Go to the SVN repository for this file.
1 /* $Id: thrdatd.h 33815 2007-05-04 17:18:18Z kazimird $ 2 *=========================================================================== 5 * National Center for Biotechnology Information 7 * This software/database is a "United States Government Work" under the 8 * terms of the United States Copyright Act. It was written as part of 9 * the author's official duties as a United States Government employee and 10 * thus cannot be copyrighted. This software/database is freely available 11 * to the public for use. The National Library of Medicine and the U.S. 12 * Government have not placed any restriction on its use or reproduction. 14 * Although all reasonable efforts have been taken to ensure the accuracy 15 * and reliability of the software and data, the NLM and the U.S. 16 * Government do not and cannot warrant the performance or results that 17 * may be obtained by using this software or data. The NLM and the U.S. 18 * Government disclaim all warranties, express or implied, including 19 * warranties of performance, merchantability or fitness for any particular 22 * Please cite the author in any work or product based on this material. 24 * =========================================================================== 26 * File Name: thrdatd.h 28 * Author: Stephen Bryant 30 * Initial Version Creation Date: 08/16/2000 34 * File Description: threader 37 /* atd.h - structure and function declarations for adaptive threading */ 38 /* Steve Bryant, 6/93 */ 40 #if !defined(THRDATD_H) 47 /* Argument data structures */ 49 typedef struct _Fld_Mtf{
/* Folding motif data structure */ 50 int n;
/* Number of residues in the structure */ 51 struct{
/* Residue-residue contact list */ 52 int*
r1;
/* Index of first residue of in a pair */ 53 int*
r2;
/* Index second residue in a pair */ 54 int*
d;
/* Distance interval in a pair */ 55 int n;
/* Number of contact pairs */ 57 struct{
/* Residue-peptide contact list */ 58 int*
r1;
/* Index of side-chain residue in a pair */ 59 int*
p2;
/* Index of the peptide group in a pair */ 60 int*
d;
/* Distance interval of a contact pair */ 61 int n;
/* Number of contact pairs */ 63 int**
mll;
/* Minimum loop lengths by residue pair */ 67 typedef struct _Cor_Def{
/* Core definition data structure */ 68 struct{
/* Core segment location limits */ 69 int*
rfpt;
/* Index of central reference residue */ 70 int*
nomn;
/* Minimun offset of core segment N-termini */ 71 int*
nomx;
/* Maxixmum offset of core segment N-termini */ 72 int*
comn;
/* Minimun offset of core segment C-termini */ 73 int*
comx;
/* Maxixmum offset of core segment C-termini */ 74 int n;
/* Number of core segments */ 76 struct{
/* Loop length limits */ 77 int*
llmn;
/* Minimum lengths, including tails */ 78 int*
llmx;
/* Maximum lengths, including tails */ 79 int*
lrfs;
/* Maximun number of residues in ref. state */ 80 int n;
/* Number of loops, one more than core segs */ 82 struct{
/* Fixed-sequence segment locations */ 83 int*
nt;
/* Fixed segment N-termini */ 84 int*
ct;
/* Fixed segment C-termini */ 85 int*
sq;
/* Motif sequence containing fixed segs */ 86 int n;
/* Number of fixed segments */ 91 typedef struct _Qry_Seq{
/* Query sequence data structure */ 92 int*
sq;
/* The sequence as an integer array */ 93 int n;
/* Number of residues in that sequence */ 94 struct{
/* Alignment contstraints for this sequence */ 95 int*
mn;
/* Minimum and maximum query sequence indices */ 96 int*
mx;
/* to be aligned with each core segment */ 97 int n;
/* Number of constraints */ 102 typedef struct _Rcx_Ptl{
/* Pairwise contact potential */ 103 int***
rre;
/* Pair energies by type and distance */ 104 int**
re;
/* Hydrophobic energies by type and distance */ 105 int***
rrt;
/* Sum of pair plus hydrophobic energies */ 106 int nrt;
/* Number or residue types */ 107 int ndi;
/* Number of distance intervals */ 108 int ppi;
/* Index of the peptide group */ 112 typedef struct _Gib_Scd{
/* Gibbs schedule parameters */ 113 int ntp;
/* number of trajectory points */ 114 int nrs;
/* Number of random starts */ 115 int nts;
/* Number of temperature steps */ 116 int crs;
/* Number of starts before convergence test */ 117 int cfm;
/* Top thread frequency convergence criterion */ 118 int csm;
/* Top thread start convergence criterion */ 119 int cet;
/* Temperature for convergence test ensemble */ 120 int cef;
