update biology/babel to properly output mm3 files.

PR:		ports/42425
Submitted by:	Glenn Johnson <glennpj@charter.net>

biology/babel/Makefile

@@ -7,7 +7,7 @@
 
 PORTNAME=	babel
 PORTVERSION=	1.6
-PORTREVISION=	2
+PORTREVISION=	3
 CATEGORIES=	biology converters
 MASTER_SITES=	http://smog.com/chem/babel/files/ \
 		http://www.ccl.net/cca/software/UNIX/babel/ \

biology/babel/files/patch-wrmm3.c

@@ -0,0 +1,92 @@
+
+$FreeBSD$
+
+--- wrmm3.c.orig	Tue Jan 21 09:53:02 1997
++++ wrmm3.c	Wed Sep  4 16:00:23 2002
+@@ -33,14 +33,17 @@
+   int METHOD; /* 0 no cojugated pi system, 1 if conjugated pi system */
+   int N; /* #of atoms */
+   int IPRINT; /* Controls amount of printout */
++  int MDERIV; /* Optimization termination; 0 for geometry, 1 for energy */
+   int NSTR; /* Restricted motion data  */
+   int INIT; /* Minimize energy  */
+   int NCONST; /* Read in new constants ? */
+   double TMAX; /* Max time */
+ 
++  int KFIXTYP; /* Atom type check; 0 for yes, 1 for no */
+   int NCON; /* Number of connected atoms */
+   int NATTACH; /*Number of attached atoms */
+-  double DEL; /* Termianation of geometry optimization */
++  double DEL; /* Termination of geometry optimization, convergence limit */
++  int ISPEED; /* Speed up minimization of crude structures, 0 is no, 1 is yes */
+   int NSYMM;/* Number of symmetry matrices */
+   int NX; /* Number of coordiante calcualtions or replacement cards */
+   int NROT; /* Reorient */
+@@ -62,17 +65,20 @@
+   strcpy(ID,OutfileName);
+ 
+ /*------ CARD 1 -------*/
+-  METHOD = 1;
++  METHOD = 0;
+   N = Atoms;
+   IPRINT = 3;
+   if (isdigit(OutputKeywords[0]))
+     IPRINT = atoi(OutputKeywords);
++  MDERIV = 1;
+   NSTR = 0;
+   INIT = 0;
+-  NCONST = 0;
++  NCONST = 1;
+   TMAX = 999.0;
+ /*------ CARD 2 -------*/
++  KFIXTYP = 0;
+   DEL = 0.00008;
++  ISPEED = 0;
+   NCON = connections;
+   NATTACH = attachments;
+   NSYMM = 0;
+@@ -86,22 +92,23 @@
+   NDRIVE = 0;
+   
+ 
+-  fprintf(file1,"%-60s%d%4d %d  %d %d  %d%-5.0f\n",
++  fprintf(file1,"%-60s%1d%4d%2d%1d%2d%2d%3d%5.0f\n",
+ 	  ID,
+ 	  METHOD,
+ 	  N,
+ 	  IPRINT,
++	  MDERIV,
+ 	  NSTR,
+ 	  INIT,
+ 	  NCONST,
+ 	  TMAX);
+ 
+-  fprintf(file1,"%1d%4d%5s%4.5f%8s%5d%5d%5d%5d%5d%5d%5d%5d%10d%5d\n",
+-	  0,
++  fprintf(file1,"%1d%4d%5s%10.7f%5d%5d%5d%5d%5d%5d%5d%5d%5d%5s%5d%5d\n",
++	  KFIXTYP,
+ 	  NCON,
+ 	  "",
+ 	  DEL,
+-	  "",
++	  ISPEED,
+ 	  NATTACH,
+ 	  NSYMM,
+ 	  NX,
+@@ -110,6 +117,7 @@
+ 	  NDC,
+ 	  NCALC,
+ 	  HFORM,
++	  "",
+ 	  MVDW,
+ 	  NDRIVE);
+ 
+@@ -145,7 +153,7 @@
+     get_output_type(i,"MM2",Type(i),temp_type,all_caps);
+     type_name = atoi(temp_type);
+     type_name = update_mm2_types(mol,i,type_name);
+-    fprintf(file1,"  %8.5f  %8.5f  %8.5f%5d(%3d)\n",
++    fprintf(file1,"%10.5f%10.5f%10.5f%5d(%3d)\n",
+ 	    X(i),
+ 	    Y(i),
+ 	    Z(i),