Module Name:	pkgsrc
Committed By:	jtb
Date:		Mon Feb 12 02:16:03 UTC 2001

Modified Files:
	pkgsrc/biology/chemtool: Makefile
	pkgsrc/biology/chemtool/files: md5 patch-sum
	pkgsrc/biology/chemtool/patches: patch-aa
	pkgsrc/biology/chemtool/pkg: PLIST
Added Files:
	pkgsrc/biology/chemtool/patches: patch-ab patch-ac

Log Message:
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.


To generate a diff of this commit:
cvs rdiff -r1.1.1.1 -r1.2 pkgsrc/biology/chemtool/Makefile
cvs rdiff -r1.1.1.1 -r1.2 pkgsrc/biology/chemtool/files/md5 \
    pkgsrc/biology/chemtool/files/patch-sum
cvs rdiff -r1.1.1.1 -r1.2 pkgsrc/biology/chemtool/patches/patch-aa
cvs rdiff -r0 -r1.1 pkgsrc/biology/chemtool/patches/patch-ab \
    pkgsrc/biology/chemtool/patches/patch-ac
cvs rdiff -r1.1.1.1 -r1.2 pkgsrc/biology/chemtool/pkg/PLIST

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.