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Gerd Fleischer
gerdfleischer@gmx.de
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xdrawchem-2.0.orig/HISTORY.txt 0000644 0001750 0001750 00000043000 10610174065 016371 0 ustar georgesk georgesk version 1.99.1:
Updated code to use Qt 4.x, with extensive contributed code.
version 1.9.9:
Updated code to use OpenBabel 2.0 (or later).
Fixed a bug when loading files with OpenBabel. Atoms are now labeled correctly.
Fixed bug #1255229, relating to correct rendering of super- and subscripts.
Added a feature to send 3-D structures to external programs ghemical and
KryoMol. More programs will be added on request.
Removed canonical SMILES generation. This feature was dependent on a cgi-bin
script that will not run on xdrawchem.org's new host. InChI, the new NIST-
IUPAC standard, should be used for canonicalization.
version 1.9.8:
Worked on bug #1236716 and #1255229, regarding XDrawChem's rendering
of text typed into the QTextEdit mini text editor.
Fixed bug #1254917, relating to segfaults when drawing symbols.
Updated database back-end to use data parsed from the PubChem Compounds
database, and updated XDrawChem to link to PubChem compound records where
available.
version 1.9.7:
Fixed sf.net bug #1221480 pertaining to QPainter errors.
Added antibody (Symbol) and biotin (pre-defined functional group).
Added support for InChI output (Tools menu; Internet access required).
Fixed a bug where drawing temporarily goes blank after certain tools or
functions are used.
version 1.9.6:
Resolved sf.net bug #1200630 relating to loading and saving formatted text.
Resolved sf.net bug #1198595, relating to segfaults in the IR tool.
Updated to use newer Qt classes (e.g., QPtrLst instead of QList). Many thanks
to Gerd Fleischer for contributing a very large patch.
Added text shape options.
Fill color can be set for ellipse/rectangle bracket types.
Updated paint/print functions to use a single global painter object. Print
and images should look the same as what you drew on screen now! Image size
is now passed to ImageMagick (if available) so images should be same size
as on-screen.
version 1.9.5:
Removed m4 / autom4te stuff from CVS and distributions!
Added arrow, symbol, ring drawing change suggested in tracker #1175966.
Resolved Edit > Cut bug, tracker #1178101.
Fixed some oddities with point moves and double bond spacing.
Tinkered with PNG output to produce nicer looking images.
-- This feature is implemented two ways, and works better if ImageMagick
-- is installed.
Added a "hot key" function for quick editing of atoms and labels.
version 1.9.4:
(contributed) Fixed buggy pointer references related to bug #1158842.
Added Edit > Insert symbol dialog.
Improvements to BUILD3D code now yield better results for fused rings,
aromtics, and other double bonds.
Updated Polish language file.
Releases will be made using "cvs export" rather than "cvs checkout"; see
sf.net bug #1169699.
version 1.9.3:
Fixed issue with color selection and color in EPS files.
Aliphatic chains are now consistently drawn correctly.
Undo and load/save correctly handle explicit "C" labels on carbons.
BUILD3D is now accessed as a CGI script, which means it is accessible for
all platforms with an Internet connection.
(contributed) Updated Polish language file.
version 1.9.2:
Fixed some small bugs in drawing behavior.
When a Tool menu option is chosen, the target molecule is now highlighted
on mouse over.
Added more options to right-click menu.
Added reverse reaction prediction.
Double clicking on text allows edit.
XDrawChem can produce 3-D structures using the external program BUILD3D.
Fixed issues with coordinate system.
version 1.9.1:
Updated German translation. Thanks to Daniel Leidert for this work.
Fixed some keyboard and text input issues. Mainly, it's possible to label
carbons again, and type characters that are not US-English letters and
numbers. This should also fix some format issues.
You can now change font settings within XDrawChem and have them saved between
sessions.
Fixed arrow behavior. All arrow types render correctly, and it's possible
to change the thickness of some arrow types.
Fixed custom rings dialog. Custom rings saved to user's home directory
now appear on menu correctly. Menu is also dynamically updated, so new
structures appear immediately without need to restart XDrawChem.
version 1.9:
Added Russian language translation file. Thanks to Vitaly Lipatov and Roman
Borisyuk for conributing this work.
Fixed dialogs that display Help. It's now possible to use the Help dialog,
and close it without closing the tool you are using.
Eliminated Elemental analysis dialog. This feature is now part of Molecule
Information.
Fixed a bug in the text tool that caused a segfault when clicking off of an
empty text field. Also updated text toopl behavior to more accurately show
what would be selected, moved, etc. on mouse click.
Fixed a bug where aromatic and other rings would have infinite scale and
random rotation if attached to an existing bond. Rings now attach
correctly, even to vertical bonds.
Keyboard input for non-English users is fixed. You can finally type letters
with umlauts (e.g., "Säure") and other accents.
You can paste text from other applications with Ctrl+V. However, you must
select the Text tool first and create a new text box.
The width of any bond (double, triple, dashed, ...) may be changed now.
version 1.8.5:
Fixed EPS output by using "ps2epsi" script supplied with GhostScript to
process the file.
Updated some deprecated functions to current version and fixed some
warnings.
