Functions and datatypes for performing and analyzing SASA calculations. More...

#include <stdio.h>

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

struct	freesasa_result
	Struct to store results of SASA calculation. More...

struct	freesasa_nodearea
	Struct to store integrated SASA values for either a full structure or a subset thereof. More...

struct	freesasa_cif_atom
	Struct to store data about a mmCIF atom site. 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...

#define	FREESASA_CONFLICTING_CLASSIFIERS "conflicting-classifiers"
	String returned by freesasa_structure_classifier_name() when structure was initialized using several different classifiers. More...

#define	FREESASA_MAX_SELECTION_NAME 50
	The maximum length of a selection name. More...

Typedefs
typedef enum freesasa_algorithm	freesasa_algorithm

typedef enum freesasa_verbosity	freesasa_verbosity

typedef enum freesasa_atom_class	freesasa_atom_class

typedef struct freesasa_structure	freesasa_structure
	Struct for structure object. More...

typedef enum freesasa_nodetype	freesasa_nodetype

typedef struct freesasa_node	freesasa_node
	Result node. More...

typedef struct freesasa_selection	freesasa_selection
	Selection struct. More...

typedef struct freesasa_classifier	freesasa_classifier
	Classifier struct. More...

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

enum	freesasa_verbosity { FREESASA_V_NORMAL , FREESASA_V_NOWARNINGS , FREESASA_V_SILENT , FREESASA_V_DEBUG }
	Verbosity levels. More...

enum	freesasa_error_codes { FREESASA_SUCCESS = 0 , FREESASA_FAIL = -1 , FREESASA_WARN = -2 }
	Error codes. More...

enum	freesasa_atom_class { FREESASA_ATOM_APOLAR = 0 , FREESASA_ATOM_POLAR = 1 , FREESASA_ATOM_UNKNOWN = 2 }
	Atom classes. More...

enum	freesasa_structure_options { FREESASA_INCLUDE_HETATM = 1 , FREESASA_INCLUDE_HYDROGEN = 1 << 2 , FREESASA_SEPARATE_MODELS = 1 << 3 , FREESASA_SEPARATE_CHAINS = 1 << 4 , FREESASA_JOIN_MODELS = 1 << 5 , FREESASA_HALT_AT_UNKNOWN = 1 << 6 , FREESASA_SKIP_UNKNOWN = 1 << 7 , FREESASA_RADIUS_FROM_OCCUPANCY = 1 << 8 }
	Options for reading structure from PDB. More...

enum	freesasa_output_options { FREESASA_OUTPUT_ATOM = 1 , FREESASA_OUTPUT_RESIDUE = 1 << 2 , FREESASA_OUTPUT_CHAIN = 1 << 3 , FREESASA_OUTPUT_STRUCTURE = 1 << 4 , FREESASA_LOG = 1 << 5 , FREESASA_RSA = 1 << 6 , FREESASA_JSON = 1 << 7 , FREESASA_XML = 1 << 8 , FREESASA_PDB = 1 << 9 , FREESASA_RES = 1 << 10 , FREESASA_SEQ = 1 << 11 , FREESASA_CIF = 1 << 12 , FREESASA_OUTPUT_SKIP_REL = 1 << 13 }
	Output options. More...

enum	freesasa_nodetype { FREESASA_NODE_ATOM , FREESASA_NODE_RESIDUE , FREESASA_NODE_CHAIN , FREESASA_NODE_STRUCTURE , FREESASA_NODE_RESULT , FREESASA_NODE_ROOT , FREESASA_NODE_NONE }
	Node types. 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...

freesasa_classifier *	freesasa_classifier_from_file (FILE *file)
	Generate a classifier from a config-file. More...

void	freesasa_classifier_free (freesasa_classifier *classifier)
	Frees a classifier object. More...

double	freesasa_classifier_radius (const freesasa_classifier classifier, const char res_name, const char *atom_name)
	Use a classifier to determine the radius of a given atom. More...

