JPRED-2 Add sources of all binaries (except alscript) to Git

[jpred.git] / sources / multicoil / options.h

diff --git a/sources/multicoil/options.h b/sources/multicoil/options.h
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+++ b/sources/multicoil/options.h
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+/* options.h contains all the compile time decisions as for what form of   *
+ * the scoring algorithm to use.                                           *
+ */
+
+#ifndef __options_h__
+#define __options_h__ 1
+
+/***/
+/* #define DEBUG_PRINTOUT */
+/***/
+#define SHOW_DISCLAIMER 
+#define NOT_PROB
+
+/** #define NoGenProline        **/   /** Make genbnk prob of proline 0 **/
+
+#define TEST_VERSION       /** Puts in extra options that aren't available **/
+                          /** in the program release.                     **/
+/**/
+#define SMALL_MEMORY  
+/***/
+
+#define AVG_WEIRD_PROBS
+#define BONNIE_END_EFFECTS 
+                            /* Controls how handle windows that go beyond */
+                             /* the end of the sequence.  **/
+
+/* #define MinDist */   /*  The algorithm for computing residue propensities */
+#define AvgDist         /*  in scscore.c is determined by which is #defined. */
+
+
+#define LOGSCALE        /* If LOGSCALE then STOCK scores are given according */
+                        /* to their scoring system. Otherwise, use           */
+                        /* e^STOCK/28.                                       */
+
+#define STOCKSTOCK       /*  Uses the stock programs singles probabilities */
+                        /*  as computed from their data sets, not ours.   */
+                        /*  This allows us to compare with the actual runs*/
+                        /*  of stock's program.                           */
+/*#define STOCKOUR*/     /*  Uses the singles probability to be the prob.  */
+                        /*  of the positives normalized by genbnk.  This  */
+                        /*  allows us to compare with stock's method on   */
+                        /*  different positive data sets.                 */
+
+
+    
+/*** For computing residue propensities in scscore.c.                  */
+#ifdef MinDist
+#define SCOREIDENTITY HUGE_VAL
+#define SCOREACCUMULATE(GSC,SC) if ((GSC) > (SC)) (GSC) = (SC)
+#endif
+#ifdef AvgDist
+#define SCOREIDENTITY 0
+#define SCOREACCUMULATE(GSC,SC) (GSC) += (SC)/functnum
+#endif
+
+/*  For determining the singles probabilities when scoring STOCK method.  */
+#ifdef STOCKOUR
+#define RELATIVE(RESIDUE,REGISTER) (pprobs[RESIDUE][REGISTER] -gprobs[RESIDUE])
+#endif
+#ifdef STOCKSTOCK
+#define RELATIVE(RESIDUE,REGISTER) (relative[RESIDUE][REGISTER])
+#endif
+
+
+#endif   /* __options_h__ */
+