(contributed) Made some pixmaps transparent to improve print quality.
version 1.8.4:
Names retrieved from the database are correctly displayed now.
Right-clicking on a molecule brings up a popup list of actions. Currently,
select molecule, cut, copy and molecule info are available this way.
version 1.8.3:
Updated Polish translation.
Pressing Escape now puts you back in select mode, regardless of current state.
Moved XDrawChem database, and eliminated dependency of frowns, sort of.
Canonical SMILES is now found by querying a cgi-bin script, so if you
have net access, you can access all DB features now.
version 1.8.2:
Zoom/magnify tools now exist.
Double bond alignment fixes. You can set a specific double bond style
by right-clicking on the double bond.
Updated configure script with Geoffrey Wossum's excellent macro for finding
Qt and setting variables. http://autoqt.sf.net/
version 1.8.1:
Improved Undo feature.
Code cleanup and arrangement: compiles much faster now.
version 1.8:
Added circle and square tools.
Changed menu structure a bit.
Added Italian language file.
Improved database -- it's now possible to get CAS number and sometimes
name from a molecule structure. Database back-end changes have also
improved lookup based on name and CAS.
Fixed some bugs, see SourceForge bug tracker.
version 1.7.8:
Added lasso tool.
Fixed bug 900782.
Updated to use OpenBabel 1.100.2 (and later)
version 1.7.7:
Bug fix release -- fixed EPS bounds and buggy text alignment.
Administrative: moved everything to SourceForge.net, put source in CVS.
version 1.7.6:
Bug fix release -- fixed null pointer bug in file save.
XDrawChem can now draw hex grid.
version 1.7.5:
EPS output should now draw text better.
A "Did You Know?" dialog was added.
configure script updated to use latest autoconf/automake.
OpenBabel is no longer bundled. You will need to download it separately.
--(from http://openbabel.sourceforge.net/ ; OB version must be 1.100.1)
Translation .po and .pot files were updated (sorry that I forgot these!)
version 1.7.4:
Program now supports English and metric units.
version 1.7.3:
Added ruler and square grid.
Added octanol-water partition (Kow) calculator.
Updated OB source directory.
version 1.7.2:
Fixed an issue with EPS/PostScript output.
Added new Danish and Polish translations.
version 1.7.1:
Improved p orbital symbols.
(Hopefully) fixed bug with saving pictures.
version 1.7:
Added half and full arrowheads for Bezier curves.
Updated documentation.
Fixed double->int conversions so that rounding is done rather than truncation.
(should improve drawing appearance)
Generated an xdrawchem.pot file for translation.
version 1.6.10:
Fixed a printing bug where lines were drawn over text.
Added pKa estimation.
version 1.6.9:
Added "wavy" bond type.
Page setup preferences (page size, orientation, etc.) are now saved.
version 1.6.8:
Bug fix release. No significant new features.
version 1.6.7:
Added file type auto-detect.
Added aliphatic chain tool.
Added Newman projection.
version 1.6.6:
Added option to not add hydrogens and format.
New text options: left, center, right justify.
version 1.6.5:
Fixed CDX/CDXML open and save operations.
Added new drawing options: box, ellipse, cubic bezier, new arrow style.
version 1.6.4:
Added new spectrum dialog.
Fixed text behaviors -- backspace and delete behavior and display of carbon.
Added option to put subscript on brackets.
version 1.6.3:
Combined open and save menus, eliminated import/export options.
Command line conversion (molecule -> image) is now possible.
version 1.6.2:
Fixed compilation to work on newer gcc.
Updated OpenBabel library code.
Updated Windows version to include OpenBabel.
version 1.6.1:
Added translation files for Danish (dk) and Japanese (jp).
Patched SMILES dialog to use OpenBabel. (contributed by Brett Saunders)
Fixed several memory leaks.
Fixed Delete key behavior.
Added symbol font.
Re-implemented (some) event handling to use Qt signal-slot architecture.
version 1.6:
Latest stable release.
Clipboard works again, and works with curve arrows and symbols correctly.
Added help to some dialogs.
version 1.5.5:
Code cleanup.
Automatic scaling on file read or import operation.
Changed behavior of select tool when moving bonds.
version 1.5.4:
File export via OpenBabel is implemented.
Fixed some namespace issues.
version 1.5.3:
Added configure switch to control whether OpenBabel is built.
Added configure switch to specify which flavor of Qt to use.
File import via OpenBabel is implemented.
version 1.5.2:
New HTML-based manual.
autoconf/automake build implemented. See INSTALL.txt
version 1.5.1:
Partial OpenBabel integration.
Numerous usability and file format fixes.
Save custom ring dialog added.
version 1.5:
(UNIX) Stereo bonds now print correctly.
The annoying ring placement bug has been fixed :)
Improved 1H NMR prediction -- chiral centers, better shift prediction.
version 1.4.2:
Limited 1H NMR prediction ability.
Fixed bug with deleting labels (again).
MDL Molfile now saved correctly.
(Windows) Stereo-down bonds are drawn correctly.
version 1.4.1:
Fixed parentheses printing (EPS mode)
Fixed bug with saving/restoring where element name saved incorrectly
Delete key on highlighted text behaves correctly now.
