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authorjtb <jtb@pkgsrc.org>2001-02-12 02:16:02 +0000
committerjtb <jtb@pkgsrc.org>2001-02-12 02:16:02 +0000
commit0384ee56748eaa490481d150d8cc3b1151a5d918 (patch)
tree2457184029c89a4b5d05fe7cd1ee18065754dace /biology/chemtool
parentcfdc9474b800c1e82efb5dca574e9633b0adc020 (diff)
downloadpkgsrc-0384ee56748eaa490481d150d8cc3b1151a5d918.tar.gz
Updated chemtool to 1.3. Changes:
1.3a1 Fixed and restored XBM export. Added a (almost empty) template menu (the beginnings of which were already hidden in 1.2a8). Fixed kerning of mixed sub- and superscripts (as in SO_4^2^-). Changed allocation of initial drawing area, calculate actual size before saving. 1.3a2 Added option menu for default bond type , added label support to template function 1.3a3 Reduced preallocated drawing area to 'windowsize+100', as the increase in 1.3a1 (which used window+1000) caused a massive slowdown at startup. Freed unneeded pixmaps in the button setup code. Fragment rotation code now stores the initial coordinates and uses them as basis for the new positions - the previous, incremental calculation was severely plagued by accumulation of errors. 1.3a4 Changed bond option menu to use small icons instead of longer and less clear text labels. Removed check for 'cursor inside marked region' in 'Move' mode to allow smooth dragging. Started populating the O and N heterocycle panels of the template menu. Fixed a duplicate bond in the tcdd example, and removed those examples that have become templates. 1.3a5 Added shortcut for some labels - pressing c,n,o,s,p,r,i,h,d or b inserts the corresponding centered element symbol at the last drawing position, 'l','1','2','3' insert the left justified labels 'Cl','CH','CH_2','CH_3'. Fixed a GC leak in export_bitmap. 1.3a6 Moved the nucleoside examples to the template system. Made marker position default to last drawing position, so that the 'Add' function is now always active. Beginnings of internationalization (.mo file for German locale added). Fixed naphthalene template, added dicyclo- pentadiene. Changed Add_atom to automatically convert blanks in label input to backslashes for storage. Prepared a few drawings for later inclusion in the template system (camphor,pteridine,caffeine,glucose, fructose,mannose,galactose,neuraminic acid, spiro[4.5]decane). 1.3a7 Template cleanup: porphine moved to heterocycle panel, spirodecane added in its place. Glc,Fru,Man,Gal transfered to carbohydrate templates, caffeine to heterocycles. Czech translation (by Radek Liboska) added. Improved bounding box coordinates for xfig compound object (used for sub/superscripted labels) Changed export functions to remove the intermediate '.f2l' files. Changed orientation in xfig header to Portrait. Adapted xfig (and xfig-based) export modes to the new XFig default depth of 100. Changed depth of xfig text (labels) to 90 and added filled white polygons at depth 95 to hide overlapping line segments (experimental, used only for sub/superscripted text at the moment). Reset default filename to 'unnamed' when the current molecule is deleted. 1.3a8 Changed buttons mark/move/rotate/flip/delete/copy from text to icon to reclaim space for the text entry box (icons created by Radek Liboska). Added white polygon to clear area under normal text as well. 1.3a9 Added program icon. Added an interface for Radek Liboskas standalone program CHT, which calculates sum formula and molecular weight from a chemtool sketch. Corrected example drawing of brevetoxin. 1.3a10 Really reset mark flag when nothing was within the marker box. Allow saving only the marked region (formula weight computation only). Helper program CHT now parses those labels that are not in its internal table of common substituents; exact mass is now returned automatically.Added status line with message history. 