svn commit: r363159 - in head/biology: babel babel/files p5-AcePerl/files povchem/files psi88/files
Adam Weinberger
adamw at FreeBSD.org
Mon Jul 28 14:22:19 UTC 2014
Author: adamw
Date: Mon Jul 28 14:22:16 2014
New Revision: 363159
URL: http://svnweb.freebsd.org/changeset/ports/363159
QAT: https://qat.redports.org/buildarchive/r363159/
Log:
Rename biology/ patch-xy patches to reflect the files they modify.
Added:
head/biology/babel/files/patch-menus.c
- copied unchanged from r363137, head/biology/babel/files/patch-ab
head/biology/p5-AcePerl/files/patch-Makefile.PL
- copied unchanged from r363137, head/biology/p5-AcePerl/files/patch-ac
head/biology/p5-AcePerl/files/patch-acelib_memsubs.c
- copied unchanged from r363137, head/biology/p5-AcePerl/files/patch-ab
head/biology/p5-AcePerl/files/patch-acelib_wh_mydirent.h
- copied, changed from r363137, head/biology/p5-AcePerl/files/patch-aa
head/biology/p5-AcePerl/files/patch-acelib_wh_mystdlib.h
- copied, changed from r363137, head/biology/p5-AcePerl/files/patch-aa
head/biology/povchem/files/patch-povchem.c
- copied unchanged from r363137, head/biology/povchem/files/patch-ab
head/biology/povchem/files/patch-povchem.cfg
- copied unchanged from r363137, head/biology/povchem/files/patch-ac
head/biology/psi88/files/patch-src_makefile
- copied unchanged from r363137, head/biology/psi88/files/patch-aa
head/biology/psi88/files/patch-unix_rpsi1
- copied unchanged from r363137, head/biology/psi88/files/patch-ba
head/biology/psi88/files/patch-unix_rpsi2
- copied unchanged from r363137, head/biology/psi88/files/patch-bb
Deleted:
head/biology/babel/files/patch-ab
head/biology/p5-AcePerl/files/patch-aa
head/biology/p5-AcePerl/files/patch-ab
head/biology/p5-AcePerl/files/patch-ac
head/biology/povchem/files/patch-ab
head/biology/povchem/files/patch-ac
head/biology/psi88/files/patch-aa
head/biology/psi88/files/patch-ba
head/biology/psi88/files/patch-bb
Modified:
head/biology/babel/Makefile
Modified: head/biology/babel/Makefile
==============================================================================
--- head/biology/babel/Makefile Mon Jul 28 14:17:02 2014 (r363158)
+++ head/biology/babel/Makefile Mon Jul 28 14:22:16 2014 (r363159)
@@ -7,13 +7,13 @@ PORTREVISION= 4
CATEGORIES= biology converters
MASTER_SITES= http://smog.com/chem/babel/files/ \
http://www.ccl.net/cca/software/UNIX/babel/
-EXTRACT_SUFX= .tar.Z
MAINTAINER= ports at FreeBSD.org
COMMENT= Converts among various molecular file formats
CONFLICTS_INSTALL= openbabel-*
+USES= tar:Z
MAKE_ARGS= CC="${CC}" CFLAGS="${CFLAGS}"
PLIST_FILES+= bin/babel libexec/babel
Copied: head/biology/babel/files/patch-menus.c (from r363137, head/biology/babel/files/patch-ab)
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/babel/files/patch-menus.c Mon Jul 28 14:22:16 2014 (r363159, copy of r363137, head/biology/babel/files/patch-ab)
@@ -0,0 +1,40 @@
+
+$FreeBSD$
+
+--- menus.c.orig Tue Jan 21 16:52:36 1997
++++ menus.c Sun Nov 18 16:43:32 2001
+@@ -63,9 +63,9 @@
+ }
+ }
+ printf("Input file name : ");
+- gets(InfileName);
++ fgets(InfileName, BUFF_SIZE, stdin);
+ printf("Keywords : ");
+- gets(InputKeywords);
++ fgets(InputKeywords, BUFF_SIZE, stdin);
+
+ if (strlen(InputKeywords) < 1)
+ strcpy(InputKeywords,"KEYWORDS GO HERE");
+@@ -108,11 +108,11 @@
+ }
+ }
+ printf("Output file name : ");
+- gets(OutfileName);
++ fgets(OutfileName, BUFF_SIZE, stdin);
+ if (has_keywords)
+ {
+ printf("Keywords : ");
+- gets(OutputKeywords);
++ fgets(OutputKeywords, BUFF_SIZE, stdin);
+ if (strlen(OutputKeywords) < 1)
+ strcpy(OutputKeywords,"KEYWORDS GO HERE");
+ }
+@@ -167,7 +167,7 @@
+ while (done == FALSE)
+ {
+ printf("Choice : ");
+- gets(choice_string);
++ fgets(choice_string, sizeof(choice_string), stdin);
+ for (i = 0; i < (int) strlen(choice_string); i++)
+ {
+ if (!isdigit(choice_string[i]))
Copied: head/biology/p5-AcePerl/files/patch-Makefile.PL (from r363137, head/biology/p5-AcePerl/files/patch-ac)
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/p5-AcePerl/files/patch-Makefile.PL Mon Jul 28 14:22:16 2014 (r363159, copy of r363137, head/biology/p5-AcePerl/files/patch-ac)
@@ -0,0 +1,20 @@
+--- Makefile.PL.orig Fri Sep 28 16:13:04 2001
++++ Makefile.PL Fri Jan 25 14:11:26 2002
+@@ -2,7 +2,7 @@
+ use ExtUtils::MakeMaker qw(prompt WriteMakefile);
+ use File::Path;
+
+-my $choice;
++my $choice = 3;
+ while (!$choice) {
+ $reply = prompt(
+ "\nWhat do you want to build?\n\n" .
+@@ -22,8 +22,6 @@
+ push @extlib,'Freesubs' if $choice >= 2;
+ push @extlib,'RPC' if $choice >= 3;
+
+-print "\n";
+-setup_sitedefs() if prompt("Do you want to install Ace::Browser? ","n") =~ /[yY]/;
+
+ my $headers = "./ace/wh";
+ WriteMakefile(
Copied: head/biology/p5-AcePerl/files/patch-acelib_memsubs.c (from r363137, head/biology/p5-AcePerl/files/patch-ab)
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/p5-AcePerl/files/patch-acelib_memsubs.c Mon Jul 28 14:22:16 2014 (r363159, copy of r363137, head/biology/p5-AcePerl/files/patch-ab)
@@ -0,0 +1,11 @@
+--- acelib/memsubs.c.orig Mon Jan 11 02:01:29 1999
++++ acelib/memsubs.c Thu Jul 27 17:18:45 2000
+@@ -21,7 +21,7 @@
+ #if defined(NEXT) || defined(HP) || defined(MACINTOSH)
+ extern void* malloc(mysize_t size) ;
+ #elif !defined(WIN32) && !defined(DARWIN)
+-#include <malloc.h> /* normal machines */
++#include <stdlib.h> /* normal machines */
+ #endif
+
+ /********** primary type definition **************/
Copied and modified: head/biology/p5-AcePerl/files/patch-acelib_wh_mydirent.h (from r363137, head/biology/p5-AcePerl/files/patch-aa)
==============================================================================
--- head/biology/p5-AcePerl/files/patch-aa Mon Jul 28 12:41:48 2014 (r363137, copy source)
+++ head/biology/p5-AcePerl/files/patch-acelib_wh_mydirent.h Mon Jul 28 14:22:16 2014 (r363159)
@@ -1,15 +1,3 @@
---- acelib/wh/mystdlib.h.orig Mon Jul 16 23:04:45 2001
-+++ acelib/wh/mystdlib.h Mon Aug 13 12:42:25 2001
-@@ -161,7 +161,8 @@
- #endif
-
- #if defined(POSIX) || defined(LINUX) || defined(SOLARIS) || defined(SGI) || \
-- defined(HP) || defined(WIN32) || defined(INTEL_SOLARIS)
-+ defined(HP) || defined(WIN32) || defined(INTEL_SOLARIS) || \
-+ defined(FREEBSD)
-
- #ifdef WIN32
- #include <mbctype.h>
--- acelib/wh/mydirent.h.orig Mon Jul 16 23:04:45 2001
+++ acelib/wh/mydirent.h Mon Aug 13 12:41:59 2001
@@ -55,7 +55,7 @@
Copied and modified: head/biology/p5-AcePerl/files/patch-acelib_wh_mystdlib.h (from r363137, head/biology/p5-AcePerl/files/patch-aa)
==============================================================================
--- head/biology/p5-AcePerl/files/patch-aa Mon Jul 28 12:41:48 2014 (r363137, copy source)
+++ head/biology/p5-AcePerl/files/patch-acelib_wh_mystdlib.h Mon Jul 28 14:22:16 2014 (r363159)
@@ -10,14 +10,3 @@
#ifdef WIN32
#include <mbctype.h>
---- acelib/wh/mydirent.h.orig Mon Jul 16 23:04:45 2001
-+++ acelib/wh/mydirent.h Mon Aug 13 12:41:59 2001
-@@ -55,7 +55,7 @@
- extern char *getwd(char *pathname) ;
- #endif /* HP || SOLARIS || WIN32 */
-
--#if defined (POSIX) || defined(SUN) || defined(SUNSVR4) || defined(SOLARIS) || defined(DEC) || defined(ALPHA) || defined(SGI) || defined(LINUX) || defined(HP) || defined (INTEL_SOLARIS)
-+#if defined (POSIX) || defined(SUN) || defined(SUNSVR4) || defined(SOLARIS) || defined(DEC) || defined(ALPHA) || defined(SGI) || defined(LINUX) || defined(HP) || defined (INTEL_SOLARIS) || defined (FREEBSD)
- #include <dirent.h>
- typedef struct dirent MYDIRENT ;
- #endif
Copied: head/biology/povchem/files/patch-povchem.c (from r363137, head/biology/povchem/files/patch-ab)
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/povchem/files/patch-povchem.c Mon Jul 28 14:22:16 2014 (r363159, copy of r363137, head/biology/povchem/files/patch-ab)
@@ -0,0 +1,188 @@
+
+$FreeBSD$
+
+--- povchem.c.orig Fri Jul 11 11:49:07 2003
++++ povchem.c Fri Jul 11 11:59:23 2003
+@@ -482,7 +482,7 @@
+ */
+
+ if (*fileName==NULL) {
+- New_String(fileName,"povchem.cfg");
++ New_String(fileName,SYSCONFDIR "/povchem.cfg");
+ if ((config=fopen(*fileName,"r"))==NULL) {
+ puts("Can't read the configuration file \"povchem.cfg\"!");
+ perror("Reason");
+@@ -731,7 +731,7 @@
+
+ no_config:
+
+- if (!PERIODIC_TABLE_FILE) New_String(&PERIODIC_TABLE_FILE,"periodic.tab");
++ if (!PERIODIC_TABLE_FILE) New_String(&PERIODIC_TABLE_FILE,DATADIR "/periodic.tab");
+ if (!FINISH) New_String(&FINISH,"Plastic");
+ if (!FINISH_DECLARATION) New_String(&FINISH_DECLARATION,"\
+ finish {\n\
+@@ -742,7 +742,7 @@
+ phong 0.3\n\
+ phong_size 50\n\
+ specular 0.0\n\
+- }\n\n");
++ };\n\n");
+
+ if (POVRAY && (!POV_OPTIONS || !POV_WIDTH) ) {
+ puts("Warning: to run POV-Ray from PovChem, you must define *all* the");
+@@ -977,10 +977,10 @@
+ if (model==CPK ||
+ (model==BALLnSTICK && ballSizeModel==PROPORTIONAL) ) {
+ if (model==BALLnSTICK)
+- fprintf(pov,"#declare Proportionality_Constant = %.*g\n",SF,ballRadius);
++ fprintf(pov,"#declare Proportionality_Constant = %.*g;\n",SF,ballRadius);
+ for (Z=0;Z<NUM_ELEMENTS;Z++) {
+ if (PeriodicTable[Z].isPresent) {
+- fprintf(pov,"#declare %s_Radius = %.*g",
++ fprintf(pov,"#declare %s_Radius = %.*g;",
+ PeriodicTable[Z].name,SF,PeriodicTable[Z].vdW);
+ if (model==BALLnSTICK)
+ fputs("*Proportionality_Constant\n",pov);
+@@ -989,13 +989,13 @@
+ }
+ }
+ } else
+- fprintf(pov,"#declare All_Atom_Radius = %.*g\n",SF,Determine_Radius(0));
++ fprintf(pov,"#declare All_Atom_Radius = %.*g;\n",SF,Determine_Radius(0));
+ fputs("\n",pov);
+
+ if (sphereColorModel==BY_ELEMENT || cylinderColorModel==BY_ELEMENT) {
+ for (Z=0;Z<NUM_ELEMENTS;Z++) {
+ if (PeriodicTable[Z].isPresent) {
+- fprintf(pov,"#declare Atom_%s_Color = color rgb <%.5g, %.5g, %.5g>\n",
++ fprintf(pov,"#declare Atom_%s_Color = color rgb <%.5g, %.5g, %.5g>;\n",
+ PeriodicTable[Z].name,RED(Z),GREEN(Z),BLUE(Z));
+ }
+ }
+@@ -1003,20 +1003,20 @@
+ }
+
+ if (sphereColorModel==ALL_THE_SAME)
+- fprintf(pov,"#declare All_Atom_Color = color rgb <%.5g, %.5g, %.5g>\n\n",
++ fprintf(pov,"#declare All_Atom_Color = color rgb <%.5g, %.5g, %.5g>;\n\n",
+ allSphereColor.r,allSphereColor.g,allSphereColor.b);
+
+ if (sphereColorModel==BY_PDB) {
+ if (ballSizeModel==CONSTANT) {
+ fputs("#declare Atom_All =\n sphere {\n",pov);
+ fputs(" <0,0,0>, All_Atom_Radius\n",pov);
+- fprintf(pov," finish { %s }\n }\n\n",FINISH);
++ fprintf(pov," finish { %s }\n };\n\n",FINISH);
+ } else {
+ for (Z=0;Z<NUM_ELEMENTS;Z++) {
+ if (PeriodicTable[Z].isPresent) {
+ fprintf(pov,"#declare Atom_%s =\n sphere {\n",PeriodicTable[Z].name);
+ fprintf(pov," <0,0,0>, %s_Radius\n",PeriodicTable[Z].name);
+- fprintf(pov," finish { %s }\n }\n",FINISH);
++ fprintf(pov," finish { %s }\n };\n",FINISH);
+ }
+ }
+ fputs("\n",pov);
+@@ -1024,7 +1024,7 @@
+ tag=firstSphereTag;
+ nTags=nSphereTags;
+ for (i=0;i<nTags;i++) {
+- fprintf(pov,"#declare Atom_%s_Color = color rgb <%.5g, %.5g, %.5g>\n",
++ fprintf(pov,"#declare Atom_%s_Color = color rgb <%.5g, %.5g, %.5g>;\n",
+ tag->name,tag->r,tag->g,tag->b);
+ tag=tag->next;
+ }
+@@ -1051,7 +1051,7 @@
+ fputs( " pigment { color All_Atom_Color }\n",pov);
+ break;
+ }
+- fprintf(pov," finish { %s }\n }\n }\n",FINISH);
++ fprintf(pov," finish { %s }\n }\n };\n",FINISH);
+ }
+ }
+
+@@ -1060,7 +1060,7 @@
+ fputs( " <0,0,0>, All_Atom_Radius\n",pov);
+ fputs( " texture {\n",pov);
+ fputs( " pigment { color All_Atom_Color }\n",pov);
+- fprintf(pov," finish { %s }\n }\n }\n",FINISH);
++ fprintf(pov," finish { %s }\n }\n };\n",FINISH);
+ }
+
+ fputs("\n",pov);
+@@ -1080,26 +1080,26 @@
+ factors[4]=HIGH_ORDER_FACTOR;
+
+ if (nOrders[H_BOND]) {
+- fprintf(pov,"#declare H_Bond_Radius = %.*g\n",SF,HBondRadius);
+- fprintf(pov,"#declare H_Bond_Color = color rgb <%.5g, %.5g, %.5g>\n",
++ fprintf(pov,"#declare H_Bond_Radius = %.*g;\n",SF,HBondRadius);
++ fprintf(pov,"#declare H_Bond_Color = color rgb <%.5g, %.5g, %.5g>;\n",
+ HBondColor.r,HBondColor.g,HBondColor.b);
+ fputs( "#declare H_Bond =\n cylinder {\n",pov);
+ fputs( " <0,0,0>, <1,0,0>, H_Bond_Radius\n",pov);
+ fputs( " texture {\n",pov);
+ fputs( " pigment { H_Bond_Color }\n",pov);
+- fprintf(pov," finish { %s }\n }\n }\n\n",FINISH);
++ fprintf(pov," finish { %s }\n }\n };\n\n",FINISH);
+ }
+
+ if (model==CYLINDER)
+- fputs("#declare All_Bond_Radius = All_Atom_Radius\n\n",pov);
++ fputs("#declare All_Bond_Radius = All_Atom_Radius;\n\n",pov);
+ else {
+ if (cylinderSizeModel==CONSTANT)
+- fprintf(pov,"#declare All_Bond_Radius = %.*g\n\n",SF,cylinderRadius);
++ fprintf(pov,"#declare All_Bond_Radius = %.*g;\n\n",SF,cylinderRadius);
+ else {
+- fprintf(pov,"#declare Single_Bond_Radius = %.*g\n",SF,cylinderRadius);
++ fprintf(pov,"#declare Single_Bond_Radius = %.*g;\n",SF,cylinderRadius);
+ for (i=DOUBLE;i<=HIGH_ORDER;i++) {
+ if (nOrders[i])
+- fprintf(pov,"#declare %sBond_Radius = Single_Bond_Radius*%.*g\n",
++ fprintf(pov,"#declare %sBond_Radius = Single_Bond_Radius*%.*g;\n",
+ orderTypes[i],SF,factors[i]);
+ }
+ fputs("\n",pov);
+@@ -1107,7 +1107,7 @@
+ }
+
+ if (cylinderColorModel==ALL_THE_SAME)
+- fprintf(pov,"#declare All_Bond_Color = color rgb <%.5g, %.5g, %.5g>\n\n",
++ fprintf(pov,"#declare All_Bond_Color = color rgb <%.5g, %.5g, %.5g>;\n\n",
+ allCylinderColor.r,allCylinderColor.g,allCylinderColor.b);
+
+ fputs( "#declare Bond =\n cylinder {\n",pov);
+@@ -1124,12 +1124,12 @@
+ } else
+ fprintf(pov," finish { %s }\n",FINISH);
+
+- fputs( " }\n\n",pov);
++ fputs( " };\n\n",pov);
+
+ if (cylinderColorModel==BY_PDB && firstCylinderTag!=firstSphereTag) {
+ tag=firstCylinderTag;
+ for (i=0;i<nCylinderTags;i++) {
+- fprintf(pov,"#declare Bond_%s_Color = color rgb <%.5g, %.5g, %.5g>\n",
++ fprintf(pov,"#declare Bond_%s_Color = color rgb <%.5g, %.5g, %.5g>;\n",
+ tag->name,tag->r,tag->g,tag->b);
+ tag=tag->next;
+ }
+@@ -2092,7 +2092,7 @@
+ * the origin, looking along +Z, sky along +Y.
+ */
+
+- fprintf(pov,"#declare Camera_Position = < %.6g, %.6g, %.6g >\n\n",
++ fprintf(pov,"#declare Camera_Position = < %.6g, %.6g, %.6g >;\n\n",
+ eye.x,eye.y,eye.z);
+
+ fputs( "camera{\n",pov);
+@@ -2317,7 +2317,7 @@
+
+ /*-------------------- the main program body --------------------------*/
+
+-void main(int argc, char *argv[])
++int main(int argc, char *argv[])
+ {
+ char *pdbName, *configName=NULL;
+ char *tgaName=NULL, *leftTga=NULL, *rightTga=NULL;
Copied: head/biology/povchem/files/patch-povchem.cfg (from r363137, head/biology/povchem/files/patch-ac)
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/povchem/files/patch-povchem.cfg Mon Jul 28 14:22:16 2014 (r363159, copy of r363137, head/biology/povchem/files/patch-ac)
@@ -0,0 +1,20 @@
+--- povchem.cfg.orig Tue Aug 8 03:13:31 2000
++++ povchem.cfg Tue Aug 8 03:16:16 2000
+@@ -294,7 +294,7 @@
+ # or leave blank the "POVRay" line, and the next five options will be ignored.
+ #
+ #POVRay = d:\graphics\povray\povray.exe
+-POVRay = /usr/local/bin/povray
++POVRay = %%LOCALBASE%%/bin/povray
+ POVWidth = 640
+ POVOptions = +V -D +Q9 +A +FT +B32
+ RunPOVRay = No
+@@ -331,7 +331,7 @@
+ # the type of image POV-Ray generates - usually TGA (also called TARGA).
+ #
+ #Viewer = c:\util\dvpeg.exe
+-Viewer = /usr/local/bin/xv
++Viewer = %%LOCALBASE%%/bin/display
+
+ # If ColorSplit is Proportional, 'Power' determines the power of the vdW radii
+ # to which the point of color change is proportional. See the manual for
Copied: head/biology/psi88/files/patch-src_makefile (from r363137, head/biology/psi88/files/patch-aa)
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/psi88/files/patch-src_makefile Mon Jul 28 14:22:16 2014 (r363159, copy of r363137, head/biology/psi88/files/patch-aa)
@@ -0,0 +1,53 @@
+--- src/makefile.orig
++++ src/makefile
+@@ -29,9 +29,6 @@
+ #
+ # SGI 4D series flags
+ #
+-f77 = f77
+-FFLAGS = -w0 -O4 -G 64
+-LFLAGS = -lfastm -lfpe -s
+ #
+ # SUN Sparc series flags version 1.3 or later compiler
+ #
+@@ -60,7 +57,6 @@
+ # Place your G88/G90 util library definition here if you wish to
+ # compile chk2psi
+ #
+-G90LIB = /usr/people/frisch/g90/libg90.a
+ #
+ # define the directory where the executables will reside
+ # usually /usr/local/bin or ~/bin to put it in your own directory
+@@ -84,13 +80,13 @@
+ #######################################################################
+ #
+
+- all: PSI1 PSICON PSI2CT PSI2HP PSI2PS PREPLOT chk2psi $(EXTRAS)
++ all: PSI1 PSICON PSI2CT PSI2HP PSI2PS PREPLOT $(EXTRAS)
+
+ #
+ # Install in the executable directory - may need to be superuser
+ # depending on where you decide to put it (/usr/local/bin for instance)
+ #
+-install: PSI1 PSICON PSI2CT PSI2HP PSI2PS PREPLOT chk2psi $(EXTRAS)
++install: PSI1 PSICON PSI2CT PSI2HP PSI2PS PREPLOT $(EXTRAS)
+ mv PSI1 $(BIN)
+ chmod +rx $(BIN)/PSI1
+ mv PSICON $(BIN)
+@@ -99,8 +95,6 @@
+ chmod +rx $(BIN)/PREPLOT
+ mv PSI2* $(BIN)
+ chmod +rx $(BIN)/PSI2*
+- mv chk2psi $(BIN)
+- chmod +rx $(BIN)/chk2psi
+
+ #
+ # This is the Density matrix generation program (PSI1/88)
+@@ -164,6 +158,6 @@
+ # Clean up when done
+ #
+ clean :
+- touch a.out foo.o core foo.u foo.f17 foo.22
++ touch a.out foo.o core foo.u foo.f17 foo.22
+ rm -f a.out *.o core *.u *.f17 *.f2*
+
Copied: head/biology/psi88/files/patch-unix_rpsi1 (from r363137, head/biology/psi88/files/patch-ba)
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/psi88/files/patch-unix_rpsi1 Mon Jul 28 14:22:16 2014 (r363159, copy of r363137, head/biology/psi88/files/patch-ba)
@@ -0,0 +1,19 @@
+*** unix/rpsi1.orig Sat May 25 03:50:02 1991
+--- unix/rpsi1 Thu Nov 12 11:25:41 1998
+***************
+*** 10,16 ****
+ #
+ # Run PSI1/88 using cmdlin.psi1 as input
+ #
+! time ./PSI1 < $1.psi1
+ #
+ # remove any old files with the target name
+ #
+--- 10,16 ----
+ #
+ # Run PSI1/88 using cmdlin.psi1 as input
+ #
+! time PSI1 < $1.psi1
+ #
+ # remove any old files with the target name
+ #
Copied: head/biology/psi88/files/patch-unix_rpsi2 (from r363137, head/biology/psi88/files/patch-bb)
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/psi88/files/patch-unix_rpsi2 Mon Jul 28 14:22:16 2014 (r363159, copy of r363137, head/biology/psi88/files/patch-bb)
@@ -0,0 +1,143 @@
+*** unix/rpsi2.orig Sat May 25 03:50:02 1991
+--- unix/rpsi2 Thu Nov 12 23:41:19 1998
+***************
+*** 13,79 ****
+ if ($1 == '-hp') goto noargs
+ if ($1 == '-ct') goto noargs
+ echo -n 'no [-ps][-pk][-hp][-ct] options - attempting to run PSI2 '
+! /bin/time PSI2 < $1.psi2
+ else
+ if ($argv[1] == '-hp') then
+ echo "Generating contours ... please wait."
+! /bin/time PSI2HP < $2.psi2
+ echo -n "Renaming HP Plotter file to "$2".hpp"
+! mv -f fort.10 $2.hpp
+ echo "Done"
+ else if ($argv[2] == '-hp') then
+ echo "Generating contours ... please wait."
+! /bin/time PSI2HP < $1.psi2
+ echo -n "Renaming HP Plotter file to "$1".hpp"
+! mv -f fort.10 $1.hpp
+ echo "Done"
+ else if ($argv[1] == '-ct') then
+ echo "Generating contours ... please wait."
+! /bin/time PSI2CT < $2.psi2
+ echo -n "Plotting for ChemText ... "
+ echo -n "Renaming ChemText Metafile to "$2".met"
+! mv -f fort.10 $2.met
+ echo "Done"
+ else if ($argv[2] == '-ct') then
+ echo "Generating contours ... please wait."
+! /bin/time PSI2CT < $1.psi2
+ echo -n "Renaming ChemText Metafile to "$1".met"
+ mv -f fort.10 $1.met
+ echo "Done"
+ else if ($argv[1] == '-pk') then
+ echo "Generating contours ... please wait."
+ # setenv OUTPUT_DEVICE PostScript
+! /bin/time PSI2PS < $2.psi2
+ echo -n "Renaming PostScript file to "$2".ps"
+ mv -f psplot $argv[2].ps
+ echo "Done"
+ else if ($argv[2] == '-pk') then
+ echo "Generating contours ... please wait."
+ # setenv OUTPUT_DEVICE PostScript
+! /bin/time PSI2PS < $1.psi2
+ echo -n "Renaming PostScript file to "$1".ps"
+ mv -f psplot $argv[1].ps
+ echo "Done"
+ else if ($argv[1] == '-ps') then
+ echo "Generating contours ... please wait."
+ setenv OUTPUT_DEVICE PostScript
+! /bin/time PSI2 < $2.psi2
+ #SYSV echo -n "Plotting on the LaserWriter ... ";lp -c /tmp/ps_plot$USER
+ #SYSV rm -f /tmp/ps_plot$USER
+! #BSD echo -n "Plotting on the LaserWriter ... ";lpr -r /tmp/ps_plot$USER
+
+! echo ' edit command file to choose print options, then remove this line'
+
+ echo "Done"
+ else if ($argv[2] == '-ps') then
+ echo "Generating contours ... please wait."
+ setenv OUTPUT_DEVICE PostScript
+! /bin/time PSI2 < $1.psi2
+ #SYSV echo -n "Plotting on the LaserWriter ... ";lp -c /tmp/ps_plot$USER
+ #SYSV rm -f /tmp/ps_plot$USER
+! #BSD echo -n "Plotting on the LaserWriter ... ";lpr -r /tmp/ps_plot$USER
+
+! echo ' edit command file to choose print options, then remove this line'
+
+ echo "Done"
+ else
+--- 13,83 ----
+ if ($1 == '-hp') goto noargs
+ if ($1 == '-ct') goto noargs
+ echo -n 'no [-ps][-pk][-hp][-ct] options - attempting to run PSI2 '
+! time PSI2 < $1.psi2
+! # PSI2 is linked to PSI2PS, then output file `psplot' will moved to $argv[1].ps
+! echo ': PSI2 is PSI2PS, now'
+! mv -f psplot $argv[1].ps
+! echo "Done"
+ else
+ if ($argv[1] == '-hp') then
+ echo "Generating contours ... please wait."
+! time PSI2HP < $2.psi2
+ echo -n "Renaming HP Plotter file to "$2".hpp"
+! mv -f fort.66 $2.hpp
+ echo "Done"
+ else if ($argv[2] == '-hp') then
+ echo "Generating contours ... please wait."
+! time PSI2HP < $1.psi2
+ echo -n "Renaming HP Plotter file to "$1".hpp"
+! mv -f fort.66 $1.hpp
+ echo "Done"
+ else if ($argv[1] == '-ct') then
+ echo "Generating contours ... please wait."
+! time PSI2CT < $2.psi2
+ echo -n "Plotting for ChemText ... "
+ echo -n "Renaming ChemText Metafile to "$2".met"
+! mv -f fort.66 $2.met
+ echo "Done"
+ else if ($argv[2] == '-ct') then
+ echo "Generating contours ... please wait."
+! time PSI2CT < $1.psi2
+ echo -n "Renaming ChemText Metafile to "$1".met"
+ mv -f fort.10 $1.met
+ echo "Done"
+ else if ($argv[1] == '-pk') then
+ echo "Generating contours ... please wait."
+ # setenv OUTPUT_DEVICE PostScript
+! time PSI2PS < $2.psi2
+ echo -n "Renaming PostScript file to "$2".ps"
+ mv -f psplot $argv[2].ps
+ echo "Done"
+ else if ($argv[2] == '-pk') then
+ echo "Generating contours ... please wait."
+ # setenv OUTPUT_DEVICE PostScript
+! time PSI2PS < $1.psi2
+ echo -n "Renaming PostScript file to "$1".ps"
+ mv -f psplot $argv[1].ps
+ echo "Done"
+ else if ($argv[1] == '-ps') then
+ echo "Generating contours ... please wait."
+ setenv OUTPUT_DEVICE PostScript
+! time PSI2 < $2.psi2
+ #SYSV echo -n "Plotting on the LaserWriter ... ";lp -c /tmp/ps_plot$USER
+ #SYSV rm -f /tmp/ps_plot$USER
+! echo -n "Plotting on the LaserWriter ... ";lpr -r /tmp/ps_plot$USER
+
+! #echo ' edit command file to choose print options, then remove this line'
+
+ echo "Done"
+ else if ($argv[2] == '-ps') then
+ echo "Generating contours ... please wait."
+ setenv OUTPUT_DEVICE PostScript
+! time PSI2 < $1.psi2
+ #SYSV echo -n "Plotting on the LaserWriter ... ";lp -c /tmp/ps_plot$USER
+ #SYSV rm -f /tmp/ps_plot$USER
+! echo -n "Plotting on the LaserWriter ... ";lpr -r /tmp/ps_plot$USER
+
+! #echo ' edit command file to choose print options, then remove this line'
+
+ echo "Done"
+ else
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