Ctrl+B, Ctrl+I, Ctrl+U, Ctrl-Plus, Ctrl-Minus shortcuts on text.
(Bold, Italic, Underline, Superscript, Subscript, respectively)
Fixed hydrogen calc and attach point for more groups: "CO", "SO"
Fixed printing of symbols (i.e., learn to print bitmaps)
version 1.4:
Bug fixes: redraw, text placement, etc. Added some templates.
Smart placement. Automatic attachment of amino acids and rings.
version 1.3.2:
Bug fix release: pointers, getenv(), -lqt vs. -lqt-mt, fonts, etc.
Really fixed EPS bug this time, I hope.
version 1.3.1:
Added pictures to menus for "standard" items.
Fixed EPS export bug.
version 1.3:
Preferences are now saved. (The directory is platform-dependent)
Simple reaction analysis: Free energy change estimate, 13C NMR comparison.
version 1.2:
Consolidated all molecule info stuff into one dialog.
Added features to group molecules into reactants and products.
Switched to GPL (woo hoo!)
version 1.1.1:
Fixed a bug with screen clearing and double buffering.
Code cleanup.
version 1.1:
Structure cleanup has improved -- aliphatics no longer drawn as straight lines.
Changed drawing of carbonyl and imine double bonds.
New CML parser - used Qt's XML parsing functions.
version 1.0.2:
Molecular weight and empirical formula are displayed on the status line
before pasting.
Can paste elemental analysis data into the drawing.
Moving towards using a Preferences class to store user settings.
version 1.0.1:
Rings are not placed automatically; click to place rings.
Screen drawing is now double-buffered. Flicker should be reduced.
More intelligent text placement. Automatically adds hydrogens.
Added symbol: stereochemical ring hydrogen.
Added ring templates: indole, purine, pyrimidine, steroid backbone.
version 1.0:
First "stable" release.
Fixed some things: memory allocation, selection issues.
Shift-drag over part of a molecule selects the entire molecule.
IR spectrum prediction improved.
Export Peak Lists from 13C NMR and IR copies peak list to clipboard.
Fixed length and angle of bond and arrow are now controlled separately.
XDrawChem can now use Babel. Added features if Babel is installed:
Can read and write PDB files.
Can output SMILES strings.
version 0.99.9:
Fixed more behavior bugs.
Double and triple bonds are drawn a little better now.
Same code compiles on Windows and UNIX. Visual C++ project file
now included.
Hydrogens added automatically in SMILES and structure cleanup.
Title bar now says "XDrawChem".
version 0.99.8:
Fixed some behavior bugs.
Fixed some code incompatibility between Windows and UNIX with conditional
compile statements.
Added SVG export support. (Under "Save picture")
Added ChemDraw(TM) XML export support. (Under "Save as...")
version 0.99.7:
Make text placement slightly smarter.
Implemented copy to system clipboard and drag and drop. This uses the
Qt library objects QImageDrag and QClipboard; I am not sure what
applications can interact with items from Qt applications.
Received (or created from old language_*.h) new translation files.
Dutch, French, German and English now supported.
Created mailing list: xdrawchem-announce@lists.sourceforge.net
version 0.99.6:
Bugfix release - conditional compiling should still allow compilation with
Qt 2.3.x, and fixed elemental analysis and EPS output.
Added translation sources (.ts files) for French (fr), German (de),
Italian (it), Dutch (nl), Spanish (es), and Portugese (pt and br - Brazil).
The text is still in English and needs translating with Qt Linguist :)
version 0.99.5:
Default print resolution is 100 dpi -- so 25 point lines on screen equal
1/4 inch on paper, etc.
Now using Qt 3.0 langauge support - no more language_*.h files.
Network access now uses Qt 3.0 HTTP support, eliminating curl dependency.
version 0.99.4:
Implemented structural diagram generation based on JMDraw.
Added SMILES interpreter.
Added molecule clean-up function.
version 0.99.3:
Fixed problem with text rendering when printing.
version 0.99.2:
Split ring menu into categories.
Added automatic text placement.
Added German manual.
version 0.99.1:
Fixed compile bug(s).
version 0.99:
Added edit functions.
Added more help strings.
Started to fix localization.
version 0.98:
Added database access components.
version 0.97:
Added French, German, and Polish languages.
version 0.96:
Added some language support.
Changed the way double bonds are handled. Aromatics etc. look nicer.
Added arrow styles - dashed, bidirectional, retrosynthetic, 90 and 270
degree curve arrows.
version 0.95:
Added colors and background.
Added bold, italic, and underline options for text.
Added page setup and tinkered with printing.
version 0.94:
Implemented Undo.
First Windows build released.
version 0.93:
Added bracket styles.
Import of binary ChemDraw (CDX) files. (not perfect, of course :)
Basic IR prediction.
version 0.92:
Finally, you can do "make install"!
Improved handling of CDXML [ChemDraw(TM) XML text] file types.
version 0.91:
Added empirical formula calculation.
Added elemental analysis.
Fixed some behaviors (text and selection).
version 0.9:
Rewrote nearly everything.
UI changes.
Added curve arrow.
Improved symbols.
