FreeBSD Bugzilla – Attachment 24865 Details for
Bug 42425
update biology/babel to properly output mm3 files
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babel-patch
babel-patch (text/plain), 2.96 KB, created by
gjohnson
on 2002-09-04 22:20:00 UTC
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Description:
babel-patch
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Creator:
gjohnson
Created:
2002-09-04 22:20:00 UTC
Size:
2.96 KB
patch
obsolete
>diff -ruN biology/babel.orig/Makefile biology/babel/Makefile >--- biology/babel.orig/Makefile Wed Sep 4 15:31:43 2002 >+++ biology/babel/Makefile Wed Sep 4 15:39:26 2002 >@@ -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/ \ >diff -ruN biology/babel.orig/files/patch-wrmm3.c biology/babel/files/patch-wrmm3.c >--- biology/babel.orig/files/patch-wrmm3.c Wed Dec 31 18:00:00 1969 >+++ biology/babel/files/patch-wrmm3.c Wed Sep 4 16:00:40 2002 >@@ -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),
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bug 42425
: 24865