This file is indexed.

/usr/lib/emboss/include/embprop.h is in emboss-lib 6.6.0-1.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  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
/* @include embprop ***********************************************************
**
** Residue/sequence properties
**
** @author Copyright (c) 1999 Alan Bleasby
** @version $Revision: 1.28 $
** @modified 24 Nov 1999 - GWW - Added embPropProtGaps and embPropProt1to3
** @modified 1 Sept 2000 - GWW - Added embPropTransition embPropTranversion
** @modified 4 July 2001 - DMAM - Modified embPropAminoRead embPropCalcMolwt
** @modified 4 July 2001 - DMAM - Added embPropCalcMolwtMod
** @modified 1 July 2008 - JISON - Added embPropGet* functions
** @modified $Date: 2011/10/18 14:24:25 $ 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.
**
******************************************************************************/

#ifndef EMBPROP_H
#define EMBPROP_H

/* ========================================================================= */
/* ============================= include files ============================= */
/* ========================================================================= */

#include "ajdefine.h"
#include "ajstr.h"
#include "ajfile.h"
#include "ajlist.h"
#include "ajseqdata.h"

AJ_BEGIN_DECLS




/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */




#define EMBPROPSIZE 29
#define EMBPROPMOLWT      0
#define EMBEMBPROPTINY    1
#define EMBPROPSMALL      2
#define EMBPROPALIPHATIC  3
#define EMBPROPAROMATIC   4
#define EMBPROPNONPOLAR   5
#define EMBPROPPOLAR      6
#define EMBPROPCHARGE     7
#define EMBPROPPOSITIVE   8
#define EMBPROPNEGATIVE   9
#define EMBPROPABSORBANCE 10

#define EMBPROPHINDEX 26
#define EMBPROPOINDEX 27
#define EMBPROPWINDEX 28

/* define monoisotopic masses for common N- and C- terminal modifications
**
**Values from Expasy
**
**http://www.expasy.org/tools/findmod/findmod_masses.html
*/

#define EMBPROPMSTN_H       1.00783
#define EMBPROPMSTN_FORMYL 29.01823
#define EMBPROPMSTN_ACETYL 43.04013

#define EMBPROPMSTC_OH     17.00274
#define EMBPROPMSTC_AMIDE  16.01804




/* ========================================================================= */
/* ============================== public data ============================== */
/* ========================================================================= */




/* @data EmbPPropAmino ********************************************************
**
** Amino acid properties
**
** @attr tiny [ajint] tiny
** @attr sm_all [ajint] small
** @attr aliphatic [ajint] aliphatic
** @attr aromatic [ajint] aromatic
** @attr nonpolar [ajint] non-polar
** @attr polar [ajint] polar
** @attr charge [float] charge
** @attr pve [ajint] positive
** @attr nve [ajint] negative
** @attr extcoeff [ajint] extinction coefficient
** @attr Padding [char[4]] padding to alignment boundary
** @@
******************************************************************************/

typedef struct EmbSPropAmino
{
    ajint     tiny;
    ajint     sm_all;
    ajint     aliphatic;
    ajint     aromatic;
    ajint     nonpolar;
    ajint     polar;
    float     charge;
    ajint     pve;
    ajint     nve;
    ajint     extcoeff;
    char      Padding[4];
} EmbOPropAmino;
#define EmbPPropAmino EmbOPropAmino*




/* @data EmbPPropMolwt ********************************************************
**
** Molecular weights
**
** @attr average [double] average molwt
** @attr mono [double] monoisotopic molwt
** @@
******************************************************************************/

typedef struct EmbSPropMolwt
{
    double average;
    double mono;
} EmbOPropMolwt;
#define EmbPPropMolwt EmbOPropMolwt*




typedef struct EmbSPropFrag	/* Enzyme digestion structure */
{
    ajint     start;
    ajint     end;
    double    molwt;
    AjBool    isfrag;
    char      Padding[4];
} EmbOPropFrag;
#define EmbPPropFrag EmbOPropFrag*




/* ========================================================================= */
/* =========================== public functions ============================ */
/* ========================================================================= */



/*
** Prototype definitions
*/

EmbPPropAmino *embPropEaminoRead(AjPFile fp);
EmbPPropMolwt *embPropEmolwtRead(AjPFile fp);
void          embPropAminoDel(EmbPPropAmino **thys);
void          embPropMolwtDel(EmbPPropMolwt **thys);

float embPropMolwtGetMolwt(const EmbPPropMolwt prop);
float embPropGetCharge(const EmbPPropAmino prop);
AjBool embPropGetProperties(const EmbPPropAmino prop, AjPStr* Pstr);
ajint embPropGetTiny(const EmbPPropAmino prop);
ajint embPropGetSmall(const EmbPPropAmino prop);
ajint embPropGetAliphatic(const EmbPPropAmino prop);
ajint embPropGetAromatic(const EmbPPropAmino prop);
ajint embPropGetNonpolar(const EmbPPropAmino prop);
ajint embPropGetPolar(const EmbPPropAmino prop);
ajint embPropGetPve(const EmbPPropAmino prop);
ajint embPropGetNve(const EmbPPropAmino prop);
ajint embPropGetExtcoeff(const EmbPPropAmino prop);



/* void    embPropAminoRead (void); */
void 	embPropCalcFragments (const char *s, ajint n,
			      AjPList *l, AjPList *pa,
			      AjBool unfavoured, AjBool overlap,
			      AjBool allpartials, ajint *ncomp, ajint *npart,
			      AjPStr *rname, AjBool nterm, AjBool cterm,
			      AjBool dorag, EmbPPropMolwt const  *mwdata,
			      AjBool mono);
double  embPropCalcMolextcoeff(const char *s, ajint start, ajint end,
			       AjBool cystine, EmbPPropAmino const *aadata);
double  embPropCalcMolwt (const char *s, ajint start, ajint end,
			  EmbPPropMolwt const *mwdata, AjBool mono);
/* new method for chemically modified ends */
double  embPropCalcMolwtMod (const char *s, ajint start, ajint end,
			     EmbPPropMolwt const *mwdata, AjBool mono,
			     double nmass, double cmass);
const char*   embPropCharToThree (char c);

void    embPropFixF(float matrix[], float missing);
const char*   embPropIntToThree (ajint c);
void    embPropNormalF(float matrix[], float missing);
AjPStr  embPropProtGaps (AjPSeq seq, ajint pad);
AjPStr  embPropProt1to3 (AjPSeq seq, ajint pad);
AjPStr  embPropProt1to3Rev (AjPSeq seq, ajint pad);
AjBool  embPropPurine (char base);
AjBool  embPropPyrimidine (char base);
AjBool  embPropTransversion (char base1, char base2);
AjBool  embPropTransition (char base1, char base2);

/*
** End of prototype definitions
*/

AJ_END_DECLS

#endif  /* !EMBPROP_H */