summaryrefslogtreecommitdiff
path: root/biology
AgeCommit message (Collapse)AuthorFilesLines
2003-09-12kill all references to gcc.buildlink2.mk and compiler.mk, and definegrant1-2/+2
USE_GCC2 or USE_GCC3 where appropriate. the functionality of the old gcc.buildlink2.mk has been rolled into compiler.mk now, which is automatically used. more changes to come later...
2003-08-30Update to version 1.6.jtb7-102/+44
New features in chemtool 1.6 - universal import mode based on BABEL (both openbabel and babel supported) - Formula weight calculator now handles all main group elements and the first row of transition elements, and accepts greek phi as phenyl substituent. - Movable hexagonal or square grid backdrop - Improved SVG export, optional preview bitmaps in EPS export, optional EMF export - Cursor key support for pixel-precise drawing and moving - The cleanup function now corrects bonds that deviate from ideal horizontal or vertical orientation by a single pixel - Color support (bonds and text can be red,green,blue,cyan,magenta or yellow). - Default bond length now configurable, additional grid positions at two and three times this length added - Added a brief help text to accompany the 'About' window in the 'Help' menu. - Added alternate text font (Times Roman) - An attachment site can be marked before saving a molecule or fragment, which act as reference point for adding this fragment to other molecules (previously, this had to be the first atom in a file). Attachment sites are marked in the preview window by a small x. - Background color can now be chosen for screen display and EPS export, and drawing whiteout boxes under labels is now an option ( off by default !). - Text at 8,10,12,14,17,20 and 24pt can now coexist in a drawing. - Increased allowed label length to 100. - Improved rendering of dashed wedge and dotted lines - Improved text kerning in xfig-based print and export. - It is now possible to place an auto-incrementing counter at the cursor position for numbering sites. - Changed double bond drawing code to no longer switch sides depending on drawing (or rotation) angle. (As a result of this, some older drawings will need fixing) - Rescaling a molecule now also scales its labels. Downscaling beyond zero size (causing strange inversions) is no longer possible. - Renamed the "Orbitals" template menu to "Symbols" and added "plus", "minus" and a rearrangement arrow to it. - Added two new bond types, a triple bond with all three lines equal, and a quadruple bond.
2003-08-11Update to 9.0.wiz4-12/+12
Changes: This release introduces the new USDA Nutrient Database, SR16, which has 6,661 foods and 125 nutrients, and includes an automatic conversion feature so that NUT 8.x installations can preserve existing meal records and have them interpreted with the latest USDA database.
2003-07-21COMMENT should start with a capital letter.martti1-2/+2
2003-07-17s/netbsd.org/NetBSD.org/grant3-6/+6
2003-07-13PKGREVISION bump for libiconv update.wiz1-2/+2
2003-07-12Update to 8.10. Not sure what has changed since 4.x, but I'd guess ratherwiz6-80/+51
much.
2003-06-11Update for the fact that 'arm' ports have been called NetBSD-*-arm for a whileabs1-2/+2
now and not NetBSD-*-arm32. Changes include one or more of: - Change MACHINE_ARCH == arm32 to also match arm - Where ONLY_FOR_PLATFORM includes NetBSD-*-arm32, add NetBSD-*-arm - Where BROKEN or worked around for arm gcc bugs, set USE_GCC3 The last may shake out a few more broken packages the next bulk build.
2003-06-02Use mk/gcc.buildlink2.mk rather than gcc/buildlink2.mk so lang/gcc3abs1-2/+2
is accepted. Suggested by Grant.
2003-06-02Use tech-pkg@ in favor of packages@ as MAINTAINER for orphaned packages.jschauma3-6/+6
Should anybody feel like they could be the maintainer for any of thewe packages, please adjust.
2003-05-10Update to version 5.1.jtb5-50/+20
Many minor enhancements and bugfixes. Manual updated.
2003-05-06Drop trailing whitespace. Ok'ed by wiz.jmmv2-3/+3
2003-05-02Dependency bumps, needed because of devel/pth's major bump, and relatedwiz1-1/+2
dependency bumps.