/* Percent of ensemble defining top threads */ 121 int isl;
/* Code for choice of starting locations */ 122 int iso;
/* Code for choice of segment sample order */ 123 int ito;
/* Code for choice of terminus sample order */ 124 int rsd;
/* Seeds for random number generator */ 125 int als;
/* Code for choice of alignment record style */ 126 int trg;
/* Code for choice of trajectory record */ 127 int*
nti;
/* Number of iterations per tempeature step */ 128 int*
nac;
/* Number of alignment cycles per iteration */ 129 int*
nlc;
/* Number of location cycles per iteration */ 130 int*
tma;
/* Temperature steps for alignment sampling */ 131 int*
tml;
/* Temperature steps for location sampling */ 132 int*
lms;
/* Iterations before local minimum test */ 133 int*
lmw;
/* Iterations in local min test interval */ 134 int*
lmf;
/* Percent of top score indicating local min */ 138 typedef struct _Thd_Tbl{
/* Thread table data structure */ 139 float*
tg;
/* Energy of this thread */ 140 float*
ps;
/* Potential energy */ 141 float*
ms;
/* Motif energy */ 142 float*
cs;
/* Conservation energy */ 143 float*
lps;
/* Loopout energy */ 144 float*
zsc;
/* Z-score */ 145 float*
g0;
/* Average total energy of shuffled seq */ 146 float*
m0;
/* Average motif score of shuffled seq */ 147 float*
errm;
/* Standard error of random motif scores */ 148 float*
errp;
/* Standard error of random contact scores */ 149 int*
tf;
/* Frequency of this thread in sampling */ 150 int*
ts;
/* Number of starts in which it was found */ 151 int*
ls;
/* Last start in which this thread was found */ 152 int**
al;
/* Alignment of query to each core segment */ 153 int**
no;
/* N-terminal offset of each core segment */ 154 int**
co;
/* C-terminal offset of each core segment */ 155 int*
pr;
/* Index of next-higher energy thread */ 156 int*
nx;
/* Index of next-lower energy thread */ 157 int mx;
/* Index of lowest energy thread in list */ 158 int mn;
/* Index of highest energy thread in list */ 159 int n;
/* Maximum number of threads in linked list */ 160 int nsc;
/* Number of core segments */ 164 typedef struct _Thd_Tst{
/* Storage for local min and convergence test */ 165 float*
bw;
/* Boltzmann weight of this thread */ 166 int nw;
/* Number of Boltzmann weight values */ 167 float*
ib;
/* Best energy found for each iteration */ 168 int nb;
/* Number of best energy values */ 169 float gb;
/* Best energy across iterations */ 170 int lm;
/* Flag for local minimum */ 171 int tf;
/* Top-thread best alignment frequency */ 172 int ts;
/* Top-thread best random start count */ 176 /* Tracking data structures for Gibb's sampling */ 178 typedef struct _Cur_Loc{
/* Location of core segments in motif */ 179 int*
no;
/* N-terminus offset from reference point */ 180 int*
co;
/* C-terminus offset from reference point */ 181 int nsc;
/* Number of core segments */ 182 int*
lp;
/* Minimum loop length derived from motif */ 183 int nlp;
/* Number of loops */ 184 int*
cr;
/* Core segment index by residue position */ 185 int nmt;
/* Number of residue positions in motif */ 189 typedef struct _Cur_Aln{
/* Aligment of query sequence with core */ 190 int*
al;
/* Query sequence index aligned with rfpt */ 191 int nsc;
/* Number of core segments */ 192 int*
sq;
/* Residue types currently assigned to motif */ 193 int*
cf;
/* Core segment indices at maximun extent */ 194 int nmt;
/* Number of residue positions in motif */ 198 typedef struct _Seg_Nsm{
/* Number of contacts by segment pair */ 199 int***
nrr;
/* Res-res counts by seg by seg by dis */ 200 int*
srr;
/* Total res-res counts by distance interval */ 201 int***
nrp;
/* Res-pep counts by seg by seg by dis */ 202 int*
srp;
/* Total res-pep counts by distance interval */ 203 int***
nrf;
/* Res-fixed contacts by seg by type by dis */ 204 int**
frf;
/* Total res-fixed contacts by type by dis */ 205 int*
srf;
/* Total res-fixed contacts by dis */ 206 int trf;
/* Total res-fixed contacts */ 207 int nsc;
/* Number of core segments */ 208 int ndi;
/* Number of distance intervals */ 209 int nrt;
/* Number of residue types */ 213 typedef struct _Seg_Cmp{
/* Segment pair amino acid composition */ 214 int**
srt;
/* Residue type counts by core segment */ 215 int nsc;
/* Number of core segments */ 216 int nrt;
/* Number of residue types */ 217 int**
lrt;
/* Residue type counts by loop segment */ 218 int nlp;
/* Number of loop segments */ 219 int*
rt;
