diff options
| author | edwin <edwin@FreeBSD.org> | 2003-01-03 16:52:41 +0800 |
|---|---|---|
| committer | edwin <edwin@FreeBSD.org> | 2003-01-03 16:52:41 +0800 |
| commit | 9e323cce15d82371bf24272bc9d9ead2bcd12315 (patch) | |
| tree | c36132d1fe23eae343106fa29cfc2ca7eaf7fbf5 | |
| parent | cb6f1f759edce5406cda9eece7451a0da6218282 (diff) | |
| download | freebsd-ports-gnome-9e323cce15d82371bf24272bc9d9ead2bcd12315.tar.gz freebsd-ports-gnome-9e323cce15d82371bf24272bc9d9ead2bcd12315.tar.zst freebsd-ports-gnome-9e323cce15d82371bf24272bc9d9ead2bcd12315.zip | |
update biology/babel to properly output mm3 files.
PR: ports/42425
Submitted by: Glenn Johnson <glennpj@charter.net>
| -rw-r--r-- | biology/babel/Makefile | 2 | ||||
| -rw-r--r-- | biology/babel/files/patch-wrmm3.c | 92 |
2 files changed, 93 insertions, 1 deletions
diff --git a/biology/babel/Makefile b/biology/babel/Makefile index 2a3aff791659..8b8f44c1139c 100644 --- a/biology/babel/Makefile +++ b/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/ \ diff --git a/biology/babel/files/patch-wrmm3.c b/biology/babel/files/patch-wrmm3.c new file mode 100644 index 000000000000..740b4930ca7e --- /dev/null +++ b/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), |