1.3a11 Internationalization support made optional (define DISABLE_NLS in the Imakefile if you do not want it) to allow compiling on systems without GNU-style locale support again. Improved ring size and position in the benzene and cyclopentadiene templates (Michael Banck). Reset all marks before loading a template. If the template menu is already open, pressing the Template button now brings it to the front. Added templates (inden,biphenyl), removed the ugly question mark placeholders. Changed handling of windowmanager events, so that using the window decorations' CLOSE button brings up the Yes/No dialog while the chemtool window is still alive. Changes in helper program CHT (cht011a): now recognizes Ac in complex substituents; correctly handles aromatic 'ring' in formula input; checks input file for identifier "Chemtool"; reads number of bonds from "bonds" line (to handle label-only files gracefully); exits on unattached labels instead of silently miscalculating formula and mass. Subsequently updated to Radek Liboskas current version 0.19, which already includes equivalent changes. Added list of abbreviations supported by cht. 1.3a12 Reset all marks before 'adding' a sketch. Adding a label on top of an existing one now replaces the old label as it should. Added a function for rescaling objects (useful for drawing reagents above the reaction arrow - but labels are not rescaled yet). Added linetype 13, a single bond with opaque background (for crossing bonds - see the bicyclooctane template). Updated the German translation. This - plus or minus some templates - is my release candidate for 1.3. 1.3a13 Dropped the internal icon, as it was only causing trouble, especially with KDE. Most window managers allow specification of an external icon anyway (added chemtool.xpm for this purpose). Moved 'delete fragment' button to the end of the button row. Updated Czech translation by Radek Liboska. Added linetype 13 to the helper program CHT, made it accept any Chemtool 1.x file, not only version 1.2. Updated the 'documentation', i.e. the README file, split out an INSTALL file. Set version number in chemtool files to 1.3. Fixed bug that left a newly 'added' structure active but unable to move. Rewrote positioning logic for subscripts and right-justified text in export modes again. Changed screen display of molecule from 'fixed' fonts to helvetica as used in the export modes - previously, labels that appeared fine on screen could overlap in the final (postscript) output. Fixed 'mannose' template that showed exactly this. Added formatting option '|' for slanted characters (as in iPr,tBu). 1.3a14 Fixed label shortcuts for CH_2 and CH_3 that could crash chemtool (buffer overrun). Fixed scaling in export function , which had been applied to labels only. Improved label size at smallest scale. Added correction factor for sub/superscript after certain characters (the joys of proportionally-spaced fonts :-( ). Handled reopening of template menu after a close via the window manager. Updated 'About' menu (mention Radek Liboska as developer, add the tu-darmstadt webpage). 1.3a15 Changed canvas bitmap allocation to avoid uncovering garbled portions when the sliders are used. Fixed fragment deletion code (deletion of the marked fragment and redisplay of the modified drawing are now performed immediately). This hopefully fixes the crashes some people have been seeing with this function. 