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
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
|
/* @source embdomain **********************************************************
**
** Algorithms for handling protein domain data.
** For use with Scop and Cath objects defined in ajdomain.h
**
** @author Copyright (c) 2004 Jon Ison (jison@hgmp.mrc.ac.uk)
** @version $Revision: 1.10 $
** @modified $Date: 2011/10/18 14:24:24 $ by $Author: rice $
** @@
**
** This library is free software; you can redistribute it and/or
** modify it under the terms of the GNU Lesser General Public
** License as published by the Free Software Foundation; either
** version 2.1 of the License, or (at your option) any later version.
**
** This library is distributed in the hope that it will be useful,
** but WITHOUT ANY WARRANTY; without even the implied warranty of
** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
** Lesser General Public License for more details.
**
** You should have received a copy of the GNU Lesser General Public
** License along with this library; if not, write to the Free Software
** Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
** MA 02110-1301, USA.
**
****************************************************************************/
#include "embdomain.h"
#include "embpdb.h"
#include "ajlib.h"
#include "ajdomain.h"
#include "ajlist.h"
/* ======================================================================= */
/* ============================ Private data ============================= */
/* ======================================================================= */
/* ======================================================================= */
/* ================= Prototypes for private functions ==================== */
/* ======================================================================= */
/* ======================================================================= */
/* ========================== Private functions ========================== */
/* ======================================================================= */
/* ======================================================================= */
/* =========================== constructors ============================== */
/* ======================================================================= */
/* @section Constructors ****************************************************
**
** All constructors return a pointer to a new instance. It is the
** responsibility of the user to first destroy any previous instance. The
** target pointer does not need to be initialised to NULL, but it is good
** programming practice to do so anyway.
**
****************************************************************************/
/* ======================================================================= */
/* =========================== destructors =============================== */
/* ======================================================================= */
/* @section Structure Destructors *******************************************
**
** All destructor functions receive the address of the instance to be
** deleted. The original pointer is set to NULL so is ready for re-use.
**
****************************************************************************/
/* ======================================================================= */
/* ============================ Assignments ============================== */
/* ======================================================================= */
/* @section Assignments *****************************************************
**
** These functions overwrite the instance provided as the first argument
** A NULL value is always acceptable so these functions are often used to
** create a new instance by assignment.
**
****************************************************************************/
/* ======================================================================= */
/* ============================= Modifiers =============================== */
/* ======================================================================= */
/* @section Modifiers *******************************************************
**
** These functions use the contents of an instance and update them.
**
****************************************************************************/
/* ======================================================================= */
/* ========================== Operators ===================================*/
/* ======================================================================= */
/* @section Operators *******************************************************
**
** These functions use the contents of an instance but do not make any
** changes.
**
****************************************************************************/
/* @func embScopToPdbid *******************************************************
**
** Read a scop identifier code and writes the equivalent pdb identifier code
**
** @param [r] scop [const AjPStr] Scop identifier code
** @param [w] pdb [AjPStr*] Pdb identifier code
**
** @return [AjPStr] Pointer to pdb identifier code.
**
** @release 2.9.0
** @@
****************************************************************************/
AjPStr embScopToPdbid(const AjPStr scop, AjPStr *pdb)
{
ajStrAssignSubS(pdb, scop, 1, 4);
return *pdb;
}
/* @func embScopToSp **********************************************************
**
** Read a scop identifier code and writes the equivalent swissprot
** identifier code. Relies on a list of Pdbtosp objects sorted by PDB
** code, which is usually obtained by a call to ajPdbtospReadAllNew.
**
** @param [r] scop [const AjPStr] Scop domain identifier code
** @param [w] spr [AjPStr*] Swissprot identifier code
** @param [r] list [const AjPList] Sorted list of Pdbtosp objects
**
** @return [AjBool] True if a swissprot identifier code was
** found for the Scop code.
**
** @release 2.9.0
** @@
****************************************************************************/
AjBool embScopToSp(const AjPStr scop, AjPStr *spr, const AjPList list)
{
AjPStr pdb = NULL;
pdb = ajStrNew();
if(embPdbidToSp(embScopToPdbid(scop, &pdb), spr, list))
{
ajStrDel(&pdb);
return ajTrue;
}
ajStrDel(&pdb);
return ajFalse;
}
/* @func embScopToAcc *********************************************************
**
** Read a scop identifier code and writes the equivalent accession number.
** Relies on a list of Pdbtosp objects sorted by PDB code, which is usually
** obtained by a call to ajPdbtospReadAllNew.
**
** @param [r] scop [const AjPStr] Scop domain identifier code
** @param [w] acc [AjPStr*] Accession number
** @param [r] list [const AjPList] Sorted list of Pdbtosp objects
**
** @return [AjBool] True if a swissprot identifier code was found for the
** Scop code.
**
** @release 2.9.0
** @@
****************************************************************************/
AjBool embScopToAcc(const AjPStr scop, AjPStr *acc, const AjPList list)
{
AjPStr pdb = NULL;
pdb = ajStrNew();
if(embPdbidToAcc(embScopToPdbid(scop, &pdb), acc, list))
{
ajStrDel(&pdb);
return ajTrue;
}
ajStrDel(&pdb);
return ajFalse;
}
/* ======================================================================= */
/* ============================== Casts ===================================*/
/* ======================================================================= */
/* @section Casts ***********************************************************
**
** These functions examine the contents of an instance and return some
** derived information. Some of them provide access to the internal
** components of an instance. They are provided for programming convenience
** but should be used with caution.
**
****************************************************************************/
/* ======================================================================= */
/* =========================== Reporters ==================================*/
/* ======================================================================= */
/* @section Reporters *******************************************************
**
** These functions return the contents of an instance but do not make any
** changes.
**
****************************************************************************/
/* ======================================================================= */
/* ========================== Input & Output ============================= */
/* ======================================================================= */
/* @section Input & output **************************************************
**
** These functions are used for formatted input and output to file.
**
****************************************************************************/
/* ======================================================================= */
/* ======================== Miscellaneous =================================*/
/* ======================================================================= */
/* @section Miscellaneous ***************************************************
**
** These functions may have diverse functions that do not fit into the other
** categories.
**
****************************************************************************/
|
