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2001-02-12Updated chemtool to 1.3. Changes:jtb7-43/+90
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.
2001-02-06Unify format of MESSAGEs, and include RCS Ids.wiz1-7/+13
2000-11-25Add and enable "chemtool". Fixes PR pkg/11377 by Jason Beegan.jtb1-1/+2
2000-11-25Initial import of new "chemtool" package:jtb7-0/+84
Program for drawing organic molecules
2000-09-27Take advantage of bsd.prefs.mk - pointed out by IWAMOTO Toshihiroagc1-24/+26
Also convert some make(1) .for loops to sh(1) for loops.
2000-08-27Convert packages to use PERL5_PACKLIST (part 1). These were the easyjlam2-81/+17
ones to do, and each compiled and installed/de-installed apparently correctly. As a side effect of the dynamic PLIST, we no longer need to have separate -static and -shared PLISTs. It's now easier than ever to make a perl5 package for NetBSD :)
2000-08-26Correct unterminated cross-reference when building man pages.jlam2-1/+15
2000-08-18Replace MIRROR_DISTFILES and NO_CDROM with the more descriptive andhubertf2-4/+8
more fine-grained NO_{BIN,SRC}_ON_{FTP,CDROM} definitions. MIRROR_DISTFILES and NO_CDROM are now dead.
2000-03-13add and enable rasmolwiz1-1/+2
2000-03-13RasMol is a molecular graphics program intended for the visualisation ofwiz9-0/+150
proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. Submitted by Marc Bauoin <babafou@babafou.eu.org> in pkg/8199, slightly enhanced.
2000-03-09remove trailing `.'wiz1-1/+1
2000-02-25remove commented out SUBDIR += lines for packages that never gotwiz1-5/+2
converted from FreeBSD, or have been disabled since. Sorted lines alphabetically, added some missing directories.
2000-02-05remove trailing '.'wiz1-1/+1
2000-01-11Initial import of nut program.garbled9-0/+106
record what you eat and analyze your meals.
1999-07-28Add and enable fastDNAmlrh1-1/+2
1999-07-28Import of fastDNAml-1.2.1, a program for estimating maximum likelihoodrh5-0/+83
phylogenetic trees from nucleotide sequences, as submitted by Marc Baudoin, thanks!
1999-07-28Enable clustalwrh1-2/+2
1999-07-28Import of clustalw-1.8, a general purpose multiple alignment programrh9-0/+87
for DNA or proteins. This is a merge of the packages submitted in PRs pkg/7075 by Brook Milligan and pkg/8094 by Marc Baudoin (with some minor modifications), thanks!
1999-07-28Import of phylip-3.573c, a Phylogeny Inference Package, as submitted byrh5-0/+117
Marc Baudoin, thanks!
1999-07-28Initial import of puzzle-4.0.2, a maximum likelihood analysis tool ofrh9-0/+112
molecular sequence data
1999-07-28Enable phyliprh1-2/+2
1999-07-28Add and enable puzzle.rh1-1/+2
1999-07-09Add package patch-sum filesagc1-0/+4
1999-04-16remove README.html from repositoryrh1-65/+0
1999-04-16Initial import of bioperl-0.04.4, based on the collection of packagesrh8-0/+288
submitted in PR pkg/7075 by Brook Milligan, with several modifications.
1999-04-15Enable bioperl.rh1-2/+2
1999-04-15Add new category biologyrh2-0/+13