RNAlib-2.1.9h
read_epars.h
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1#ifndef __VIENNA_RNA_PACKAGE_READ_EPARS_H__
2#define __VIENNA_RNA_PACKAGE_READ_EPARS_H__
3
22enum parset {
23 /* misc identifiers */
24 UNKNOWN = -1,
25 QUIT = 0, /* end of parameter file */
26
27 /*
28 The following enumeration identifiers are used throughout the library
29 to indicate read/write from/to the regular energy contribution arrays,
30 i.e. the ones used in all folding recursions for base pair types <= 7.
31 For simplicity and to keep things clear we associate these arrays with
32 RNA contributions althought they can be filled with contributions for
33 any kind of interaction via the read_parameter_file() function
34 */
35
36 /* RNA loop type specific identifiers */
37 S, S_H,
38 HP, HP_H,
39 B, B_H,
40 IL, IL_H,
41 INT11, INT11_H, INT21, INT21_H, INT22, INT22_H,
42 ML,
43 /* RNA mismatch identifiers */
44 MMH, MMH_H,
45 MMI, MMI_H,
46 MMI1N, MMI1N_H, MMI23, MMI23_H,
47 MMM, MMM_H,
48 MME, MME_H,
49 /* RNA dangling end identifiers */
50 D5, D5_H,
51 D3, D3_H,
52 /* RNA special hairpin identifiers */
53 TRI, TL, HEX,
54 /* RNA other identifiers */
55 NIN, MISC,
56
57 /*
58 Below are the identifiers used for DNA parameters in all the hybridisation
59 routines. Note that they will be used only if RNA/DNA hybridisation is
60 activated (base pair types >= 7 are occuring)
61 */
62
63 /* DNA loop type specific identifiers */
64 S_DNA, S_H_DNA,
65 HP_DNA, HP_H_DNA,
66 B_DNA, B_H_DNA,
67 IL_DNA, IL_H_DNA,
68 INT11_DNA, INT11_H_DNA, INT21_DNA, INT21_H_DNA, INT22_DNA, INT22_H_DNA,
69 ML_DNA,
70 /* RNA mismatch identifiers */
71 MMH_DNA, MMH_H_DNA,
72 MMI_DNA, MMI_H_DNA,
73 MMI1N_DNA, MMI1N_H_DNA, MMI23_DNA, MMI23_H_DNA,
74 MMM_DNA, MMM_H_DNA,
75 MME_DNA, MME_H_DNA,
76 /* DNA dangling end identifiers */
77 D5_DNA, D5_H_DNA,
78 D3_DNA, D3_H_DNA,
79 /* DNA special hairpin identifiers */
80 TRI_DNA, TL_DNA, HEX_DNA,
81 /* DNA other identifiers */
82 NIN_DNA, MISC_DNA,
83
84 /* Finally, the RNA/DNA hybrid identifiers */
85
86 /* RNA/DNA hybrid loop type specific identifiers */
87 S_HYBRID, S_H_HYBRID,
88 HP_HYBRID, HP_H_HYBRID,
89 B_HYBRID, B_H_HYBRID,
90 IL_HYBRID, IL_H_HYBRID,
91 INT11_HYBRID, INT11_H_HYBRID, INT21_HYBRID, INT21_H_HYBRID, INT22_HYBRID, INT22_H_HYBRID,
92 ML_HYBRID,
93 /* RNA/DNA hybrid mismatch identifiers */
94 MMH_HYBRID, MMH_H_HYBRID,
95 MMI_HYBRID, MMI_H_HYBRID,
96 MMI1N_HYBRID, MMI1N_H_HYBRID, MMI23_HYBRID, MMI23_H_HYBRID,
97 MMM_HYBRID, MMM_H_HYBRID,
98 MME_HYBRID, MME_H_HYBRID,
99 /* RNA/DNA hybrid dangling end identifiers */
100 D5_HYBRID, D5_H_HYBRID,
101 D3_HYBRID, D3_H_HYBRID,
102 /* RNA/DNA hybrid special hairpin identifiers */
103 TRI_HYBRID, TL_HYBRID, HEX_HYBRID,
104 /* RNA/DNA hybrid other identifiers */
105 NIN_HYBRID, MISC_HYBRID,
106
107 /* This dummy must be the last entry in this enum! */
108 DUMMY
109};
110
111#define VRNA_PARAMETER_FILE_RNA 1
112#define VRNA_PARAMETER_FILE_DNA 2
113#define VRNA_PARAMETER_FILE_HYBRID 4
114
115
121void read_parameter_file(const char fname[]);
122
128void write_parameter_file(const char fname[]);
129
130void write_parameter_file_full(const char fname[], int options);
131
136enum parset gettype(const char *ident);
137
142const char *settype(enum parset s);
143
148#endif
void read_parameter_file(const char fname[])
Read energy parameters from a file.
parset
Identifiers for energy contribution parameters in parameter files.
Definition read_epars.h:22
void write_parameter_file(const char fname[])
Write energy parameters to a file.