freesasa_atom_class	freesasa_classifier_class (const freesasa_classifier classifier, const char res_name, const char *atom_name)
	Use a classifier to determine the class of a given atom. More...

const char *	freesasa_classifier_class2str (freesasa_atom_class atom_class)
	Names for freesasa_atom_class. More...

const char *	freesasa_classifier_name (const freesasa_classifier *classifier)
	The name of a classifier. More...

freesasa_selection *	freesasa_selection_new (const char command, const freesasa_structure structure, const freesasa_result *result)
	Get area of a selection. More...

void	freesasa_selection_free (freesasa_selection *selection)
	Free selection. More...

const char *	freesasa_selection_name (const freesasa_selection *selection)
	Name of the selection. More...

const char *	freesasa_selection_command (const freesasa_selection *selection)
	Command that was used to generate the selection. More...

double	freesasa_selection_area (const freesasa_selection *selection)
	Area of the selection. More...

int	freesasa_selection_n_atoms (const freesasa_selection *selection)
	Number of atoms that matched the selection. 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...

freesasa_structure *	freesasa_structure_new (void)
	Allocate empty structure. More...

void	freesasa_structure_free (freesasa_structure *structure)
	Free structure. More...

freesasa_structure *	freesasa_structure_from_pdb (FILE pdb, const freesasa_classifier classifier, int options)
	Init structure with coordinates from pdb-file. More...

freesasa_structure **	freesasa_structure_array (FILE pdb, int n, const freesasa_classifier *classifier, int options)
	Init array of structures from PDB. More...

int	freesasa_structure_add_atom (freesasa_structure structure, const char atom_name, const char residue_name, const char residue_number, char chain_label, double x, double y, double z)
	Add individual atom to structure using default behavior. More...

int	freesasa_structure_add_atom_wopt (freesasa_structure structure, const char atom_name, const char residue_name, const char residue_number, char chain_label, double x, double y, double z, const freesasa_classifier *classifier, int options)
	Add individual atom to structure. More...

int	freesasa_structure_add_cif_atom (freesasa_structure structure, freesasa_cif_atom atom, const freesasa_classifier *classifier, int options)
	Add atoms from a mmCIF file to a structure. More...

freesasa_structure *	freesasa_structure_get_chains (const freesasa_structure structure, const char chains, const freesasa_classifier *classifier, int options)
	Create new structure consisting of a selection chains from the provided structure. More...

const char *	freesasa_structure_chain_labels (const freesasa_structure *structure)
	Get string listing all chains in structure. More...

int	freesasa_structure_n (const freesasa_structure *structure)
	Get number of atoms. More...

int	freesasa_structure_n_residues (const freesasa_structure *structure)
	Get number of residues. More...

int	freesasa_structure_n_chains (const freesasa_structure *structure)
	Get number of chains. More...

const double *	freesasa_structure_radius (const freesasa_structure *structure)
	Returns a pointer to an array of the radii of each atom. More...

void	freesasa_structure_set_radius (freesasa_structure structure, const double radii)
	Override the radii set when the structure was initialized. More...

const char *	freesasa_structure_atom_name (const freesasa_structure *structure, int i)
	Get atom name. More...

const char *	freesasa_structure_atom_res_name (const freesasa_structure *structure, int i)
	Get residue name. More...

const char *	freesasa_structure_atom_res_number (const freesasa_structure *structure, int i)
	Get residue number. More...

char	freesasa_structure_atom_chain (const freesasa_structure *structure, int i)
	Get chain label. More...

const char *	freesasa_structure_atom_symbol (const freesasa_structure *structure, int i)
	Get atom symbol. More...

double	freesasa_structure_atom_radius (const freesasa_structure *structure, int i)
	Get atom radius. More...

void	freesasa_structure_atom_set_radius (freesasa_structure *structure, int i, double radius)
	Set atom radius. More...