13C NMR prediction.
version 0.85:
Added Rotate functions (under Edit menu).
Consolidated Flip functions (under Edit menu).
Added Insert menu under Edit menu; can now insert CML/XML files.
Started to migrate pre-defined rings to CML format.
Can read simple ChemDraw XML (text only!) files.
Can write simple Encapsulated PostScript (EPS) files.
version 0.84:
Added Info window and functions.
Fixed MW calculator.
Fixed some things in Format menu.
Changed Alignment functions; now under Tools menu.
Alignment functions now collected as Auto Layout.
Better support for XML documents. (Auto scale and placement)
Changed ring dialog; added all common amino acids and nucleic acids.
version 0.83:
Bug fixes, add more rings, update manual, etc.
Improved MDL Molfile support (still doesn't meet spec, but closer now)
Improved XDrawChem file format to store element info.
Added Undo (may not be able to undo everything!).
Added Mass Calculator.
Changed and improved text editor - now can properly do super- and subscript,
and support multi-line entry.
Added some support for 2-D CML (Chemical Markup Language) files.
version 0.82:
Added support for PNG image files.
Ability to flip horizontal/vertical.
Dashed line support.
Symbol support.
Changed install procedure and Makefile to point to correct ring file location.
version 0.81:
Added more rings. (This will probably happen every release.)
Wrote more manual pages. (This will also probably happen every release.)
Bug fixes. (I really hope to do this every release too.)
Added color.
Changed ring dialog so "tool tips" appear to identify each ring.
Line drawing now tells length and angle of the line being drawn.
Manual is not modal anymore, so you can continue working with the manual open.
There is now a user-defined page size which allows you to specify the pixel
size of the drawing widget (this is most useful for creating images).
You can now set the fixed angle used in fixed length/angle mode.
version 0.8:
First public release.
xdrawchem-2.0.orig/README.txt 0000644 0001750 0001750 00000004727 10465520507 016206 0 ustar georgesk georgesk Welcome to XDrawChem! (version 1.9.9)
Mostly written by Bryan Herger, bherger@users.sourceforge.net
See acknowledgements below for specific contributions.
The XDrawChem web site is http://xdrawchem.sourceforge.net/
Please report bugs and suggest features to me at the e-mail listed above,
or using links to the sf.net tracker on the project web page.
This program is released under the terms of the GNU General Public License.
Portions of the source code are copyright by others.
Please see the files COPYRIGHT.txt and GPL.txt included in this package.
NOTE: This is a mostly stable version, but probably still has bugs!
See LICENSE.txt for copyright and limitation of liability.
Please report bugs to bherger@users.sourceforge.net
XDrawChem is a two-dimensional molecule drawing program for Unix
operating systems. It is similar in functionality to other molecule
drawing programs such as ChemDraw (TM, CambridgeSoft). It can read
and write MDL Molfiles and CML files to allow sharing between
XDrawChem and other chemistry applications. XDrawChem has been tested
on Linux, Sun Solaris and SGI IRIX. XDrawChem was designed with Qt
3.0 or later, available free from http://www.trolltech.com/
XDrawChem also depends on the OpenBabel library, http://openbabel.sf.net/
Please read INSTALL.txt which gives instructions on how to install
XDrawChem.
XDrawChem features an online manual. Run the program and press F1 (or
select Manual under the Help menu) for instructions.
The HISTORY file lists changes made in each revision.
Please subscribe to the xdrawchem-announce mailing list for
information about future releases. Send a blank message to
xdrawchem-announce-request@lists.sourceforge.net
You should also subscribe to xdrawchem-user, the discussion list for
XDrawChem. Send a blank message to
xdrawchem-user-request@lists.sourceforge.net
Acknowledgements and many thanks to the following people who have
contributed:
Thomas LeClerc
Masao Kawamura
Guy Brand
Sven Bornemann
Kuznik Nikodem
Ralf Ahlbrink
Eduardo Sanchez
Ronald Bialozyt
Egon Willighagen
Armando Navarro
Bojan Ivancic
Brett Saunders
Geoffrey Wossum (for autoconf macros, http://autoqt.sf.net/)
Brian Kelley (for Frowns project, http://frowns.sf.net/)
Christian Becke (for pixmaps)
Everyone who works on OpenBabel (http://openbabel.sf.net/)
Vitaly Lipatov and Roman Borisyuk (for Russian language translation)
Daniel Leidert (for German language translation)
Thomas Shattuck
Gerd Fleischer
...and others not listed yet...
xdrawchem-2.0.orig/xdrawchem.pro 0000644 0001750 0001750 00000014011 10612715032 017170 0 ustar georgesk georgesk TEMPLATE = app
TARGET = xdrawchem2
!exists(config.mak) {
error(Please run the configure script first.)
