rwresprop.cpp File Reference

Library routines to read and write residue properties. More...

#include "rwresprop.h"
#include "star.h"
#include "mol_tags.h"
#include "seq_util.h"
#include "linked_list.h"
#include "utilities.h"

Classes
struct	resprop

Functions
Bresidue_type *	residue_type_add (Bresidue_type **rtype, char c)
Bresidue_type *	read_residue_prop_star (Bstring &filename)
Bresidue_type *	read_residue_properties (Bstring &filename)
int	write_residue_prop_star (Bstring &filename, Bresidue_type *rt)
Bresidue_matrix *	read_residue_mat_star (Bstring &filename)
Bresidue_type *	get_residue_properties (Bstring &filename)
	Reading residue properties from parameter files. More...
int	write_residue_properties (Bstring &filename, Bresidue_type *rt)
	Writing residue properties from a parameter file. More...
Bresidue_matrix *	get_residue_matrix (Bstring &filename)
	Reading a residue matrix from a file. More...
int	residue_matrix_kill (Bresidue_matrix *resmat)
	Deallocating a residue matrix. More...

Variables
int	verbose
struct resprop	defaultprops []
char	defaultcode [] = "-*ABCDEFGHIKLMNPQRSTVWXYZ"
float	defaultsim []

Detailed Description

Library routines to read and write residue properties.

Author

Bernard Heymann

Date

Created: 19991114

Modified: 20210328

Function Documentation

get_residue_matrix()

Bresidue_matrix * get_residue_matrix

(

Bstring &

filename

)

Reading a residue matrix from a file.

Parameters

&filename

file name.

Returns

Bresidue_matrix* residue matrix property structure, NULL on failure.

get_residue_properties()

Bresidue_type * get_residue_properties

(

Bstring &

filename

)

Reading residue properties from parameter files.

Parameters

&filename

file name.

Returns

Bresidue_type* the residue property structure, NULL on failure.

read_residue_mat_star()

Bresidue_matrix * read_residue_mat_star

(

Bstring &

filename

)

read_residue_prop_star()

Bresidue_type * read_residue_prop_star

(

Bstring &

filename

)

read_residue_properties()

Bresidue_type * read_residue_properties

(

Bstring &

filename

)

residue_matrix_kill()

int residue_matrix_kill

(

Bresidue_matrix *

resmat

)

Deallocating a residue matrix.

Parameters

*resmat

the residue matrix property structure.

Returns

int 0.

residue_type_add()

Bresidue_type * residue_type_add	(	Bresidue_type **	rtype,
		char	c
	)

write_residue_prop_star()

int write_residue_prop_star	(	Bstring &	filename,
		Bresidue_type *	rt
	)

write_residue_properties()

int write_residue_properties	(	Bstring &	filename,
		Bresidue_type *	rt
	)

Writing residue properties from a parameter file.

Parameters

&filename	file name.
*rt	the residue property structure.

Returns

int error code (<0 means failure).

Variable Documentation

defaultcode

char defaultcode[] = "-*ABCDEFGHIKLMNPQRSTVWXYZ"

defaultprops

struct resprop defaultprops[]

Initial value:

= {
    {'-',   0.00,   0.0,  0.0,  0.00,  0.0,  0.0},
    {'*',   0.00,   0.0,  0.0,  0.00,  0.0,  0.0},
    {'A',  89.09,  89.0,  3.4,  0.10,  0.0, -1.6},
    {'B', 132.61, 118.0,  5.5,  0.50, -0.5,  7.0},
    {'C', 121.15, 103.0,  4.4,  0.24,  0.0, -2.0},
    {'D', 133.10, 114.0,  5.5,  0.50, -1.0,  9.2},
    {'E', 147.13, 139.0,  6.1,  0.50, -1.0,  8.2},
    {'F', 165.19, 199.0,  6.7,  0.32,  0.0, -3.7},
    {'G',  75.07,  64.0,  2.3,  0.07,  0.0, -1.0},
    {'H', 155.16, 157.0,  6.0,  0.50,  0.5,  3.0},
    {'I', 131.17, 163.0,  5.1,  0.22,  0.0, -3.1},
    {'K', 146.19, 165.0,  6.7,  0.50,  1.0,  8.8},
    {'L', 131.17, 163.0,  5.5,  0.20,  0.0, -2.8},
    {'M', 149.21, 166.0,  6.1,  0.45,  0.0, -3.4},
    {'N', 132.12, 122.0,  5.5,  0.50,  0.0,  4.8},
    {'P', 115.13, 122.0,  4.4,  0.50,  0.0,  0.2},
    {'Q', 146.15, 147.0,  6.1,  0.50,  0.0,  4.1},
    {'R', 174.23, 191.0,  7.3,  0.50,  1.0, 12.0},
    {'S', 105.09,  94.0,  4.4,  0.50,  0.0, -0.6},
    {'T', 119.12, 120.0,  4.5,  0.50,  0.0, -1.2},
    {'V', 117.15, 138.0,  4.5,  0.12,  0.0, -2.6},
    {'W', 204.23, 226.0,  7.4,  0.61,  0.0, -1.9},
    {'X', 128.16, 144.0,  5.5,  0.50,  0.0,  0.0},
    {'Y', 181.19, 195.0,  7.3,  0.50,  0.0,  0.7},
    {'Z', 146.64, 143.0,  6.1,  0.50, -0.5,  6.2},
}

defaultsim

float defaultsim[]

Initial value:

= {
    1.0,1.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,
    1.0,1.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,-4.0,
    -4.0,-4.0,4.0,-2.0,0.0,-2.0,-1.0,-2.0,0.0,-2.0,-1.0,-1.0,-1.0,-1.0,-2.0,-1.0,-1.0,-1.0,1.0,0.0,0.0,-3.0,0.0,-2.0,-1.0,
    -4.0,-4.0,-2.0,4.0,-3.0,4.0,1.0,-3.0,-1.0,0.0,-3.0,0.0,-4.0,-3.0,3.0,-2.0,0.0,-1.0,0.0,-1.0,-3.0,-4.0,-1.0,-3.0,1.0,
    -4.0,-4.0,0.0,-3.0,9.0,-3.0,-4.0,-2.0,-3.0,-3.0,-1.0,-3.0,-1.0,-1.0,-3.0,-3.0,-3.0,-3.0,-1.0,-1.0,-1.0,-2.0,-2.0,-2.0,-3.0,
    -4.0,-4.0,-2.0,4.0,-3.0,6.0,2.0,-3.0,-1.0,-1.0,-3.0,-1.0,-4.0,-3.0,1.0,-1.0,0.0,-2.0,0.0,-1.0,-3.0,-4.0,-1.0,-3.0,1.0,
    -4.0,-4.0,-1.0,1.0,-4.0,2.0,5.0,-3.0,-2.0,0.0,-3.0,1.0,-3.0,-2.0,0.0,-1.0,2.0,0.0,0.0,-1.0,-2.0,-3.0,-1.0,-2.0,4.0,
    -4.0,-4.0,-2.0,-3.0,-2.0,-3.0,-3.0,6.0,-3.0,-1.0,0.0,-3.0,0.0,0.0,-3.0,-4.0,-3.0,-3.0,-2.0,-2.0,-1.0,1.0,-1.0,3.0,-3.0,
    -4.0,-4.0,0.0,-1.0,-3.0,-1.0,-2.0,-3.0,6.0,-2.0,-4.0,-2.0,-4.0,-3.0,0.0,-2.0,-2.0,-2.0,0.0,-2.0,-3.0,-2.0,-1.0,-3.0,-2.0,
    -4.0,-4.0,-2.0,0.0,-3.0,-1.0,0.0,-1.0,-2.0,8.0,-3.0,-1.0,-3.0,-2.0,1.0,-2.0,0.0,0.0,-1.0,-2.0,-3.0,-2.0,-1.0,2.0,0.0,
    -4.0,-4.0,-1.0,-3.0,-1.0,-3.0,-3.0,0.0,-4.0,-3.0,4.0,-3.0,2.0,1.0,-3.0,-3.0,-3.0,-3.0,-2.0,-1.0,3.0,-3.0,-1.0,-1.0,-3.0,
    -4.0,-4.0,-1.0,0.0,-3.0,-1.0,1.0,-3.0,-2.0,-1.0,-3.0,5.0,-2.0,-1.0,0.0,-1.0,1.0,2.0,0.0,-1.0,-2.0,-3.0,-1.0,-2.0,1.0,
    -4.0,-4.0,-1.0,-4.0,-1.0,-4.0,-3.0,0.0,-4.0,-3.0,2.0,-2.0,4.0,2.0,-3.0,-3.0,-2.0,-2.0,-2.0,-1.0,1.0,-2.0,-1.0,-1.0,-3.0,
    -4.0,-4.0,-1.0,-3.0,-1.0,-3.0,-2.0,0.0,-3.0,-2.0,1.0,-1.0,2.0,5.0,-2.0,-2.0,0.0,-1.0,-1.0,-1.0,1.0,-1.0,-1.0,-1.0,-1.0,
    -4.0,-4.0,-2.0,3.0,-3.0,1.0,0.0,-3.0,0.0,1.0,-3.0,0.0,-3.0,-2.0,6.0,-2.0,0.0,0.0,1.0,0.0,-3.0,-4.0,-1.0,-2.0,0.0,
    -4.0,-4.0,-1.0,-2.0,-3.0,-1.0,-1.0,-4.0,-2.0,-2.0,-3.0,-1.0,-3.0,-2.0,-2.0,7.0,-1.0,-2.0,-1.0,-1.0,-2.0,-4.0,-2.0,-3.0,-1.0,
    -4.0,-4.0,-1.0,0.0,-3.0,0.0,2.0,-3.0,-2.0,0.0,-3.0,1.0,-2.0,0.0,0.0,-1.0,5.0,1.0,0.0,-1.0,-2.0,-2.0,-1.0,-1.0,3.0,
    -4.0,-4.0,-1.0,-1.0,-3.0,-2.0,0.0,-3.0,-2.0,0.0,-3.0,2.0,-2.0,-1.0,0.0,-2.0,1.0,5.0,-1.0,-1.0,-3.0,-3.0,-1.0,-2.0,0.0,
    -4.0,-4.0,1.0,0.0,-1.0,0.0,0.0,-2.0,0.0,-1.0,-2.0,0.0,-2.0,-1.0,1.0,-1.0,0.0,-1.0,4.0,1.0,-2.0,-3.0,0.0,-2.0,0.0,
    -4.0,-4.0,0.0,-1.0,-1.0,-1.0,-1.0,-2.0,-2.0,-2.0,-1.0,-1.0,-1.0,-1.0,0.0,-1.0,-1.0,-1.0,1.0,5.0,0.0,-2.0,0.0,-2.0,-1.0,
    -4.0,-4.0,0.0,-3.0,-1.0,-3.0,-2.0,-1.0,-3.0,-3.0,3.0,-2.0,1.0,1.0,-3.0,-2.0,-2.0,-3.0,-2.0,0.0,4.0,-3.0,-1.0,-1.0,-2.0,
    -4.0,-4.0,-3.0,-4.0,-2.0,-4.0,-3.0,1.0,-2.0,-2.0,-3.0,-3.0,-2.0,-1.0,-4.0,-4.0,-2.0,-3.0,-3.0,-2.0,-3.0,11.0,-2.0,2.0,-3.0,
    -4.0,-4.0,0.0,-1.0,-2.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-2.0,-1.0,-1.0,0.0,0.0,-1.0,-2.0,-1.0,-1.0,-1.0,
    -4.0,-4.0,-2.0,-3.0,-2.0,-3.0,-2.0,3.0,-3.0,2.0,-1.0,-2.0,-1.0,-1.0,-2.0,-3.0,-1.0,-2.0,-2.0,-2.0,-1.0,2.0,-1.0,7.0,-2.0,
    -4.0,-4.0,-1.0,1.0,-3.0,1.0,4.0,-3.0,-2.0,0.0,-3.0,1.0,-3.0,-1.0,0.0,-1.0,3.0,0.0,0.0,-1.0,-2.0,-3.0,-1.0,-2.0,4.0,
}

verbose

int verbose

extern