bg_bg_atom_atom_overlaps(), core::pack::interaction_graph::InvRotamerDots::overlap_exposed(), and core::pack::interaction_graph::InvRotamerDots::write_circle_intersection_mask_to_kinemage().

void core::scoring::sasa::get_legrand_orientation	(	Vector const &	a_xyz,
		Vector const &	b_xyz,
		int &	phi_index,
		int &	theta_index,
		Real	distance_ijxyz
	)

Gets the orientation of a to b (i to j, see below). Does this by calculating two angles, aphi and theta. (j)

sasa.cc::get_orientation

Detailed:: ronj This function is used to get two indexes (phi and theta) which are used to get the index of a dot on the ronj surface of the 'a' sphere. When calculating how much surface area sphere b covers on a, we can get the degree ronj of overlap from the function above, but it's not necessarily the case that the vector that connects the center ronj of atom 'a' and atom 'b' goes through one of the predetermined dot locations on the surface of 'a'. In fact, ronj it's very unlikely that the vector goes through a predetermined dot. Instead, what is done is the actual point ronj of intersection (the outermost point of a on the line from the center of 'a' to center of 'b') is converted ronj to spherical polar coordinates. Then, the values are used to find the location of the closest predetermined ronj point on the surface of 'a' using a lookup table. So what this function needs to do is convert the ronj cartesian coordinate of the actual point of intersection into polar coordinates. ronj ronj To get the spherical, polar coordinates of a cartesian point x,y,z, use these equations: ronj r = sqrt( x^2 + y^2 + z^2 ) ronj theta = arccos( z / r ) ronj phi = arctan( y / x )

ronj Then, once we have the true phi and theta, we need to translate this into an index (or offset) for the correct ronj value in the database file. There are 64 phi angle bin and 64 theta bins in the database file sampling/SASA-angles.dat. ronj We need to convert the phi and theta into indexes for this file by multiplying them by num_phi / 2*pi. ronj Note: I think phi and theta have been reversed in the function below. The code below uses the following: ronj phi = arccos( z ) ronj theta = arctan( y / x )

ronj After a couple of weeks trying to write tests for this function, I have been unsuccessful in figuring out why ronj it's doing what it does. Despite using the wrong equations, it seems to work. Comparing the total residue ronj SASA values calculated by calc_per_atom_sasa() below results in a correlation of 0.98 against what the program ronj NACCESS finds for the same residues. This test was done on a small 110aa protein. I also looked at the per-atom ronj total SASA and the correlation for all atoms (mini v. NACCESS) was approximately 0.94. I'm using exactly the same ronj van der Waals radii for both programs so I feel like the correlations should be 1.0. Explanations for the ronj differences can be 1) this method is doing something wrong in calculating the closest surface point, 2) this ronj method is correct but the masks that are in the database are not aligned to the surface points correctly, 3) the ronj differences are solely due to the different way that the two program calculate surface area.

Detailed:: This function is used to get two indexes (phi and theta) which are used to get the index of a dot on the surface of the 'a' sphere. When calculating how much surface area sphere b covers on a, we can get the degree of overlap from the function above, but it's not necessarily the case that the vector that connects the center of atom 'a' and atom 'b' goes through one of the predetermined dot locations on the surface of 'a'. In fact, it's very unlikely that the vector goes through a predetermined dot. Instead, what is done is the actual point of intersection (the outermost point of a on the line from the center of 'a' to center of 'b') is converted to spherical polar coordinates. Then, the values are used to find the location of the closest predetermined point on the surface of 'a' using a lookup table. So what this function needs to do is convert the cartesian coordinate of the actual point of intersection into polar coordinates.

To get the spherical, polar coordinates of a cartesian point x,y,z, use these equations: r = sqrt( x^2 + y^2 + z^2 ) theta = arccos( z / r ) phi = arctan( y / x )

Then, once we have the true phi and theta, we need to translate this into an index (or offset) for the correct value in the database file. There are 64 phi angle bin and 64 theta bins in the database file sampling/SASA-angles.dat. We need to convert the phi and theta into indexes for this file by multiplying them by num_phi / 2*pi. Note: I think phi and theta have been reversed in the function below. The code below uses the following: phi = arccos( z ) theta = arctan( y / x )

After a couple of weeks trying to write tests for this function, I have been unsuccessful in figuring out why it's doing what it does. Despite using the wrong equations, it seems to work. Comparing the total residue SASA values calculated by calc_per_atom_sasa() below results in a correlation of 0.98 against what the program NACCESS finds for the same residues. This test was done on a small 110aa protein. I also looked at the per-atom total SASA and the correlation for all atoms (mini v. NACCESS) was approximately 0.94. I'm using exactly the same van der Waals radii for both programs so I feel like the correlations should be 1.0. Explanations for the differences can be 1) this method is doing something wrong in calculating the closest surface point, 2) this method is correct but the masks that are in the database are not aligned to the surface points correctly, 3) the differences are solely due to the different way that the two program calculate surface area. (ronj)

References num_phi, num_theta, pi_2, numeric::sin_cos_range(), and sin_cos_range().