}
include(config.mak)
DESTDIR = bin
target.path = $${PREFIX}/$${DESTDIR}
INSTALLS = target
unix {
MOC_DIR = .moc
UI_DIR = .ui
OBJECTS_DIR = .obj
# for includes and libs
DEFINES += UNIX
DEFINES += RINGHOME=\"$${PREFIX}/share/xdrawchem2\"
# DEFINES += QT3_SUPPORT_WARNINGS
ringdir.path = $${PREFIX}/share/xdrawchem2
ringdir.files = ring/*
doc.path = $${PREFIX}/share/xdrawchem2/doc
doc.files = doc/*
INSTALLS += ringdir doc
QMAKE_CXXFLAGS_DEBUG += -O0
QMAKE_CXXFLAGS_DEBUG += -g3
}
DEFINES += QT_NO_CAST_TO_ASCII
#DEFINES += QT_NO_CAST_FROM_ASCII
CONFIG += qt debug
QT += xml network
#RESOURCES = xdrawchem/xdrawchem.qrc
HEADERS = xdrawchem/aa_xpm.h \
xdrawchem/application.h \
xdrawchem/arrow.h \
xdrawchem/arrows.h \
xdrawchem/atom.h \
xdrawchem/biotools.h \
xdrawchem/bondedit.h \
xdrawchem/bond.h \
xdrawchem/boshcp.h \
xdrawchem/bracket.h \
xdrawchem/brackets.h \
xdrawchem/CDXConstants.h \
xdrawchem/cdxml_reader.h \
xdrawchem/charsel.h \
xdrawchem/chemdata.h \
xdrawchem/colorbutton.h \
xdrawchem/clipboard.h \
xdrawchem/cml.h \
xdrawchem/crings_dialog.h \
xdrawchem/cubicbezier.h \
xdrawchem/curvearrow.h \
xdrawchem/defs.h \
xdrawchem/dpoint.h \
xdrawchem/drawable.h \
xdrawchem/dyk.h \
xdrawchem/fixeddialog.h \
xdrawchem/gobject.h \
xdrawchem/graphdata.h \
xdrawchem/graphdialog.h \
xdrawchem/graphwidget.h \
xdrawchem/helpwindow.h \
xdrawchem/http.h \
xdrawchem/ioiface.h \
xdrawchem/justifytools.h \
xdrawchem/lines.h \
xdrawchem/magnifytools.h \
xdrawchem/moldata.h \
xdrawchem/molecule.h \
xdrawchem/molecule_sssr.h \
xdrawchem/molinfodialog.h \
xdrawchem/myfiledialog.h \
xdrawchem/na_xpm.h \
xdrawchem/netaccess.h \
xdrawchem/netchoosedialog.h \
xdrawchem/netdialog.h \
xdrawchem/ngw.h \
xdrawchem/pagesetupdialog.h \
xdrawchem/paintable.h \
xdrawchem/peak.h \
xdrawchem/peptidebuilder.h \
xdrawchem/prefs.h \
xdrawchem/previewwidget.h \
xdrawchem/render2d.h \
xdrawchem/renderarea.h \
xdrawchem/ringdialog.h \
xdrawchem/ring.h \
xdrawchem/rings.h \
xdrawchem/ring_xpm.h \
xdrawchem/sdg.h \
xdrawchem/setofrings.h \
xdrawchem/smilesdialog.h \
xdrawchem/sorf.h \
xdrawchem/sugar_xpm.h \
xdrawchem/symbol.h \
xdrawchem/symbol_xpm.h \
xdrawchem/text.h \
xdrawchem/textshapedialog.h \
xdrawchem/tool_13c_nmr.h \
xdrawchem/tool_1h_nmr.h \
xdrawchem/tool_2d3d.h \
xdrawchem/tooldialog.h \
xdrawchem/tool_ir.h \
xdrawchem/xdc_event.h \
xdrawchem/xdc_toolbutton.h \
xdrawchem/xml_cml.h \
xdrawchem/xml_reader.h \
xdrawchem/xruler.h
SOURCES = xdrawchem/application.cpp \
xdrawchem/application_ob.cpp \
xdrawchem/application_ring.cpp \
xdrawchem/arrow.cpp \
xdrawchem/biotools.cpp \
xdrawchem/bond.cpp \
xdrawchem/bondedit.cpp \
xdrawchem/boshcp.cpp \
xdrawchem/bracket.cpp \
xdrawchem/cdx2cdxml.cpp \
xdrawchem/cdxml_reader.cpp \
xdrawchem/charsel.cpp \
xdrawchem/chemdata_cdx.cpp \
xdrawchem/chemdata_cdxml.cpp \
xdrawchem/chemdata_cml.cpp \
xdrawchem/chemdata.cpp \
xdrawchem/chemdata_edit.cpp \
xdrawchem/chemdata_event.cpp \
xdrawchem/chemdata_mdl.cpp \
xdrawchem/chemdata_rw.cpp \
xdrawchem/chemdata_rxn.cpp \
xdrawchem/chemdata_tools.cpp \
xdrawchem/chemdata_xdc.cpp \
xdrawchem/chemdata_xml.cpp \
xdrawchem/colorbutton.cpp \
xdrawchem/crings_dialog.cpp \
xdrawchem/curvearrow.cpp \
xdrawchem/drawable.cpp \
xdrawchem/dyk.cpp \
