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 
22 enum 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 
121 void read_parameter_file(const char fname[]);
122 
128 void write_parameter_file(const char fname[]);
129 
130 void write_parameter_file_full(const char fname[], int options);
131 
136 enum parset gettype(const char *ident);
137 
142 const char *settype(enum parset s);
143 
148 #endif
void read_parameter_file(const char fname[])
Read energy parameters from a file.
void write_parameter_file(const char fname[])
Write energy parameters to a file.
parset
Identifiers for energy contribution parameters in parameter files.
Definition: read_epars.h:22