const char *	freesasa_structure_residue_name (const freesasa_structure *structure, int r_i)
	Get name of residue. More...

const char *	freesasa_structure_residue_number (const freesasa_structure *structure, int r_i)
	Get residue number. More...

char	freesasa_structure_residue_chain (const freesasa_structure *structure, int r_i)
	Get chain residue belongs to. More...

int	freesasa_structure_model (const freesasa_structure *structure)
	Get model number for structure. More...

const double *	freesasa_structure_coord_array (const freesasa_structure *structure)
	Get array of coordinates. More...

int	freesasa_structure_residue_atoms (const freesasa_structure structure, int r_i, int first, int *last)
	Get indices of first and last atoms of a residue. More...

int	freesasa_structure_chain_atoms (const freesasa_structure structure, char chain, int first, int *last)
	Get indices of first and last atoms of a chain. More...

int	freesasa_structure_chain_residues (const freesasa_structure structure, char chain, int first, int *last)
	Get indices of first and last residues of a chain. More...

const char *	freesasa_structure_classifier_name (const freesasa_structure *structure)
	Name of classifier used to generate structure. More...

freesasa_node *	freesasa_tree_new (void)
	Generates empty freesasa_node of type FREESASA_NODE_ROOT. More...

freesasa_node *	freesasa_tree_init (const freesasa_result result, const freesasa_structure structure, const char *name)
	Init tree based on result and structure. More...

int	freesasa_tree_add_result (freesasa_node tree, const freesasa_result result, const freesasa_structure structure, const char name)
	Add a new set of results to a tree. More...

int	freesasa_tree_join (freesasa_node tree1, freesasa_node *tree2)
	Join two trees. More...

int	freesasa_tree_export (FILE output, freesasa_node root, int options)
	Outputs result in format specified by options. More...

int	freesasa_node_free (freesasa_node *root)
	Free tree. More...

const freesasa_nodearea *	freesasa_node_area (const freesasa_node *node)
	The freesasa_nodearea of all atoms belonging to a node. More...

freesasa_node *	freesasa_node_children (freesasa_node *node)
	The children of a node. More...

freesasa_node *	freesasa_node_next (freesasa_node *node)
	Next sibling of a node. More...

freesasa_node *	freesasa_node_parent (freesasa_node *node)
	The parent of a node. More...

freesasa_nodetype	freesasa_node_type (const freesasa_node *node)
	The type of a node. More...

const char *	freesasa_node_name (const freesasa_node *node)
	The name of a node. More...

const char *	freesasa_node_classified_by (const freesasa_node *node)
	The name of the classifier used to generate the node. More...

int	freesasa_node_atom_is_polar (const freesasa_node *node)
	Is atom polar. More...

int	freesasa_node_atom_is_mainchain (const freesasa_node *node)
	Does atom belong to the main chain/backbone. More...

double	freesasa_node_atom_radius (const freesasa_node *node)
	Atom radius. More...

const char *	freesasa_node_atom_pdb_line (const freesasa_node *node)
	Line in PDB atom was generated from. More...

const char *	freesasa_node_atom_residue_number (const freesasa_node *node)
	Atom residue number. More...

const char *	freesasa_node_atom_residue_name (const freesasa_node *node)
	Atom residue name. More...

char	freesasa_node_atom_chain (const freesasa_node *node)
	Atom chain. More...

const char *	freesasa_node_residue_number (const freesasa_node *node)
	Residue number. More...

int	freesasa_node_residue_n_atoms (const freesasa_node *node)
	Number of atoms in a residue. More...

const freesasa_nodearea *	freesasa_node_residue_reference (const freesasa_node *node)
	The reference area for a node from the classifier used to generate the tree. More...

int	freesasa_node_chain_n_residues (const freesasa_node *node)
	The number of residues in a chain. More...