xdrawchem/fixeddialog.cpp \
xdrawchem/gobject.cpp \
xdrawchem/graphdialog.cpp \
xdrawchem/graphwidget.cpp \
xdrawchem/helpwindow.cpp \
xdrawchem/ioiface.cpp \
xdrawchem/main.cpp \
xdrawchem/molecule_1h_nmr.cpp \
xdrawchem/molecule.cpp \
xdrawchem/molecule_obmol.cpp \
xdrawchem/molecule_smiles.cpp \
xdrawchem/molecule_sssr.cpp \
xdrawchem/molecule_tools_1.cpp \
xdrawchem/molecule_tools_2.cpp \
xdrawchem/molinfodialog.cpp \
xdrawchem/myfiledialog.cpp \
xdrawchem/netaccess.cpp \
xdrawchem/netchoosedialog.cpp \
xdrawchem/netdialog.cpp \
xdrawchem/ngw.cpp \
xdrawchem/pagesetupdialog.cpp \
xdrawchem/peptidebuilder.cpp \
xdrawchem/previewwidget.cpp \
xdrawchem/render2d.cpp \
xdrawchem/render2d_draw.cpp \
xdrawchem/render2d_event.cpp \
xdrawchem/render2d_print.cpp \
xdrawchem/render2d_select.cpp \
xdrawchem/render2d_text.cpp \
xdrawchem/renderarea.cpp \
xdrawchem/retro.cpp \
xdrawchem/ringdialog.cpp \
xdrawchem/smilesdialog.cpp \
xdrawchem/symbol.cpp \
xdrawchem/text.cpp \
xdrawchem/textshapedialog.cpp \
xdrawchem/to3d.cpp \
xdrawchem/tool_13c_nmr.cpp \
xdrawchem/tool_1h_nmr.cpp \
xdrawchem/tool_2d3d.cpp \
xdrawchem/tooldialog.cpp \
xdrawchem/tool_ir.cpp \
xdrawchem/xdc_toolbutton.cpp \
xdrawchem/xml_cml.cpp \
xdrawchem/xml_reader.cpp \
xdrawchem/xruler.cpp
xdrawchem-2.0.orig/configure 0000755 0001750 0001750 00000002115 10610174065 016400 0 ustar georgesk georgesk #!/bin/sh
PREFIX="/usr/local"
ONLY_HELP="no"
if [ -n "$*" ] ; then
for arg in "$@" ; do
if [ "$arg" == "--help" ] ; then
cat << EOF
XDrawChem configure
Usage:
./configure [options]
Options:
--prefix=PREFIX install in PREFIX (optional, default is /usr/local)
--help show this help
EOF
ONLY_HELP="yes"
else
cut_arg="`echo "$arg"|cut -c-9`"
if [ "$cut_arg" == "--prefix=" ] ; then
PREFIX="`echo "$arg"|cut -c10-`"
fi
fi
done
fi
if [ "$ONLY_HELP" == "no" ] ; then
rm -f config.mak
#openbabel includes and libs
pkg-config openbabel-2.0 --atleast-version=2.0
if [ $? -eq 0 ] ; then
ob_incs=`pkg-config openbabel-2.0 --cflags-only-I|cut -c3-`
ob_libs=`pkg-config openbabel-2.0 --libs-only-l|cut -c3-`
echo "INCLUDEPATH += $ob_incs" >> config.mak
echo "LIBS += -l$ob_libs" >> config.mak
else
echo "Error: openbabel-2.0 libs not found or too old!"
exit 1
fi
echo "PREFIX = $PREFIX" >> config.mak
echo -e "\nWill install in $PREFIX."
echo -n "Creating Makefiles..."
qmake4 -o Makefile xdrawchem.pro
echo -e " done.\n"
fi
exit 0
xdrawchem-2.0.orig/TODO.txt 0000644 0001750 0001750 00000001351 10465520507 016004 0 ustar georgesk georgesk to fix immediately:
Improve printing of diagrams.
(Improve) Compute pKa's of functional groups.
Add more lone pair/orbital symbols.
Longer term:
- Improve interoperability with OpenBabel (perhaps abolishing my custom
Molecule classes in favor of OBMol)
- Browser plugin (Mozilla for Linux/MacOSX, .NET on Windows)
- Retrosynthesis
- Implement Convert to 3D.
- Link to 3-D visualization programs of some sort
- Improved XML support -- standards like SAX and DOM...
For Qt4
- antialias option
- cmake, qmake or autotools?
- use Qt resource system instead of RingDir?
- find a way to replace Q3PointArray (beziers)
- use more pass by reference (const QString &)
- make use of Qt's Postscript and SVG output capabilities?
