ARB
ed4_protein_2nd_structure.hxx
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1 
30 #ifndef ED4_PROTEIN_2ND_STRUCTURE_HXX
31 #define ED4_PROTEIN_2ND_STRUCTURE_HXX
32 
33 #ifndef AW_WINDOW_HXX
34 #include "aw_window.hxx"
35 #endif
36 
37 // #define SHOW_PROGRESS ///< Print information about progress to screen (for finding and extending structures and resolving overlaps).
38 
39 #define PFOLD_AWAR_ENABLE "Pfold/enable"
40 #define PFOLD_AWAR_SELECTED_SAI "Pfold/selected_SAI"
41 #define PFOLD_AWAR_PAIR_TEMPLATE "Pfold/pairs/%s"
42 #define PFOLD_AWAR_SYMBOL_TEMPLATE "Pfold/symbols/%s"
43 #define PFOLD_AWAR_SYMBOL_TEMPLATE_2 "Pfold/symbols2"
44 #define PFOLD_AWAR_MATCH_METHOD "Pfold/match_method"
45 #define PFOLD_AWAR_SAI_FILTER "Pfold/SAI_filter"
46 
47 // TODO: move static variables to .cpp file?
48 
57  BETA_SHEET = 1,
58  BETA_TURN = 2,
60 // THREE_TURN = 4, ///< Three turn
61 // FOUR_TURN = 5, ///< Four turn
62 // FIVE_TURN = 6 ///< Five turn
63 };
64 
67  const char *name;
68  int value;
69 };
70 
80 };
81 
84 
85 #define PFOLD_PAIRS 6
86 
88 extern char *pfold_pairs[PFOLD_PAIRS];
89 
91 extern char *pfold_pair_chars[PFOLD_PAIRS];
92 
100 #define PFOLD_PAIR_CHARS_2 "##++~~-- "
101 
108 };
109 
117 #define cf_former(aa, strct) ((strct!=2) ? cf_parameters[aa][strct] : cf_parameters_norm[aa][strct])
118 
127 #define cf_breaker(aa, strct) ((strct!=2) ? cf_parameters[aa][strct+2] : 0)
128 
129 
130 // General ED4 functions //////////////////////////////////////////////////////////////////////////////////////////////////////////
131 
132 
133 
180 GB_ERROR ED4_pfold_calculate_secstruct_match(const unsigned char *structure_sai, const unsigned char *structure_cmp, int start, int end, char *result_buffer, PFOLD_MATCH_METHOD match_method = SECSTRUCT_SEQUENCE);
181 
198 GB_ERROR ED4_pfold_set_SAI(char **protstruct, GBDATA *gb_main, const char *alignment_name, long *protstruct_len = NULp);
199 
200 
201 // AW related functions ///////////////////////////////////////////////////////////////////////////////////////////////
202 
225 AW_window *ED4_pfold_create_props_window(AW_root *awr, const WindowCallback *refreshCallback);
226 
227 #endif
const char * GB_ERROR
Definition: arb_core.h:25
Compare two protein secondary structures.
#define PFOLD_PAIRS
GB_ERROR ED4_pfold_calculate_secstruct_match(const unsigned char *structure_sai, const unsigned char *structure_cmp, int start, int end, char *result_buffer, PFOLD_MATCH_METHOD match_method=SECSTRUCT_SEQUENCE)
Compares a protein secondary structure with a primary structure or another secondary structure...
static char * alignment_name
AW_window * ED4_pfold_create_props_window(AW_root *awr, const WindowCallback *refreshCallback)
Creates the "Protein Match Settings" window.
Compare an amino acid sequence with a reference protein secondary structure.
name_value_pair pfold_match_type_awars[]
Awars for the match type; binds the PFOLD_MATCH_TYPE to the corresponding awar name.
static HelixNrInfo * start
Unknown structure.
char * pfold_pairs[PFOLD_PAIRS]
Match pair definition (see PFOLD_MATCH_TYPE) as used for match methods SECSTRUCT_SECSTRUCT and SECSTR...
PFOLD_MATCH_TYPE
Match quality for secondary structure match.
PFOLD_MATCH_METHOD
Defines the methods for match computation. For details refer to ED4_pfold_calculate_secstruct_match()...
const char * name
Name or description.
Defines a name-value pair (e.g. for awars, menu entries, etc.).
Compare a full prediction of the protein secondary structure from its amino acid sequence with a refe...
char * pfold_pair_chars[PFOLD_PAIRS]
Symbols for the match quality (defined by PFOLD_MATCH_TYPE) as used for match methods SECSTRUCT_SECST...
PFOLD_STRUCTURE
Protein secondary structure types.
int value
Value attached to name.
GB_ERROR ED4_pfold_set_SAI(char **protstruct, GBDATA *gb_main, const char *alignment_name, long *protstruct_len=NULp)
Sets the reference protein secondary structure SAI.
#define NULp
Definition: cxxforward.h:97
GBDATA * gb_main
Definition: adname.cxx:33