1.3 Added Check for no (or no selected) atoms before trying to delete a fragment, fixed bug that could deletion of a fragment to fail. Changed functions for horizontal and vertical flip to transform the atom(s) directly bonded to the marked fragment as well. Added current filename (if any) to window title. Use xfig's own arrow type in export of regular arrows (Michael Banck). Some code cleanup: removed dead code, fixed unnecessary parameter passing between functions, tidied formatting with GNU indent. Removed Imakefile and provided regular Makefile (the build process relies on gtk-config, not xmkmf, since 1.2), added install targets for the localization files and manpage. Updated cht to version 1.3.
Diffstat (limited to 'biology/chemtool')
-rw-r--r--biology/chemtool/Makefile29
-rw-r--r--biology/chemtool/files/md54
-rw-r--r--biology/chemtool/files/patch-sum6
-rw-r--r--biology/chemtool/patches/patch-aa48
-rw-r--r--biology/chemtool/patches/patch-ab12
-rw-r--r--biology/chemtool/patches/patch-ac10
-rw-r--r--biology/chemtool/pkg/PLIST24
7 files changed, 90 insertions, 43 deletions
diff --git a/biology/chemtool/Makefile b/biology/chemtool/Makefile
index cf9f290974b..f71e6fa97b7 100644
--- a/biology/chemtool/Makefile
+++ b/biology/chemtool/Makefile
@@ -1,29 +1,24 @@
-# $NetBSD: Makefile,v 1.1.1.1 2000/11/25 20:10:55 jtb Exp $
+# $NetBSD: Makefile,v 1.2 2001/02/12 02:16:02 jtb Exp $
-DISTNAME= chemtool-1.2
+DISTNAME= chemtool-1.3
CATEGORIES= biology
MASTER_SITES= http://www.uni-ulm.de/~s_tvolk/chemtool/stable/
MAINTAINER= jtb@netbsd.org
-HOMEPAGE= http://www.uni-ulm.de/~s_tvolk/chemtool/
+HOMEPAGE= http://www.uni-ulm.de/~s_tvolk/chemtool.html
DEPENDS+= gtk+>=1.0.0:../../x11/gtk
-USE_IMAKE= YES
-USE_X11BASE= YES
-
-do-install:
- ${INSTALL_PROGRAM} ${WRKSRC}/chemtool ${PREFIX}/bin
+post-install:
${INSTALL_DATA_DIR} ${PREFIX}/share/examples/chemtool
+ @for f in ${WRKSRC}/examples/*; do \
+ i="${INSTALL_DATA} $$f ${PREFIX}/share/examples/chemtool/"; \
+ ${ECHO} $$i; $$i; \
+ done
${INSTALL_DATA_DIR} ${PREFIX}/share/doc/chemtool
- @(cd ${WRKSRC}; \
- for i in examples/*; \
- do \
- ${INSTALL_DATA} $$i ${PREFIX}/share/examples/chemtool; \
- done; \
- for j in README TODO ChangeLog; \
- do \
- ${INSTALL_DATA} $$j ${PREFIX}/share/doc/chemtool; \
- done)
+ @for f in README TODO; do \
+ i="${INSTALL_DATA} ${WRKSRC}/$$f ${PREFIX}/share/doc/chemtool/"; \
+ ${ECHO} $$i; $$i; \
+ done
.include "../../mk/bsd.pkg.mk"
diff --git a/biology/chemtool/files/md5 b/biology/chemtool/files/md5
index f02f8e1fc6a..920b90e4073 100644
--- a/biology/chemtool/files/md5
+++ b/biology/chemtool/files/md5
@@ -1,3 +1,3 @@
-$NetBSD: md5,v 1.1.1.1 2000/11/25 20:10:55 jtb Exp $
+$NetBSD: md5,v 1.2 2001/02/12 02:16:03 jtb Exp $
-MD5 (chemtool-1.2.tar.gz) = 9ff4ebb7be5101c1f9110de106af10d4
+MD5 (chemtool-1.3.tar.gz) = bc66cf300fb12e6b308c0c3ef33c8491
diff --git a/biology/chemtool/files/patch-sum b/biology/chemtool/files/patch-sum
index a31ce05ca5c..b8d15483343 100644
--- a/biology/chemtool/files/patch-sum
+++ b/biology/chemtool/files/patch-sum
@@ -1,3 +1,5 @@
-$NetBSD: patch-sum,v 1.1.1.1 2000/11/25 20:10:55 jtb Exp $
+$NetBSD: patch-sum,v 1.2 2001/02/12 02:16:03 jtb Exp $
-MD5 (patch-aa) = af8067738f13a84bfe85195ec8a9652d
+MD5 (patch-aa) = 0854349a7060d6a8020b776d315c331c
+MD5 (patch-ab) = 0f990b1e1f3dc5c5176a748870d713ba
+MD5 (patch-ac) = 1c1b963e57d809d6332ada09004d2e58
diff --git a/biology/chemtool/patches/patch-aa b/biology/chemtool/patches/patch-aa
index 986d294dbcb..0b02a6aee62 100644
--- a/biology/chemtool/patches/patch-aa
+++ b/biology/chemtool/patches/patch-aa
@@ -1,10 +1,40 @@
-$NetBSD: patch-aa,v 1.1.1.1 2000/11/25 20:10:55 jtb Exp $
+$NetBSD: patch-aa,v 1.2 2001/02/12 02:16:03 jtb Exp $
---- Imakefile.orig Sat May 13 10:01:16 2000
-+++ Imakefile
-@@ -9,5 +9,3 @@
- NormalProgramTarget(chemtool,$(OBJS), , , )