ObjexxFCL::FArray2D_int const & core::scoring::sasa::get_legrand_sasa_angles ( )

Returns const access to the angles FArray, which contains the information in the SASA database file sampling/SASA-angles.dat. Adding this in so that the values in the SASA database files can be used in SASA-based scores. (ronj)

Return total SASA for side chains. : Uses Naccess radii by default for all atom. Not for general use. Values returned used to generate SVM for ProQ/ProQ2.

get_angles

Returns const access to the angles FArray, which contains the information in the SASA database file sampling/SASA-angles.dat. Adding this in so that the values in the SASA database files can be used in SASA-based scores. (ronj)

References angles(), and input_legrand_sasa_dats().

Referenced by core::pack::interaction_graph::RotamerDots::initialize_sasa_arrays().

ObjexxFCL::FArray2D_ubyte const & core::scoring::sasa::get_legrand_sasa_masks ( )

Returns const access to the masks FArray, which contains the information in the SASA database file sampling/SASA-masks.dat. Adding this in so that the values in the SASA database files can be used in SASA-based scores. (ronj)

get_masks

References input_legrand_sasa_dats(), and masks().

Referenced by core::pack::interaction_graph::RotamerDots::initialize_sasa_arrays().

SasaMethodEnum core::scoring::sasa::get_sasa_method_from_string ( std::string method )

Gets sasa enum from string passed by options system.

Enum Management. Can go in separate file if it gets large.

References LeGrand.

Referenced by core::scoring::sasa::SasaCalc::set_defaults().

std::string core::scoring::sasa::get_sasa_radii_parameter_name ( SasaRadii radii_set )

Get string name of SASA radii used to obtain extra parameter index from atom_type_set.

References chothia, legacy, LJ, naccess, reduce, and SasaRadii_total.

Referenced by core::scoring::sasa::LeGrandSasa::calculate().

SasaRadii core::scoring::sasa::get_sasa_radii_set_from_string ( std::string radii_set )

Gets sasa radii enum from string passed by options system.

References chothia, legacy, LJ, naccess, and reduce.

Referenced by core::scoring::sasa::SasaCalc::set_defaults().

std::pair< Real, Real > core::scoring::sasa::get_sc_bb_sasa	(	const pose::Pose &	pose,
		const id::AtomID_Map< Real > &	atom_sasa
	)

Calculate the sidechain and backbone sasa from atom sasa.

Convenience Functions

References core::chemical::ResidueType::all_bb_atoms(), core::chemical::ResidueType::all_sc_atoms(), core::id::AtomID_Map< T >::n_residue(), and core::pose::Pose::residue_type().

std::pair< utility::vector1< Real >, utility::vector1< Real > > core::scoring::sasa::get_sc_bb_sasa_per_res	(	const pose::Pose &	pose,
		const id::AtomID_Map< Real > &	atom_sasa
	)

References core::chemical::ResidueType::all_bb_atoms(), core::chemical::ResidueType::all_sc_atoms(), core::id::AtomID_Map< T >::n_residue(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

void core::scoring::sasa::input_legrand_sasa_dats ( )

Reads in the SASA database files sampling/SASA-angles.dat and sampling/SASA-masks.dat into FArrays above.

sasa.cc::input_sasa_dats

References angles(), utility::io::izstream::close(), basic::database::full_name(), core::init::init(), masks(), num_bytes, num_orientations, num_overlaps, num_phi, num_theta, and skip.

Referenced by get_legrand_sasa_angles(), and get_legrand_sasa_masks().

ObjexxFCL::FArray2D_ubyte core::scoring::sasa::masks	(	num_bytes	,
		num_overlaps *	num_orientations
	)

Referenced by get_legrand_sasa_masks(), and input_legrand_sasa_dats().

Variable Documentation

int const core::scoring::sasa::num_bytes = 21

Referenced by input_legrand_sasa_dats().

int const core::scoring::sasa::num_orientations = 162

Referenced by input_legrand_sasa_dats().

int const core::scoring::sasa::num_overlaps = 100

Referenced by input_legrand_sasa_dats().

int const core::scoring::sasa::num_phi = 64

Referenced by get_legrand_2way_orientation(), get_legrand_orientation(), and input_legrand_sasa_dats().

int const core::scoring::sasa::num_theta = 64

Referenced by get_legrand_2way_orientation(), get_legrand_orientation(), and input_legrand_sasa_dats().

Typedefs
typedef utility::pointer::owning_ptr < LeGrandSasa >	LeGrandSasaOP

typedef utility::pointer::owning_ptr < LeGrandSasa const >	LeGrandSasaCOP

typedef utility::pointer::owning_ptr < SasaCalc >	SasaCalcOP

typedef utility::pointer::owning_ptr < SasaCalc const >	SasaCalcCOP

typedef utility::pointer::owning_ptr < SasaMethod >	SasaMethodOP

typedef utility::pointer::owning_ptr < SasaMethod const >	SasaMethodCOP

Classes

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation