/usr/lib/emboss/include/embprop.h is in emboss-lib 6.6.0+dfsg-6.
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 */
|