-
- InstallProgram(chemtool,$(BINDIR))
--
--#InstallAppDefaults(Chemtool)
+--- Makefile.orig Tue Feb 6 18:52:54 2001
++++ Makefile
+@@ -1,15 +1,15 @@
+-PREFIX=/usr/local
+-LOCALEDIR=/usr/share/locale
+-CFLAGS=-O2 -Wall
+-CC=gcc
+-CP=/bin/cp
+-RM=/bin/rm -f
++#PREFIX=/usr/local
++LOCALEDIR=${PREFIX}/share/locale
++#CFLAGS=-O2 -Wall
++#CC=gcc
++#CP=/bin/cp
++#RM=/bin/rm -f
+
+ SRCS = main.c chemproc.c graph.c draw.c inout.c
+ OBJS = main.o chemproc.o graph.o draw.o inout.o
+
+
+-EXTRA_INCLUDES = `gtk-config --cflags` # -DDISABLE_NLS
++EXTRA_INCLUDES = `gtk-config --cflags` -I${LOCALBASE}/include # -DDISABLE_NLS
+ SYS_LIBRARIES = `gtk-config --libs` -lm
+
+ all: chemtool cht
+@@ -25,9 +25,9 @@
+ ${CC} ${CFLAGS} ${EXTRA_INCLUDES} -c ${SRCS}
+
+ install: chemtool src-cht/cht
+- ${CP} chemtool src-cht/cht ${PREFIX}/bin
+- ${CP} chemtool.1 ${PREFIX}/man/man1
+- for L in `ls locales`; do ${CP} locales/$$L/chemtool.mo ${LOCALEDIR}/$$L/LC_MESSAGES;done
++ ${BSD_INSTALL_PROGRAM} chemtool src-cht/cht ${PREFIX}/bin
++ ${BSD_INSTALL_MAN} chemtool.1 ${PREFIX}/man/man1
++ for L in `ls locales`; do ${BSD_INSTALL_DATA} locales/$$L/chemtool.mo ${LOCALEDIR}/$$L/LC_MESSAGES;done
+
+ clean:
+ ${RM} *.o *~ src-cht/*.o src-cht/*~ chemtool src-cht/cht
diff --git a/biology/chemtool/patches/patch-ab b/biology/chemtool/patches/patch-ab
new file mode 100644
index 00000000000..6a032027ea8
--- /dev/null
+++ b/biology/chemtool/patches/patch-ab
@@ -0,0 +1,12 @@
+$NetBSD: patch-ab,v 1.1 2001/02/12 02:16:03 jtb Exp $
+
+--- src-cht/cht-1.3.c.orig Tue Feb 6 18:38:02 2001
++++ src-cht/cht-1.3.c
+@@ -16,6 +16,7 @@
+
+
+ #include <stdio.h>
++#include <limits.h>
+
+ #define DOUBLE double
+
diff --git a/biology/chemtool/patches/patch-ac b/biology/chemtool/patches/patch-ac
new file mode 100644
index 00000000000..9e9aeaf8a2c
--- /dev/null
+++ b/biology/chemtool/patches/patch-ac
@@ -0,0 +1,10 @@
+$NetBSD: patch-ac,v 1.1 2001/02/12 02:16:03 jtb Exp $
+
+--- src-cht/Makefile.orig Mon Feb 12 02:13:11 2001
++++ src-cht/Makefile
+@@ -1,4 +1,4 @@
+ default: cht
+
+ cht: cht-1.3.c
+- gcc -O cht-1.3.c -lm -o cht
++ $(CC) $(CFLAGS) cht-1.3.c -lm -o cht
diff --git a/biology/chemtool/pkg/PLIST b/biology/chemtool/pkg/PLIST
index c21bc22330b..6c277a832d1 100644
--- a/biology/chemtool/pkg/PLIST
+++ b/biology/chemtool/pkg/PLIST
@@ -1,31 +1,29 @@
-@comment $NetBSD: PLIST,v 1.1.1.1 2000/11/25 20:10:55 jtb Exp $
+@comment $NetBSD: PLIST,v 1.2 2001/02/12 02:16:03 jtb Exp $
bin/chemtool
-share/doc/chemtool/ChangeLog
+bin/cht
share/doc/chemtool/README
share/doc/chemtool/TODO
share/examples/chemtool/AAMP
-share/examples/chemtool/A_Fur
share/examples/chemtool/A_Fur_big
-share/examples/chemtool/A_Ph
-share/examples/chemtool/A_Pyr
-share/examples/chemtool/A_ad
-share/examples/chemtool/A_ch_ch
-share/examples/chemtool/N_ade
share/examples/chemtool/N_ado
-share/examples/chemtool/N_cyt
-share/examples/chemtool/N_gua
-share/examples/chemtool/N_hx
-share/examples/chemtool/N_thy
-share/examples/chemtool/N_ura
+share/examples/chemtool/Neu1
+share/examples/chemtool/Neu2
share/examples/chemtool/amp.cht
share/examples/chemtool/breve.cht
+share/examples/chemtool/camphor
share/examples/chemtool/claisen.cht
+share/examples/chemtool/coronen
share/examples/chemtool/example1
share/examples/chemtool/example2
share/examples/chemtool/example3
share/examples/chemtool/example4
share/examples/chemtool/example5
share/examples/chemtool/example7
+share/examples/chemtool/indigo
+share/examples/chemtool/label
+share/examples/chemtool/pteridin
share/examples/chemtool/tcdd.cht
+share/locale/cs/LC_MESSAGES/chemtool.mo
+share/locale/de/LC_MESSAGES/chemtool.mo
@dirrm share/examples/chemtool
@dirrm share/doc/chemtool