2003-03-29Place WRKSRC where it belongs, to make pkglint happy; ok'ed by wiz.jmmv1-3/+2
2003-02-25Use new IMAKE_MAN_PATH variables in PLISTs to make these packages morejschauma2-3/+4
portable. Bump PKGREVISION accordingly.
2002-12-01Fix thinko, /usr -> ${PREFIX}.salo2-4/+4
2002-11-30USE_PKGLOCALEDIR.salo4-22/+26
2002-10-27Use buildlink2. Use perl5/module.mk.seb1-6/+3
2002-09-29buildlink1 -> buildlink2jlam1-5/+5
2002-09-21buildlink1 -> buildlink2jlam3-19/+13
2002-09-12Standardize.wiz1-3/+3
2002-06-07Small pkglint white-space complaint.cjep1-2/+1
2002-05-20Add NetBSD tags.cjep3-0/+3
2002-05-03Update to version 1.4.1. Numerous bug fixes since 1.3.jtb7-56/+80
2002-04-20Avoid egcs internal compiler error by using gcc-2.95.3 on arm32.cjep1-1/+7
2001-12-06Include x11.buildlink.mkjmc1-1/+2
2001-11-28Buildlinkify.jlam1-2/+3
2001-11-14Replace "${GTAR} cf - . | (cd ... ; ${GTAR} xf - )" pipelines with aagc1-3/+2
single instance of ${PAX}.
2001-10-31Move pkg/ files into package's toplevel directoryzuntum18-12/+12
2001-09-09Deprecate NO_WRKSUBDIR, replacing it with an explicit assignment of:agc1-2/+3
WRKSRC= ${WRKDIR} This is much cleaner, much more indicative of what happens, and removes another of the negative definitions (NO_.* = value).
2001-08-17Remove explicit settings of FOO_CONFIG=${BUILDLINK_CONFIG_WRAPPER.foo} injlam1-2/+1
MAKE_ENV as they are now added by the buildlink files themselves.
2001-07-08Update to 5.0.jtb6-68/+58
Among the many changes: * New MPI version * Now uses autoconf/automake See the ChangeLog for full details.
2001-06-30Converted to use buildlink.mkzuntum3-10/+13
2001-04-28Remove redundant echoing, quoting, and input redirection to sed.jtb1-9/+4
2001-04-26chemtool.1 is a leftover from the i386 bulk build.jtb1-1/+2
2001-04-19move to sha digest, and add distfile size.agc1-2/+3
2001-04-19Move to sha1 digests, and add distfile sizes.agc7-13/+20
2001-04-17+ move the distfile digest/checksum value from files/md5 to distinfoagc19-48/+32
+ move the patch digest/checksum values from files/patch-sum to distinfo
2001-04-14Change MAINTAINER section to packages@netbsd.orgjtb1-2/+2
2001-04-05Updated to bioperl-0.7.0.jtb7-93/+40
Revision history for Bioperl core modules 0.7 Large number of changes, including refactoring of the Object system, new parsers, new functionality and all round better system. Highlights are: o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI; Bio::Root::IO for I/O and file/handle capabilities. o Imported BPlite modules from Ian Korf for BLAST parsing. This is considered the supported BLAST parser; Bio::Tools::Blast.pm will eventually phase out due to lack of support. o Improved Sequence Feature model. Added complete location modelling (with fuzzy and compound locations). See Bio::LocationI and the modules under Bio/Location. Added support in Genbank/EMBL format parsing to completely parse feature tables for complex locations. o Moved special support for databanks etc to specialized modules under Bio/Seq/. One of these supports very large sequences through a temporary file as a backend. o Explicit Gene, Transcript and Exon SeqFeature objects, supporting CDS retrieval and exon shuffling. o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and DB/GDB (the latter has platform-specific limitations). o New analysis parser framework for HT sequence annotation (see Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory) o New Alignment IO framework o New Index modules (Swissprot) o New modules for running Blast within perl (Bio::Tools::Run::StandAloneBlast). Added modules for running Multiple Sequence Alignment tools ClustalW and TCoffee (Bio::Tools::Run::Alignment). o New Cookbook-style tutorial (see bptutorial.pl). Improved documentation across the package. o Much improved cross platform support. Many known incompatibilities have been fixed; however, NT and Mac do not work across the entire setup (see PLATFORMS). o Many bug fixes, code restructuring, etc. Overall stability and maintainability benefit a lot. o A total of 957 automatic tests 0.6.2 There are very few functionality changes but a large number of software improvements/bug fixes across the package. o The EMBL/GenBank parsing are improved. o The Swissprot reading is improved. Swissprot writing is