[med-svn] [Git][med-team/raster3d][upstream] New upstream version 3.0-8
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Wed Sep 24 19:35:49 BST 2025
Étienne Mollier pushed to branch upstream at Debian Med / raster3d
Commits:
e9c76352 by Étienne Mollier at 2025-09-24T19:15:43+02:00
New upstream version 3.0-8
- - - - -
15 changed files:
- CHANGELOG
- Makefile
- Makefile.incl
- README
- VERSION
- VERSION.incl
- avs2ps.c
- doc/normal3d.l
- doc/rastep.l
- html/normal3d.html
- label3d
- local.c
- stereo3d
- ungz.c
- worms
Changes:
=====================================
CHANGELOG
=====================================
@@ -1,3 +1,4 @@
+05-May-2025 revise function declaration and prototypes to make gcc15 (default C23) happy
29-Sep-2020 Package 3.0-7
13-May-2020 -std=legacy seems to reduce pedantry from gfortran 10.1
10-May-2020 gfortran 10.1 is insanely picky - must wrap hex constants in INT(...)
=====================================
Makefile
=====================================
@@ -7,6 +7,9 @@ default: all
include Makefile.incl
include VERSION
+NAME = Raster3D_3.0-8
+TARFILE = $(NAME).tar.gz
+
LIBS = $(LIBDIRS) $(CLIBS) $(TLIBS) $(GDLIBS) $(SLIBS)
DEFINES = $(GDEFS) $(IDEFS) $(TDEFS) $(GDDEFS) $(SDEFS) $(OSDEFS)
@@ -15,6 +18,7 @@ FLAGS = $(INCDIRS) $(DEFINES)
PROGS = avs2ps balls rastep render ribbon rings3d rods normal3d
SCRIPTS = stereo3d worms
+
clean:
rm -f *.o $(PROGS) core *~
rm -f render_small render_small.f parse_small.f qinp_small.f parameters_small.incl
@@ -90,13 +94,13 @@ osx-intel:
@echo CC = icc >> Makefile.incl
@echo CFLAGS = -g -Wall >> Makefile.incl
@echo FC = ifort >> Makefile.incl
- @echo FFLAGS = -g -w -O3 -Wtabs -132 >> Makefile.incl
+ @echo FFLAGS = -g -w -O3 -132 >> Makefile.incl
@echo RM = /bin/rm -f >> Makefile.incl
@echo OSDEFS = -DOSX -DNETWORKBYTEORDER >> Makefile.incl
@echo include Makefile.package >> Makefile.incl
@echo >> Makefile.incl
@echo qinp.o: qinp.f >> Makefile.incl
- @echo " \$$(FC) -g -O0 -w -Wtabs -132 -c -o qinp.o qinp.f" >> Makefile.incl
+ @echo " \$$(FC) -g -O0 -w -132 -c -o qinp.o qinp.f" >> Makefile.incl
@echo >> Makefile.incl
osx-fink:
@@ -109,13 +113,13 @@ osx-fink:
@echo LIBDIRS = -L/sw/lib >> Makefile.incl
@echo CFLAGS = -g -Wall -Dgfortran >> Makefile.incl
@echo FC = /sw/bin/gfortran >> Makefile.incl
- @echo FFLAGS = -g -w -O3 -Wtabs -ffixed-line-length-132 >> Makefile.incl
+ @echo FFLAGS = -g -w -O3 -Wno-tabs -ffixed-line-length-132 >> Makefile.incl
@echo RM = /bin/rm -f >> Makefile.incl
@echo OSDEFS = -DOSX -DNETWORKBYTEORDER >> Makefile.incl
@echo include Makefile.package >> Makefile.incl
@echo >> Makefile.incl
@echo qinp.o: qinp.f >> Makefile.incl
- @echo " \$$(FC) -g -O0 -Wall -Wtabs -c -o qinp.o qinp.f" >> Makefile.incl
+ @echo " \$$(FC) -g -O0 -Wall -Wno-tabs -c -o qinp.o qinp.f" >> Makefile.incl
@echo >> Makefile.incl
irix5:
@@ -279,3 +283,8 @@ render_small.o parse_small.o qinp_small.o: parameters_small.incl
render_small.f parse_small.f qinp_small.f: %_small.f: %.f
sed 's/parameters.incl/parameters_small.incl/;' $< >$@
+dist: clean $(TARFILE)
+
+$(TARFILE):
+ echo "make new tar file"
+ tar --directory=.. --exclude='.git' --exclude='.gitignore' -cvf $(TARFILE) Raster3D/
=====================================
Makefile.incl
=====================================
@@ -0,0 +1,72 @@
+#
+# makefile template for Raster3D distribution 3.0
+#
+# You may want to edit some of the lines below to select
+# options or directories appropriate to your local installation.
+#
+include VERSION
+#
+# Where to install the program, data files, and manuals
+#
+prefix = /usr/local
+bindir = $(prefix)/bin
+datadir = $(prefix)/share/Raster3D/materials
+mandir = $(prefix)/man/manl
+htmldir = $(prefix)/share/Raster3D/html
+examdir = $(prefix)/share/Raster3D/examples
+
+INCDIRS = -I/usr/include -I/usr/local/include
+LIBDIRS = -L/usr/local/lib
+
+#
+# TIFF support (enabled by default)
+# add -DTIFF_SUPPORT to the DEFINES statement.
+# add -ltiff to the LIBS definition.
+# The TIFF_INVERT option is a work-around for broken programs
+# (e.g. PhotoShop) that don't properly read the TIFF header.
+#
+ TLIBS = -ltiff
+ TDEFS = -DTIFF_SUPPORT -DTIFF_INVERT
+# TDEFS = -DTIFF_SUPPORT
+
+#
+# libgd support for PNG and JPEG output (enabled by default)
+# add -DGD_SUPPORT to the DEFINES statement.
+# add -lgd to the LIBS definition.
+ GDLIBS = -lgd
+ GDDEFS = -DGD_SUPPORT
+
+#
+# Everybody (I think) needs these
+#
+ CLIBS = -lm
+
+#
+# Support for on-the-fly decompression of input files using gunzip
+# (may not work on all systems)
+ GDEFS = -DGUNZIP
+
+#
+# Support for SGI imagetools library (-sgi output option to render)
+# This probably makes sense only on an Irix workstation, and only
+# if you have installed the libimage library.
+# Commented out by default.
+# SLIBS = -limage
+# SDEFS = -DLIBIMAGE_SUPPORT
+
+#
+# Any stuff you see below this comment was added by the "make OS" command.
+# You can edit it if you like, but it will be lost if you "make OS" again.
+#
+OS = linux
+CC = gcc
+CFLAGS = -g -Wall -Dgfortran
+FC = gfortran -std=legacy
+FFLAGS = -g -w -O3 -Wno-tabs -ffixed-line-length-132
+RM = /bin/rm -f
+OSDEFS = -DLINUX -DNETWORKBYTEORDER
+include Makefile.package
+
+qinp.o: qinp.f
+ $(FC) -g -O0 -Wall -Wno-tabs -c -o qinp.o qinp.f
+
=====================================
README
=====================================
@@ -1,11 +1,11 @@
-Most recent change: 29-Sep-2020
+Most recent change: 05-May-2025
-The file Raster3D_3.0-7.tar.gz contains the full source distribution for
+The file Raster3D_3.0-8.tar.gz contains the full source distribution for
version 3.0 of Raster3D.
See CHANGELOG for a history of changes to the package.
Basically nothing has changed since verison 3.0-3 (2014) except for
- minor tweaks to accommodate newer Fortran versions.
+ minor tweaks to accommodate newer Fortran and C compiler versions.
Note: The programs from Raster3D are included in the CCP4 crystallography
suite. You might find it easier to use that pre-built version.
=====================================
VERSION
=====================================
@@ -1 +1 @@
-VERSION = "3.0-7"
+VERSION = "3.0-8"
=====================================
VERSION.incl
=====================================
@@ -1,2 +1,2 @@
CHARACTER*8 VERSION
- PARAMETER (VERSION='V3.0.5 ')
+ PARAMETER (VERSION='V3.0.8 ')
=====================================
avs2ps.c
=====================================
@@ -16,6 +16,11 @@
#define random rand
#endif
+/* function prototypes */
+void dither(int nx, float *line1, float *line2,
+ unsigned char *pixels, int *index, int *done);
+float warpf(unsigned char c);
+
/*
* I added a lookup table for warping, since calculating it on the fly
* was taking about 20% of the CPU time on a DECstation 5000.
@@ -28,16 +33,12 @@
#define NO (0)
#define YES (1)
-int main(argc,argv)
-int argc;
-char *argv[];
+int main( int argc, char *argv[] )
{
int xsize, ysize;
int i, j;
float red, green, blue, alpha;
-extern float warpf();
extern float warpm[];
-extern void dither();
float *inbuf1, *inbuf2, *tbuf;
int *index;
int *done;
@@ -227,11 +228,8 @@ static float avail[4][5] = {
void
-dither( nx, line1, line2, pixels, index, done )
-int nx;
-float *line1, *line2;
-unsigned char *pixels;
-int *index, *done;
+dither(int nx, float *line1, float *line2, unsigned char *pixels,
+ int *index, int *done)
{
int i, j, k;
int it;
@@ -294,8 +292,7 @@ int *index, *done;
* It's computationally expensive (applied 3 times per pixel),
* so I dumped it into a lookup table for speed.
*/
-float warpf( rgbval )
-unsigned char rgbval;
+float warpf(unsigned char rgbval)
{
float temp;
=====================================
doc/normal3d.l
=====================================
@@ -37,7 +37,7 @@ degrees with respect to the original view angle.
.PP
In-line and normalize all instances of file indirection in the input stream.
This results in a single input file containing no file indirection.
-The default is to simply copy file indirection lines (those begining
+The default is to simply copy file indirection lines (those beginning
with @) to the new input file without opening them or normalizing their
contents.
=====================================
doc/rastep.l
=====================================
@@ -38,7 +38,7 @@ colors, and send it for immediate rendering into a PNG file
.PP
rastep < infile.pdb | render -png picture.png
.PP
-To describe the same ellipsoids colored by Biso, omiting header records so that
+To describe the same ellipsoids colored by Biso, omitting header records so that
the resulting input file can be merged with other scene components
.PP
rastep -h -Bcolor 10. 30. < infile.pdb > ellipsoids.r3d
=====================================
html/normal3d.html
=====================================
@@ -34,7 +34,7 @@ format specifiers (which are set to *). <p>
<dd>The <i>-expand</i> flag causes the program to
In-line and normalize all instances of file indirection in the input stream.
This results in a single render input file containing no file indirection.
- The default is to simply copy file indirection lines (those begining
+ The default is to simply copy file indirection lines (those beginning
with @) to the new input file without opening them or normalizing their
contents.</dd>
<dt><i>-h</i></dt>
=====================================
label3d
=====================================
@@ -63,7 +63,7 @@ else
echo "label3d version 2.7a"
echo "unrecognized option: $option" 1>&2
echo "Usage: label3d [-tiff [out.tiff]] [-png [out.png]] < in.r3d > outfile"
- exit -1
+ exit 1
fi
fi
previous="$option"
@@ -94,7 +94,7 @@ render -labels ${tmp}_label3d.ps -fontscale $FONTSCALE -${img} ${tmp}_render.${i
if [ ! -e ${tmp}_render.${img} ]; then
echo "label3d: could not find output ${tmp}_render.${img} from render" 1>&2
rm -f ${tmp}_*
- exit -1
+ exit 1
fi
if [ ! -e ${tmp}_label3d.ps ]; then
cat ${tmp}_render.${img}
@@ -113,7 +113,7 @@ then
else
echo "label3d: GhostScript error" 1>&2
rm -f ${tmp}_*
- exit -1
+ exit 1
fi
#
=====================================
local.c
=====================================
@@ -100,15 +100,14 @@ int or(i,j) int *i,*j; {return (*i | *j);}
#endif
#if defined(gfortran)
-int and_(i,j) int *i,*j; {return (*i & *j);}
-int or_(i,j) int *i,*j; {return (*i | *j);}
+int and_(int *i, int *j) {return (*i & *j);}
+int or_(int *i,int *j) {return (*i | *j);}
#endif
size_t trimwhitespace(char *out, size_t len, const char *str);
-int local_(option,buffer1,buffer2,buffer3,buffer4)
- int *option;
- short *buffer1, *buffer2, *buffer3, *buffer4;
+int local_( int *option,
+ short *buffer1, short *buffer2, short *buffer3, short *buffer4)
{
/* Everyone needs these */
@@ -137,7 +136,9 @@ int local_(option,buffer1,buffer2,buffer3,buffer4)
static TIFF *tfile;
static unsigned char *scanline;
unsigned short rows_per_strip;
- void my_write_tiff();
+ void my_write_tiff( TIFF *fp,
+ short buf1[], short buf2[], short buf3[], short buf4[],
+ int size, unsigned char scanline[]);
#endif
@@ -220,6 +221,12 @@ if (*option == 0)
mode = 1;
invert = !invert;
}
+ else if (strncmp( (char *)buffer1, "-v", 2) == 0
+ || strncmp( (char *)buffer1, "--v", 3) == 0)
+ {
+ fprintf(stderr, "%s\n",program_name);
+ exit(-1);
+ }
else if (strncmp( (char *)buffer1, " ", 2) != 0)
{
fprintf(stderr, "\n%s",program_name);
@@ -369,7 +376,7 @@ else if (*option == 1)
TIFFSET(tfile,TIFFTAG_ROWSPERSTRIP,rows_per_strip);
if (alpha_channel)
{
- uint16 extra_samples, sample_info[1];
+ uint16_t extra_samples, sample_info[1];
extra_samples=1;
sample_info[0]=EXTRASAMPLE_ASSOCALPHA;
TIFFSetField(tfile,TIFFTAG_EXTRASAMPLES,extra_samples,&sample_info[0]);
@@ -637,11 +644,10 @@ return 0;
}
#ifdef TIFF_SUPPORT
-void my_write_tiff(fp, buf1, buf2, buf3, buf4, size, scanline)
-TIFF *fp;
-short buf1[], buf2[], buf3[], buf4[];
-int size;
-unsigned char scanline[];
+void my_write_tiff(
+ TIFF *fp,
+ short buf1[], short buf2[], short buf3[], short buf4[],
+ int size, unsigned char scanline[])
{
static int row=0;
int i;
@@ -672,12 +678,11 @@ row++;
/*
* _addlabel()
*/
-int addlabel_(fontname, fontsize, fontscale, fontalign, xp, yp, zp, red, grn, blu,
- labelstring, font_len, label_len)
- int *fontalign;
- float *fontsize, *fontscale, *xp, *yp, *zp, *red, *grn, *blu;
- char *fontname, *labelstring;
- long int font_len, label_len;
+int addlabel_( int *fontalign,
+ float *fontsize, float *fontscale, float *xp, float *yp, float *zp,
+ float *red, float *grn, float *blu,
+ char *fontname, char *labelstring,
+ long int font_len, long int label_len )
{
#ifdef GD_SUPPORT
static double last_x = 0.0, last_y = 0.0, last_z = 0.0;
=====================================
stereo3d
=====================================
@@ -97,7 +97,7 @@ then
echo "stereo3d: normal3d seems to be OK" 1>&2
else
echo "stereo3d: normal3d failed" 1>&2
- exit -1
+ exit 1
fi
echo "@${tmp}_stereo3d.tmp" >> ${tmp}_left.r3d
=====================================
ungz.c
=====================================
@@ -9,8 +9,7 @@
#define ungz_ ungz
#endif
-int ungz_( origname, tempname )
-char *origname, *tempname;
+int ungz_( char *origname, char *tempname )
{
char command[128];
char *t;
=====================================
worms
=====================================
@@ -1,4 +1,4 @@
-#!/bin/csh
+#!/bin/sh
#
# Wrapper for rods program that splits main/sidechain atoms for
# separate treatment. The backbone is drawn as a radius 0.3 worm.
@@ -10,12 +10,12 @@ cat > worms.tmp.0
# Backbone first, with or without header as determined by $1 (-h)
#
rm -rf worms.tmp.1
-if ($1 == "-h") then
+if [ "$1" = "-h" ] ; then
echo "# Worms version 1.0" > worms.tmp.1
echo "# Backbone atoms" >> worms.tmp.1
else
touch worms.tmp.1
-endif
+fi
grep -E -w '(^COLOUR.*)|(N)|(C)|(CA)' worms.tmp.0 | rods $1 -r 0.3 >> worms.tmp.1
#
# Now the sidechains (actually everything but the backbone carbonyl bond)
View it on GitLab: https://salsa.debian.org/med-team/raster3d/-/commit/e9c763526ae3c078b87b947fa171043b35e40b5e
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View it on GitLab: https://salsa.debian.org/med-team/raster3d/-/commit/e9c763526ae3c078b87b947fa171043b35e40b5e
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