Core

The core functions to perform a calculation. More...

Data Structures
struct	freesasa_parameters
	Struct to store parameters for SASA calculation. More...
struct	freesasa_result
	Struct to store results of SASA calculation. More...

Macros
#define	FREESASA_DEF_ALGORITHM   FREESASA_LEE_RICHARDS
	Default algorithm. More...
#define	FREESASA_DEF_PROBE_RADIUS   1.4
	Default probe radius (in Ångström). More...
#define	FREESASA_DEF_SR_N   100
	Default number of test points in S&R. More...
#define	FREESASA_DEF_LR_N   20
	Default number of slices per atom in L&R. More...
#define	freesasa_default_classifier   freesasa_protor_classifier
	Default freesasa_classifier. More...

Enumerations
enum	freesasa_algorithm { FREESASA_LEE_RICHARDS , FREESASA_SHRAKE_RUPLEY }
	The FreeSASA algorithms. More...

Functions
freesasa_result *	freesasa_calc_structure (const freesasa_structure *structure, const freesasa_parameters *parameters)
	Calculates SASA based on a given structure. More...
freesasa_result *	freesasa_calc_coord (const double *xyz, const double *radii, int n, const freesasa_parameters *parameters)
	Calculates SASA based on a given set of coordinates and radii. More...
freesasa_node *	freesasa_calc_tree (const freesasa_structure *structure, const freesasa_parameters *parameters, const char *name)
	Calculates SASA for a structure and returns as a tree of freesasa_node. More...
freesasa_nodearea	freesasa_result_classes (const freesasa_structure *structure, const freesasa_result *result)
	Results by classes. More...
void	freesasa_result_free (freesasa_result *result)
	Frees a freesasa_result object. More...
int	freesasa_set_verbosity (freesasa_verbosity v)
	Set the global verbosity level. More...
freesasa_verbosity	freesasa_get_verbosity (void)
	Get the current verbosity level. More...
void	freesasa_set_err_out (FILE *err)
	Set where to write errors. More...
FILE *	freesasa_get_err_out (void)
	Get pointer to error file. More...

Variables
const int	FREESASA_DEF_NUMBER_THREADS
	Default number of threads. More...
const freesasa_parameters	freesasa_default_parameters
	The default parameters for FreeSASA.

Detailed Description

The core functions to perform a calculation.

Macro Definition Documentation

FREESASA_DEF_ALGORITHM

#define FREESASA_DEF_ALGORITHM   FREESASA_LEE_RICHARDS

Default algorithm.

Definition at line 115 of file freesasa.h.

FREESASA_DEF_PROBE_RADIUS

#define FREESASA_DEF_PROBE_RADIUS   1.4

Default probe radius (in Ångström).

Definition at line 116 of file freesasa.h.

FREESASA_DEF_SR_N

#define FREESASA_DEF_SR_N   100

Default number of test points in S&R.

Definition at line 117 of file freesasa.h.

FREESASA_DEF_LR_N

#define FREESASA_DEF_LR_N   20

Default number of slices per atom in L&R.

Definition at line 118 of file freesasa.h.

freesasa_default_classifier

#define freesasa_default_classifier   freesasa_protor_classifier

Default freesasa_classifier.

Definition at line 124 of file freesasa.h.

Enumeration Type Documentation

freesasa_algorithm

enum freesasa_algorithm

The FreeSASA algorithms.

Enumerator
FREESASA_LEE_RICHARDS	Lee & Richards' algorithm.
FREESASA_SHRAKE_RUPLEY	Shrake & Rupley's algorithm.

Definition at line 89 of file freesasa.h.

Function Documentation

freesasa_calc_structure()

freesasa_result * freesasa_calc_structure	(	const freesasa_structure *	structure,
		const freesasa_parameters *	parameters
	)

Calculates SASA based on a given structure.

This function allows direct access to the results array, for most users freesasa_calc_tree() is more appropriate.

Return value is dynamically allocated, should be freed with freesasa_result_free().

Parameters

structure	The structure
parameters	Parameters for the calculation, if NULL defaults are used.

Returns

The result of the calculation, NULL if something went wrong.

freesasa_calc_coord()

freesasa_result * freesasa_calc_coord	(	const double *	xyz,
		const double *	radii,
		int	n,
		const freesasa_parameters *	parameters
	)

Calculates SASA based on a given set of coordinates and radii.

Return value is dynamically allocated, should be freed with freesasa_result_free().

Parameters

xyz	Array of coordinates in the form x1,y1,z1,x2,y2,z2,...,xn,yn,zn.
radii	Radii, this array should have n elements..
n	Number of coordinates (i.e. xyz has size 3*n, radii size n).
parameters	Parameters for the calculation, if NULL defaults are used.

Returns

The result of the calculation, NULL if something went wrong.

freesasa_calc_tree()

freesasa_node * freesasa_calc_tree	(	const freesasa_structure *	structure,
		const freesasa_parameters *	parameters,
		const char *	name
	)

Calculates SASA for a structure and returns as a tree of freesasa_node.

Return value is dynamically allocated, should be freed with freesasa_node_free()

Parameters

structure	A structure
parameters	Parameters for the calculation, if NULL, defaults are used.
name	Name of input structure to be used in output.

Returns

The result of the calculation, NULL if something went wrong.

freesasa_result_classes()

freesasa_nodearea freesasa_result_classes	(	const freesasa_structure *	structure,
		const freesasa_result *	result
	)

Results by classes.

Adds up the SASA of Polar/Apolar/Unknown atoms, and main-chain/side-chain atoms for the whole protein. Uses the classes defined by the classifier used when generating the structure.

Parameters

structure	The structure the results are based on
result	The results

Returns

A struct with all the results.

freesasa_result_free()

void freesasa_result_free

(

freesasa_result *

result

)

Frees a freesasa_result object.

Parameters

result

the object to be freed.

freesasa_set_verbosity()

int freesasa_set_verbosity

(

freesasa_verbosity

v

)

Set the global verbosity level.

Parameters

v	the verbosity level

Returns

FREESASA_SUCCESS. If v is invalid FREESASA_FAIL.

See also

freesasa_verbosity

freesasa_get_verbosity()

freesasa_verbosity freesasa_get_verbosity

(

void

)

Get the current verbosity level.

Returns

the verbosity level.

freesasa_set_err_out()

void freesasa_set_err_out

(

FILE *

err

)

Set where to write errors.

By default stderr is used, this function can be called to redirect error output elsewhere.

Parameters

err	The file to write to. If NULL, stderr will be used.

freesasa_get_err_out()

FILE * freesasa_get_err_out

(

void

)

Get pointer to error file.

NULL means stderr is used.

Returns

The error file.

Variable Documentation

FREESASA_DEF_NUMBER_THREADS

const int FREESASA_DEF_NUMBER_THREADS

extern

Default number of threads.

Value will depend on if library was compiled with or without thread support. (2 with threads, 1 without).