int	freesasa_node_structure_n_chains (const freesasa_node *node)
	The number of chains in a structure. More...

int	freesasa_node_structure_n_atoms (const freesasa_node *node)
	The number of atoms in a structure. More...

const char *	freesasa_node_structure_chain_labels (const freesasa_node *node)
	All chain labels in a structure. More...

int	freesasa_node_structure_model (const freesasa_node *node)
	Model number of a structure (from input PDB) More...

const freesasa_result *	freesasa_node_structure_result (const freesasa_node *node)
	Raw results for a structure. More...

const freesasa_selection **	freesasa_node_structure_selections (const freesasa_node *node)
	Selection results for a structure. More...

int	freesasa_node_structure_add_selection (freesasa_node node, const freesasa_selection selection)
	Add a selection result to a structure node. More...

const freesasa_parameters *	freesasa_node_result_parameters (const freesasa_node *node)
	Parameter values used to calculate result. More...

int	freesasa_select_area (const char command, char name, double area, const freesasa_structure structure, const freesasa_result *result)
	Get area of a selection. More...

void	freesasa_structure_set_model (freesasa_structure *structure, int model)

Variables
const int	FREESASA_DEF_NUMBER_THREADS
	Default number of threads. More...

const freesasa_parameters	freesasa_default_parameters
	The default parameters for FreeSASA.

const freesasa_classifier	freesasa_protor_classifier
	ProtOr classifier. More...

const freesasa_classifier	freesasa_naccess_classifier
	NACCESS classifier. More...

const freesasa_classifier	freesasa_oons_classifier
	OONS classifier. More...

Detailed Description

Functions and datatypes for performing and analyzing SASA calculations.

Author: Simon Mitternacht

Copyright: MIT License

This header provides the functions and data types necessary to perform and analyze a SASA calculation using FreeSASA. They are all listed on this page, but also divided into Core, Structure, Classifier, Node and Selection modules. The page FreeSASA API shows how to set up and perform a simple SASA calculation.

Definition in file freesasa.h.

Typedef Documentation

◆ freesasa_algorithm

typedef enum freesasa_algorithm freesasa_algorithm

Definition at line 95 of file freesasa.h.

◆ freesasa_verbosity

typedef enum freesasa_verbosity freesasa_verbosity

Definition at line 111 of file freesasa.h.

◆ freesasa_atom_class

typedef enum freesasa_atom_class freesasa_atom_class

Definition at line 170 of file freesasa.h.

◆ freesasa_nodetype

typedef enum freesasa_nodetype freesasa_nodetype

Definition at line 318 of file freesasa.h.

Enumeration Type Documentation

◆ freesasa_verbosity

enum freesasa_verbosity

Verbosity levels.

See also: freesasa_set_verbosity(); freesasa_get_verbosity()

Enumerator
FREESASA_V_NORMAL	Print all errors and warnings.
FREESASA_V_NOWARNINGS	Print only errors.
FREESASA_V_SILENT	Print no errors and warnings.
FREESASA_V_DEBUG	Print all errors, warnings and debug messages.

Definition at line 103 of file freesasa.h.

◆ freesasa_error_codes

enum freesasa_error_codes

Error codes.

Can rely upon FREESASA_SUCCESS being 0 and the errors having negative numbers.

Enumerator
FREESASA_SUCCESS	All is ok (value will always be zero).
FREESASA_FAIL	Something went seriously wrong (value will always be negative).
FREESASA_WARN	Something went wrong, but results might still be meaningful (value will always be negative).

Definition at line 151 of file freesasa.h.

Data Structures

Macros

Typedefs

Enumerations

Functions

Variables

Detailed Description

Typedef Documentation

◆ freesasa_algorithm

◆ freesasa_verbosity

◆ freesasa_atom_class

◆ freesasa_nodetype

Enumeration Type Documentation

◆ freesasa_verbosity

◆ freesasa_error_codes