1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
|
/*******************************************************************************
* Copyright (c) 2005, Arun S Konagurthu, The University of Melbourne.
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification are permitted provided that the following conditions are met:
*
* (1) Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
* (2) Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
* (3) Neither the name of the University of Melbourne nor the names of its
* contributors may be used to endorse or promote products derived from this
* software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
* BUSINESSINTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
* IN CONTRACT, STRICT LIABILITY,OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
******************************************************************************/
#ifndef GLOBALS_H
#define GLOBALS_H
//*********************************
//MACROS
#define NSTRUCTS_ULIMIT 20
#define CP_WINDOW_SIZE 6
#define MIN_CP_WINDOW_SIZE 6 // default Minimum Contact Pattern Window size used in length-proportional
// edge-weights routine.
#define MIN_WINDOW_WIDTH 15 // default size of maximal sub-structure for Quaternion-superposition
#define RMSD_THRESH 0.5
#define RMSD_THRESH_JOINT 0.5
#define RMSD_THRESH_MAXIMAL 1.80
#define JOINT_RMSD_THRESH_MAXIMAL 6.5
#define RMSD_THRESH_4 0.7
#define RMSD_THRESH_5 0.9
#define NINFO_LOCAL_LIBRARY 10
#define ALIGNMENT_RMSD 8.0
//MACRO ENDS HERE
extern const char INSTALL_DIR[] ;
//STRUCT TEMPLATES
struct residues
{
char three_letter_code[4] ;
char single_letter_code ;
};
struct pdb_info // Contains only the backbone info
{
char res_num[10] ; //as it appears in PDB
int res_indx ; //count from 0
char res_name ;
float N_coords[3] ;
float CA_coords[3] ;
float C_coords[3] ;
float O_coords[3] ;
float occupancy ;
float backbone_occupancies[4] ;
float Phi , Psi, Omega ;
pdb_info()
{
res_num[0] = '\0' ; res_indx = 0 ; res_name = 'Z' ;
for( int i = 0 ; i < 3 ; i++ )
{
N_coords[i] = -999 ; CA_coords[i] = -999 ;
C_coords[i] = -999 ; O_coords[i] = -999 ;
}
for( int i = 0 ; i < 4 ; i++ ) backbone_occupancies[i] = -9999 ;
occupancy = -1 ;
Phi = Psi = Omega = -999 ;
}
};
struct Complete_pdb_info // Contains entire info; used to generate superposed pdbs
{
char atom_name[6];
char residue[4] ;
char residue_num[6];
float coords[3] ;
float sup_coords[3] ;
float occupancy ;
float B_factor ;
struct Complete_pdb_info *link;
};
struct ramaplot
{
float Phi_Ulimit ;
float Phi_Llimit ;
float Psi_Ulimit ;
float Psi_Llimit ;
int Region_Code ;
} ;
struct SecondaryStruct_identifier
{
int SS_code ;
int start ;
int end ;
SecondaryStruct_identifier()
{
SS_code = start = end = -1 ;
}
} ;
struct glob_lib
{
int **mates;
int sizes[2] ;
};
struct maximal_fragments
{
int start[2] ;
int size ;
float rmsd ;
struct maximal_fragments *link ;
};
struct loc_lib
{
int frag_start[2] ;
int frag_size ;
float frag_rmsd ;
struct loc_lib *link ;
};
struct merge_lib
{
int *mates[2];
int *res_indices[2] ;
int sizes[2] ;
int seq_index[2] ;
struct merge_lib *link;
};
struct tree_info
{
int node_num ;
char leaf_flag;
int child_node_nums[2] ;
int node_size ;
int *node_list ;
float branch_lengths[2] ;
} ;
struct node_composition_from_Tree
{
int num ;
int *list ;
} ;
//STRUCT TEMPLATES ENDS HERE
extern char *STRUCT_PATH ;
extern char **struct_names;
extern char **struct_paths ;
extern char *OUTPUT_IDENTIFIER ;
extern char cmdlineparam_o[500] ;
extern int param_o_flag ;
extern int param_a_flag ;
extern int param_i_flag ;
extern int param_f_flag ;
extern int param_P_flag ;
extern int param_H_flag ;
extern int param_s_flag ;
extern int param_p_flag ;
extern int param_r_flag ;
extern int param_Fhtml_flag , param_Fps_flag,
param_Fpir_flag, param_Ffasta_flag ,
param_Fmsf_flag;
extern int param_D_flag ;
extern int NSTRUCTS ;
extern char OUTPUT_FILENAME_PREFIX[200];
extern struct pdb_info **PROT ;
extern int **secondary_stuct_identifier ;
extern struct Complete_pdb_info ***COMPLETE_PDBs ;
extern struct ramaplot efimov_regions[] ;
extern struct SecondaryStruct_identifier **SS_identifier ;
extern int *PROT_SIZES ;
extern int *PDB_SIZES ;
extern struct residues res_names[] ;
extern float ***distance_matrices;
extern float ***Edge_Weights ;
extern struct glob_lib *Global_Library ;
extern struct loc_lib **Local_Library ;
extern struct maximal_fragments **Max_Frags_Library ;
extern struct merge_lib **Merged_Library ;
extern float ***Extended_Edge_Weights;
extern char **ALGN ;
extern int **I_ALGN ; // contains alignment of residue indices
extern int **ALGN_QUALITY ; // a boolean mask containing which will help to decide whether or not residues
//in a column of multiple alignment are correctly aligned.
extern int ALGN_LEN ;
extern float CA_CA_DIAMETER ;
//extern struct glob_lib Pair_Algn[] ;
//extern float Pair_Algn_Costs[];
#endif /*GLOBALS_H*/
|