- improve previewwidget xdrawchem-2.0.orig/Doxyfile 0000644 0001750 0001750 00000023740 10465520507 016212 0 ustar georgesk georgesk # Doxyfile 1.4.1-KDevelop
#---------------------------------------------------------------------------
# Project related configuration options
#---------------------------------------------------------------------------
PROJECT_NAME = xdrawchem2.kdevelop
PROJECT_NUMBER = $VERSION$
OUTPUT_DIRECTORY =
CREATE_SUBDIRS = NO
OUTPUT_LANGUAGE = English
USE_WINDOWS_ENCODING = NO
BRIEF_MEMBER_DESC = YES
REPEAT_BRIEF = YES
ABBREVIATE_BRIEF = "The $name class" \
"The $name widget" \
"The $name file" \
is \
provides \
specifies \
contains \
represents \
a \
an \
the
ALWAYS_DETAILED_SEC = NO
INLINE_INHERITED_MEMB = NO
FULL_PATH_NAMES = YES
STRIP_FROM_PATH = /home/gerd/prog/svn/klinpopup/
STRIP_FROM_INC_PATH =
SHORT_NAMES = NO
JAVADOC_AUTOBRIEF = NO
MULTILINE_CPP_IS_BRIEF = NO
DETAILS_AT_TOP = NO
INHERIT_DOCS = YES
DISTRIBUTE_GROUP_DOC = NO
TAB_SIZE = 8
ALIASES =
OPTIMIZE_OUTPUT_FOR_C = NO
OPTIMIZE_OUTPUT_JAVA = NO
SUBGROUPING = YES
#---------------------------------------------------------------------------
# Build related configuration options
#---------------------------------------------------------------------------
EXTRACT_ALL = NO
EXTRACT_PRIVATE = NO
EXTRACT_STATIC = NO
EXTRACT_LOCAL_CLASSES = YES
EXTRACT_LOCAL_METHODS = NO
HIDE_UNDOC_MEMBERS = NO
HIDE_UNDOC_CLASSES = NO
HIDE_FRIEND_COMPOUNDS = NO
HIDE_IN_BODY_DOCS = NO
INTERNAL_DOCS = NO
CASE_SENSE_NAMES = YES
HIDE_SCOPE_NAMES = NO
SHOW_INCLUDE_FILES = YES
INLINE_INFO = YES
SORT_MEMBER_DOCS = YES
SORT_BRIEF_DOCS = NO
SORT_BY_SCOPE_NAME = NO
GENERATE_TODOLIST = YES
GENERATE_TESTLIST = YES
GENERATE_BUGLIST = YES
GENERATE_DEPRECATEDLIST= YES
ENABLED_SECTIONS =
MAX_INITIALIZER_LINES = 30
SHOW_USED_FILES = YES
SHOW_DIRECTORIES = YES
FILE_VERSION_FILTER =
#---------------------------------------------------------------------------
# configuration options related to warning and progress messages
#---------------------------------------------------------------------------
QUIET = NO
WARNINGS = YES
WARN_IF_UNDOCUMENTED = YES
WARN_IF_DOC_ERROR = YES
WARN_NO_PARAMDOC = NO
WARN_FORMAT = "$file:$line: $text"
WARN_LOGFILE =
#---------------------------------------------------------------------------
# configuration options related to the input files
#---------------------------------------------------------------------------
INPUT = /other/video/kde4/xdrawchem-qt4
FILE_PATTERNS = *.c \
*.cc \
*.cxx \
*.cpp \
*.c++ \
*.java \
*.ii \
*.ixx \
*.ipp \
*.i++ \
*.inl \
*.h \
*.hh \
*.hxx \
*.hpp \
*.h++ \
*.idl \
*.odl \
*.cs \
*.php \
*.php3 \
*.inc \
*.m \
*.mm \
*.dox \
*.C \
*.CC \
*.C++ \
*.II \
*.I++ \
*.H \
*.HH \
*.H++ \
*.CS \
*.PHP \
*.PHP3 \
*.M \
*.MM \
*.C \
*.H \
*.tlh \
*.diff \
*.patch \
*.moc \
*.xpm \
*.dox
RECURSIVE = yes
EXCLUDE =
EXCLUDE_SYMLINKS = NO
EXCLUDE_PATTERNS =
EXAMPLE_PATH =
EXAMPLE_PATTERNS = *
EXAMPLE_RECURSIVE = NO
IMAGE_PATH =
INPUT_FILTER =
FILTER_PATTERNS =
FILTER_SOURCE_FILES = NO
#---------------------------------------------------------------------------
# configuration options related to source browsing
#---------------------------------------------------------------------------
SOURCE_BROWSER = NO
INLINE_SOURCES = NO
STRIP_CODE_COMMENTS = YES
REFERENCED_BY_RELATION = YES
REFERENCES_RELATION = YES
VERBATIM_HEADERS = YES
#---------------------------------------------------------------------------
# configuration options related to the alphabetical class index
#---------------------------------------------------------------------------
ALPHABETICAL_INDEX = NO
COLS_IN_ALPHA_INDEX = 5
IGNORE_PREFIX =
#---------------------------------------------------------------------------
# configuration options related to the HTML output
#---------------------------------------------------------------------------
GENERATE_HTML = YES
HTML_OUTPUT = html
HTML_FILE_EXTENSION = .html
HTML_HEADER =
HTML_FOOTER =
HTML_STYLESHEET =
HTML_ALIGN_MEMBERS = YES
GENERATE_HTMLHELP = NO
CHM_FILE =
HHC_LOCATION =
GENERATE_CHI = NO
BINARY_TOC = NO
TOC_EXPAND = NO
DISABLE_INDEX = NO
ENUM_VALUES_PER_LINE = 4
GENERATE_TREEVIEW = NO
TREEVIEW_WIDTH = 250
#---------------------------------------------------------------------------
# configuration options related to the LaTeX output
#---------------------------------------------------------------------------
GENERATE_LATEX = YES
LATEX_OUTPUT = latex
LATEX_CMD_NAME = latex
MAKEINDEX_CMD_NAME = makeindex
COMPACT_LATEX = NO
