JPRED-2 Add alscript to the Git repository

[jpred.git] / sources / alscript / src / mzcons.c

diff --git a/sources/alscript/src/mzcons.c b/sources/alscript/src/mzcons.c
new file mode 100644 (file)
index 0000000..fd67769
--- /dev/null
+++ b/sources/alscript/src/mzcons.c
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+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <gjutil.h>
+
+int GJindex(char *str,char c);
+
+float mzcons(unsigned char *pos,int n)
+
+/* calculate conservation value according to Zvelebil et al for a set
+   of amino acids and gaps stored in string pos of length n
+
+   Copyright:  Geoffrey J. Barton (1992,1997)
+
+   email: geoff@ebi.ac.uk
+   Please see the README file for details of conditions for use of this program.
+
+   $Id: mzcons.c,v 1.2 1998/09/17 16:55:07 geoff Exp $
+   $Log: mzcons.c,v $
+   Revision 1.2  1998/09/17 16:55:07  geoff
+   Check consistency with archive
+
+
+*/
+
+{
+
+/* --  conmat contains a table like that shown in the JMB paper
+       order of amino acids is GAP,ARNDCQEGHILKMFPSTWYBZX
+*/
+    static char *acids = " ARNDCQEGHILKMFPSTWYBZX";
+    static int conmat[24][10] = {
+       {1,1,1,1,1,1,1,1,1,1},
+       {1,0,0,0,0,1,1,0,0,0},
+       {0,1,0,1,1,0,0,0,0,0},
+       {0,0,0,1,0,1,0,0,0,0},
+       {0,0,1,1,1,1,0,0,0,0}, 
+       {1,0,0,0,0,1,0,0,0,0},
+       {0,0,0,1,0,0,0,0,0,0},
+       {0,0,1,1,1,0,0,0,0,0},
+       {1,0,0,0,0,1,1,0,0,0}, 
+       {1,1,0,1,1,0,0,0,1,0},
+       {1,0,0,0,0,0,0,1,0,0},
+       {1,0,0,0,0,0,0,1,0,0},
+       {1,1,0,1,1,0,0,0,0,0},
+       {1,0,0,0,0,0,0,0,0,0},
+       {1,0,0,0,0,0,0,0,1,0},
+       {0,0,0,0,0,1,0,0,0,1},
+       {0,0,0,1,0,1,1,0,0,0},
+       {1,0,0,1,0,1,0,0,0,0},
+       {1,0,0,1,0,0,0,0,1,0},
+       {1,0,0,1,0,0,0,0,1,0},
+       {1,0,0,0,0,1,0,1,0,0},
+       {0,0,0,1,0,0,0,0,0,0},
+       {0,0,0,1,0,0,0,0,0,0},
+       {1,1,1,1,1,1,1,1,1,1}
+    };
+
+    int concnt,it,i,j,k,l,tcnt,ibseq;
+    int nide, facid;
+
+    concnt = 0;
+    for(j=0;j<10;++j){
+       /*found: outer loop over properties
+       set IT to the value of the first amino acid*/
+       it = conmat[GJindex(acids,pos[0])][j];
+       /*loop over remaining acids, if a difference occurs then
+        set tcnt to 1*/
+        tcnt = 0;
+        for(k=1;k<n;++k){
+           if(it != conmat[GJindex(acids,pos[k])][j]){
+                tcnt = 1;
+          }
+       }
+       /*add tcnt to concnt*/
+        concnt += tcnt;
+    }
+    /* check for total identity at this position*/
+    facid = pos[0];
+    nide = 0;
+    for(k=1;k<n;++k){
+       if(facid == pos[k]){
+             ++nide;
+       }
+    }
+
+    /*calculate the conservation*/
+    if(concnt == 10){
+      con = 0.0;
+    }else if(concnt == 0){
+       if(nide == n){
+           /*total identity*/
+            con = 1.0;
+       }else{
+            /*not identity, but same properties*/
+              con = 0.9;
+       }
+    }else{
+        con = 0.9 - 0.1 * concnt;
+    }
+    return con;
+}
+
+
+int GJindex(char *str,char c)
+{
+    char *t;
+    t = strchr(str,c);
+    if(t == NULL) return NULL;
+    return (int) (t - str);
+}
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