disabled as it doesn't work at all. This needs to wait for 0.7 release o BLAST reports with no hits are correctly parsed. o Several other bugs of the BLAST parser (regular expressions, ...) fixed. o Old syntax calls have been replaced with more modern syntax o Modules that did not work at all, in particular the Sim4 set have been removed o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair have improved compliance with interface specs and documentation o Mailing list documentation updated throughout the distribution o Most minor bug fixes have happened. o The scripts in /examples now work and have the modern syntax rather than the deprecated syntax 0.6.1 Sun April 2 2000 o Sequences can have Sequence Features attached to them - The sequence features can be read from or written to EMBL and GenBank style flat files o Objects for Annotation, including References (but not full medline abstracts), Database links and Comments are provided o A Species object to represent nodes on a taxonomy tree is provided o The ability to parse HMMER and Sim4 output has been added o The Blast parsing has been improved, with better PSI-BLAST support and better overall behaviour. o Flat file indexed databases provide both random access and sequential access to their component sequences. o A CodonTable object has been written with all known CodonTables accessible. o A number of new lightweight analysis tools have been added, such as molecular weight determination. The 0.6 release also has improved software engineering o The sequence objects have been rewritten, providing more maintainable and easier to implement objects. These objects are backwardly compatible with the 0.05.1 objects o Many objects are defined in terms of interfaces and then a Perl implementation has been provided. The interfaces are found in the 'I' files (module names ending in 'I'). This means that it is possible to wrap C/CORBA/SQL access as true "bioperl" objects, compatible with the rest of bioperl. o The SeqIO system has been overhauled to provide better processing and perl-like automatic interpretation of <> over arguments. o Many more tests have been added (a total of 172 automatic tests are now run before release). 0.05.1 Tue Jun 29 05:30:44 1999 - Central distribution now requires Perl 5.004. This was done to get around 5.003-based problems in Bio/Index/* and SimpleAlign. - Various bug fixes in the Bio::Tools::Blast modules including better exception handling and PSI-Blast support. See Bio/Tools/Blast/CHANGES for more. - Fixed the Parse mechanism in Seq.pm to use readseq. Follow the instructions in README for how to install it (basically, you have to edit Parse.pm). - Improved documentation of Seq.pm, indicating where objects are returned and where strings are returned. - Fixed uninitialized warnings in Bio::Root::Object.pm and Bio::Tools::SeqPattern.pm. - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52. 0.05 Sun Apr 25 01:14:11 1999 - Bio::Tools::Blast modules have less memory problems and faster parsing. Webblast uses LWP and supports more functionality. See Bio/Tools/Blast/CHANGES for more. - The Bio::SeqIO system has been started, moving the sequence reformatting code out of the sequence object - The Bio::Index:: system has been started, providing generic index capabilities and specifically works for Fasta formatted databases and EMBL .dat formatted databases - The Bio::DB:: system started, providing access to databases, both via flat file + index (see above) and via http to NCBI - The scripts/ directory, where industrial strength scripts are put has been started. - Many changes - a better distribution all round.
2001-04-01Fix quotingzuntum2-4/+4
2001-03-04Use ${PKGLOCALEDIR}.jtb3-5/+7
2001-02-16Not needed any more -- COMMENTs are in Makefiles now.wiz1-1/+0
2001-02-16Update to new COMMENT style: COMMENT var in Makefile instead of pkg/COMMENT.wiz1-9/+11
While I'm here, unify category Makefiles to more standard style. (If you have tools depending on the previous form, please fix them.)
2001-02-16Update to new COMMENT style: COMMENT var in Makefile instead of pkg/COMMENT.wiz16-16/+16
2001-02-15It appears that the source has moved. Fixes i386 bulk build problem.jtb1-2/+2
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