PAPER_TYPE = a4wide
EXTRA_PACKAGES =
LATEX_HEADER =
PDF_HYPERLINKS = NO
USE_PDFLATEX = NO
LATEX_BATCHMODE = NO
LATEX_HIDE_INDICES = NO
#---------------------------------------------------------------------------
# configuration options related to the RTF output
#---------------------------------------------------------------------------
GENERATE_RTF = NO
RTF_OUTPUT = rtf
COMPACT_RTF = NO
RTF_HYPERLINKS = NO
RTF_STYLESHEET_FILE =
RTF_EXTENSIONS_FILE =
#---------------------------------------------------------------------------
# configuration options related to the man page output
#---------------------------------------------------------------------------
GENERATE_MAN = NO
MAN_OUTPUT = man
MAN_EXTENSION = .3
MAN_LINKS = NO
#---------------------------------------------------------------------------
# configuration options related to the XML output
#---------------------------------------------------------------------------
GENERATE_XML = yes
XML_OUTPUT = xml
XML_SCHEMA =
XML_DTD =
XML_PROGRAMLISTING = YES
#---------------------------------------------------------------------------
# configuration options for the AutoGen Definitions output
#---------------------------------------------------------------------------
GENERATE_AUTOGEN_DEF = NO
#---------------------------------------------------------------------------
# configuration options related to the Perl module output
#---------------------------------------------------------------------------
GENERATE_PERLMOD = NO
PERLMOD_LATEX = NO
PERLMOD_PRETTY = YES
PERLMOD_MAKEVAR_PREFIX =
#---------------------------------------------------------------------------
# Configuration options related to the preprocessor
#---------------------------------------------------------------------------
ENABLE_PREPROCESSING = YES
MACRO_EXPANSION = NO
EXPAND_ONLY_PREDEF = NO
SEARCH_INCLUDES = YES
INCLUDE_PATH =
INCLUDE_FILE_PATTERNS =
PREDEFINED =
EXPAND_AS_DEFINED =
SKIP_FUNCTION_MACROS = YES
#---------------------------------------------------------------------------
# Configuration::additions related to external references
#---------------------------------------------------------------------------
TAGFILES =
GENERATE_TAGFILE = xdrawchem2.tag
ALLEXTERNALS = NO
EXTERNAL_GROUPS = YES
PERL_PATH = /usr/bin/perl
#---------------------------------------------------------------------------
# Configuration options related to the dot tool
#---------------------------------------------------------------------------
CLASS_DIAGRAMS = YES
HIDE_UNDOC_RELATIONS = YES
HAVE_DOT = NO
CLASS_GRAPH = YES
COLLABORATION_GRAPH = YES
GROUP_GRAPHS = YES
UML_LOOK = NO
TEMPLATE_RELATIONS = NO
INCLUDE_GRAPH = YES
INCLUDED_BY_GRAPH = YES
CALL_GRAPH = NO
GRAPHICAL_HIERARCHY = YES
DIRECTORY_GRAPH = YES
DOT_IMAGE_FORMAT = png
DOT_PATH =
DOTFILE_DIRS =
MAX_DOT_GRAPH_WIDTH = 1024
MAX_DOT_GRAPH_HEIGHT = 1024
MAX_DOT_GRAPH_DEPTH = 1000
DOT_TRANSPARENT = NO
DOT_MULTI_TARGETS = NO
GENERATE_LEGEND = YES
DOT_CLEANUP = YES
#---------------------------------------------------------------------------
# Configuration::additions related to the search engine
#---------------------------------------------------------------------------
SEARCHENGINE = NO
xdrawchem-2.0.orig/COPYRIGHT.txt 0000644 0001750 0001750 00000002217 10465520507 016611 0 ustar georgesk georgesk Portions copyright by Christoph Steinbeck, the JChemPaint project and
others. The following files contain copyright and license info for
the code they contain:
boshcp.h sdg.h sorf.h setofrings.h ring.h atom.h
-- XDrawChem copyright begins here --
XDrawChem
Copyright (C) 2004, 2005 Bryan Herger -- bherger@users.sourceforge.net
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
(Author's note: the license is in the file GPL.txt, which is included
in the source directory.)
xdrawchem-2.0.orig/ring/ 0000755 0001750 0001750 00000000000 11561261606 015435 5 ustar georgesk georgesk xdrawchem-2.0.orig/ring/biphenyl.cml 0000644 0001750 0001750 00000007143 10465520507 017751 0 ustar georgesk georgesk
Mon Jun 10 15:29:32 2002
XDrawChem 1.3.2
C
103.399
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256.241
C
63.3992
238.921
C
73.3993
221.601
C
93.3993
221.601
C
123.399
238.921
C
133.399
221.601
C
153.399
221.601
C
133.399
256.242
C
163.399
238.922
C
153.399
256.242
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xdrawchem-2.0.orig/ring/dashtool.png 0000644 0001750 0001750 00000000477 10465520507 017770 0 ustar georgesk georgesk PNG
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