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
|
/* @source embmol *************************************************************
**
** Routines for molecular weight matching.
**
** @author Copyright (c) 1999 Alan Bleasby
** @version $Revision: 1.23 $
** @modified $Date: 2012/07/14 14:52:40 $ 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 "ajlib.h"
#include "embmol.h"
#include "embprop.h"
#include "ajarr.h"
#include <string.h>
#include <stdlib.h>
#include <limits.h>
#include <stdio.h>
#include <math.h>
static ajint embMolFragSort(const void* a, const void* b);
/* @func embMolGetFrags *******************************************************
**
** Create a sorted list of molwt fragments
**
** @param [r] thys [const AjPStr] sequence
** @param [r] rno [ajint] 1=Trypsin 2=LysC 3=ArgC 4=AspN 5=V8b 6=V8p
** 7=Chy 8=CNBr
** @param [r] mwdata [EmbPPropMolwt const *] molecular weight data
** @param [r] mono [AjBool] true for monoisotopic data
** @param [w] l [AjPList*] list for results
** @return [ajint] number of fragments
**
** @release 1.13.0
******************************************************************************/
ajint embMolGetFrags(const AjPStr thys, ajint rno, EmbPPropMolwt const *mwdata,
AjBool mono, AjPList *l)
{
static struct enz
{
const char *ename;
const char *residues;
const char *type;
const char *partial;
} zyme[]=
{
{"Trypsin","KR","CC","KRIFL"},
{"Lys-C","K","C",""},
{"Arg-C","R","C",""},
{"Asp-N","D","N",""},
{"V8b","E","C","KR"},
{"V8p","DE","CC",""},
{"Chymotrypsin","FYWLM","CCCCC",""},
{"CNBr","M","C",""}
};
EmbPMolFrag frag = NULL;
EmbPMolFrag *ptr = NULL;
ajint len;
ajint pos;
const char *p;
static AjPInt defcut =NULL;
ajint defcnt;
ajint beg;
ajint end;
ajint i;
double mw;
if(!defcut)
defcut=ajIntNew();
--rno;
len = ajStrGetLen(thys);
p = ajStrGetPtr(thys);
defcnt=0;
/* Positions of complete digest cuts */
for(pos=0;pos<len;++pos)
{
if(!strchr(zyme[rno].residues,(ajint)p[pos]))
continue;
if(len==pos+1)
continue;
if(p[pos+1]=='P' && rno!=3 && rno!=7)
continue;
if(rno==4 && p[pos+1]=='E')
continue;
ajIntPut(&defcut,defcnt++,pos);
}
/* Molwts of definite cuts */
beg = 0;
for(i=0;i<defcnt;++i)
{
end = ajIntGet(defcut,i);
if(strchr(zyme[rno].type,(ajint)'N'))
--end;
mw = embPropCalcMolwt(p,beg,end, mwdata, mono);
if(rno==7)
mw -= (double)(17.0079 + 31.095);
AJNEW0(frag);
frag->begin = beg+1;
frag->end = end+1;
frag->mwt = mw;
ajListPush(*l,(void *)frag);
beg = end+1;
}
if(defcnt)
{
mw = embPropCalcMolwt(p,beg,len-1,mwdata,mono);
if(rno==7)
mw -= (double)(17.0079 + 31.095);
AJNEW0(frag);
frag->begin = beg+1;
frag->end = len;
frag->mwt = mw;
ajListPush(*l,(void *)frag);
}
/* Overlaps */
if(defcnt)
{
ajListReverse(*l);
ajListToarray(*l,(void ***)&ptr);
for(i=0;i<defcnt-1;++i)
{
beg = ptr[i]->begin;
end = ptr[i+1]->end;
AJNEW0(frag);
frag->begin = beg;
frag->end = end;
mw = embPropCalcMolwt(p,beg-1,end-1,mwdata,mono);
frag->mwt = mw + EMBMOLPARDISP;
ajListPush(*l,(void *)frag);
}
AJFREE(ptr);
}
ajListSort(*l, &embMolFragSort);
ajIntDel(&defcut);
return (ajuint) ajListGetLength(*l);
}
/* @funcstatic embMolFragSort *************************************************
**
** Sort routine for molwt fragments
**
** @param [r] a [const void*] EmbPMolFrag pointer
** @param [r] b [const void*] EmbPMolFrag pointer
**
** @return [ajint] molwt difference
**
** @release 1.5.0
******************************************************************************/
static ajint embMolFragSort(const void* a, const void* b)
{
return (ajint)((*(EmbPMolFrag const *)a)->mwt -
(*(EmbPMolFrag const *)b)->mwt);
}
|