/* Total residue type counts */ 220 int*
rto;
/* Residue type counts from previous thread */ 224 typedef struct _Seg_Gsm{
/* Current contact energies by segmenmt pair */ 225 int**
gss;
/* Potential energies by core segment pair */ 226 int*
gs;
/* Potential energies by core segment */ 227 int*
ms;
/* Motif energies by core segment */ 228 int*
cs;
/* Conservation energies by core segment */ 229 int*
ls;
/* Loopout energies by by core segment */ 230 int*
s0;
/* Expected motif energies by core segment */ 231 int nsc;
/* The number of segments */ 235 typedef struct _Thd_Cxe{
/* Expected energy of pairwise contacts */ 236 float*
rp;
/* Residue frequencies, from type counts */ 237 float**
rrp;
/* Mass action residue pair probabilities */ 238 int nrt;
/* Number of residue types */ 239 float*
rre;
/* Expected energy of a res-res contact */ 240 float*
rpe;
/* Expected energy of a res-pep contact */ 241 float*
rfe;
/* Expected energy of a res-fix contact */ 242 int ndi;
/* Number of distance intervals */ 246 typedef struct _Thd_Gsm{
/* Total thread energy */ 247 int g;
/* G(r|m), sum of potentials */ 248 float g0;
/* G0(r|m), reference state energy for potential */ 249 float dg;
/* Overall thread energy */ 250 float ps;
/* G(r|m)-G0(r|m)-overall potential energy */ 251 float ms;
/* Overall motif energy */ 252 float m0;
/* Average motif score for random assignment*/ 253 float cs;
/* Overall conservation energy */ 254 float ls;
/* Overall loopout energy */ 258 typedef struct _Cxl_Als{
/* Contacts by segment for alignment sampling */ 259 struct{
/* Residue-residue contact list */ 260 int*
r1;
/* Index of first residue in a pair */ 261 int*
r2;
/* Index second residue in a pair */ 262 int***
e;
/* Energy of each type pair at these pos. */ 263 int n;
/* Number of contact pairs */ 265 struct{
/* Residue-hfo/pep/fix contact list */ 266 int*
r;
/* Index of a position with contacts */ 267 int**
e;
/* Energy of each residue type at this pos. */ 268 int n;
/* Number of residue-peptide contact terms */ 273 typedef struct _Cxl_Los{
/* Contacts by segment for extent sampling */ 274 struct{
/* Residue-residue contact list */ 275 int*
r1;
/* Index of first residue in a pair */ 276 int*
r2;
/* Index second residue in a pair */ 277 int*
d;
/* Contact distance interval */ 278 int*
e;
/* Energy of a contact at these positions */ 279 int n;
/* Number of contact pairs */ 281 struct{
/* Residue-peptide contact list */ 282 int*
r1;
/* Index of first residue in a pair */ 283 int*
p2;
/* Index second residue in a pair */ 284 int*
d;
/* Contact distance interval */ 285 int*
e;
/* Energy of the pair, given alignment */ 286 int n;
/* Number of contact pairs */ 288 struct{
/* Residue-fixed environment contact list */ 289 int*
r1;
/* Index of a position with contacts */ 290 int*
t2;
/* Type of second residue in the pair */ 291 int*
d;
/* Contact distance interval */ 292 int*
e;
/* Energy of the pair, given alignment */ 293 int n;
/* Number of residue-peptide contact terms */ 298 typedef struct _Seg_Ord{
/* Sampling order for core segments */ 299 int*
si;
/* Indices of variables for sampling */ 300 int*
so;
/* Sample order for variables */ 301 int*
to;
/* Flags first terminus for extent sampling */ 302 int nsc;
/* Number of core segments */ 306 typedef struct _Rnd_Smp{
/* Random-sampling and permutation parameters */ 307 int n;
/* Number of values a variable may adopt */ 308 float*
p;
/* Probabilitites associated with each value */ 309 float*
e;
/* Energies associated with each value */ 310 int*
lsg;
/* Start/stop sites of loop segments in structure */ 311 int*
aqi;
/* Indeces of the residues to be shuffled */ 312 int*
r,*
o;
/* Shuffled values and order permutation */ 313 int*
sq;
/* Permuted sequence */ 317 typedef struct _Seq_Mtf{
/* Sequence motif parameters */ 318 int**
ww;
/* Weights */ 319 int**
freqs;
/* residue frequencies */ 320 int n;
/* Number of residues in structure */ 322 float ww0;
/* Expected energy of template profile term */ 326 /*----------------------------------------------------------------------------*/ 328 /*----------------------------------------------------------------------------*/ 329 #define BIGNEG -1000000000. 330 #define NERZRO .000001RetroSearch is an open source project built by @garambo | Open a GitHub Issue
Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo
HTML:
3.2
| Encoding:
UTF-8
| Version:
0.7.4