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y*5f6ԂU[`|۪5nc..:̞ LZn ; bkchem-0.13.0/INSTALL 0000644 0001756 0000144 00000005160 10265403554 012703 0 ustar beda users Note: This file describes the installation of source release of BKchem. If you have
downloaded the binary release, please read the INSTALL.binary file instead.
Installation of BKchem is very simple. But before you can run the program you
must install the following:
1/ Python.
On www.python.org get a distribution of Python for your platform. Note that
BKchem will run only on Python 2.3 or newer.
2/ pycairo
This library is optional and is available only for Linux. It enables high quality
export to PDF and PNG formats with support for antialiased unicode texts.
It requires the cairo library. Both can be found on http://cairographics.org/snapshots/.
The current and tested version is 0.5.1.
--- Single directory deployment ---
No installation is needed to run BKchem. This means that you can run the program
directly after unpacking the downloaded sources.
Simply run the bkchem.py located in the 'bkchem-X.Y.Z/bkchem' directory, where X,Y,Z
are version numbers of BKchem release.
example:
on Unix do
>cd "the dir where you have downloaded the BKchem package"
>tar -xzf bkchem-X.X.X.tgz -C "the dir where you want to unpack BKchem"
>cd "the dir where you have unpacked BKchem"/bkchem-X.Y.Z/bkchem
>python bkchem.py
--- System-wide install ---
Under Linux and other Unix systems you have the possibility to use a 'classic'
way of installing software. Major advantage of doing this is that it you will have
a "bkchem" program in your path, thus easily startable from any path.
For the purpose of installation BKchem uses a standard for installation of
python modules - distutils. The installation is accomplished by simply running
the setup.py script from the bkchem directory with 'install' argument:
>python setup.py install
NOTE: usually you have to be root in order to be able to perform the install!
This way all python sources will be installed in a standard directory for
third-party modules - usually something like '/usr/lib/python/site-packages'.
The templates, pixmaps and other such stuff will go into 'prefix/share/bkchem',
where prefix is usually 'usr' or 'usr/local'.
Documentation will be put in 'prefix/share/doc/bkchem'.
Finally a sh-script 'prefix/bin/bkchem' will be created so that you can run
bkchem from anywhere you want.
To influence the paths that are used during install - especially the 'prefix'
run:
>python setup.py install --help
to see the available options.
Running
>python setup.py --help
will give you another set of options available for the install.
Any comments or reports on installation process are especially welcome as this
is very hard to test thoroughly on a single machine. bkchem-0.13.0/dtd/ 0000755 0001756 0000144 00000000000 11150507660 012420 5 ustar beda users bkchem-0.13.0/dtd/ftext.dtd 0000644 0001756 0000144 00000001243 10107136666 014254 0 ustar beda users
bkchem-0.13.0/dtd/cdml.xsd 0000644 0001756 0000144 00000025334 10107136666 014073 0 ustar beda users
]>
The root element of all BKchem CDML documents
Contains document metadata
Application used to create this document
RGB color either in #rrggbb format or in 'r g b' format
bkchem-0.13.0/dtd/cdml.dtd 0000644 0001756 0000144 00000004767 10107136666 014057 0 ustar beda users
bkchem-0.13.0/progress.log 0000644 0001756 0000144 00000150411 11150506124 014210 0 ustar beda users RELEASE 0.13.0
----------------------------------------
* bugfixes - InChI generation is now compatibile with old InChI versions (1.0 and 1.0.1)
(thanks to Michal Bozon for reporting this)
* enhancements - double bonds in 3D rotated molecules look much better now
(z-coordinate is taken into account when the bond is drawn)
* info - this version is shipped with OASA 0.13.0
RELEASE 0.12.6
----------------------------------------
* bugfixes - Spanish and Italian translations were not packaged with last release
- import of Molfiles containing disconnected molecules no longer crashes
- when a bond was drawn under precisely 45 degree angle, it disappeared
* enhancements - new 3D rotation options - it is possible to fix a bond an rotate around it;
when Shift key is held, only one part of the molecule will rotate, allowing
for conformation adjustments
- InChI code updated to work with standard InChI
- InChIKey is generated alongside InChI
* translations - German updated by Bernhard Radzio
- traditional Chinese updated by I-Yuan Chiang
* info - this version is shipped with OASA 0.12.7
RELEASE 0.12.5
----------------------------------------
* bugfixes - Segmentation fault on Ubuntu 8.10 caused by some glitch in the BLT library
was fixed (sidestepped)
- CML generation for charged atoms was fixed
- some missed strings were made translatable
(thanks to Angel Herráez and Alan Mangiaferro)
- polylines were missing in ODF export
* changes - dashed stereo bonds are no longer by default "rectangular", but
triangular instead
- BKchem.pot file for translators is not part of the source-code distribution
* enhancements - monoisotopic mass is calculated as part of the Chemistry->Info output
* translations - Italian translation was added (thanks to Alan Mangiaferro)
- Spanish translation was added (thanks to Angel Herráez)
* acknowledgments - Alan Mangiaferro and Angel Herráez for great work on Italian
and Spanish translations
RELEASE 0.12.4
----------------------------------------
* bugfixes - an error preventing new users (those without saved personal standard)
from reopening saved files was fixed
RELEASE 0.12.3
----------------------------------------
* bugfixes - a crash that resulted from changing standard values and applying them to selected arrows was fixed
- scroll region updates automatically to always contain all of the drawing -
no part of the drawing should be unreachable after resizing and similar operations
* enhancements - many more paper sizes were added
- a simple minor mode (available under the last mode icon) for drawing of wavy lines was added
- arrows are rotatable in 2D
- trying to rotate an object that does not support it pops up an error message
- it is now possible to set the default value for "show hydrogens" in the "standard dialog".
RELEASE 0.12.2
----------------------------------------
* bugfixes - positioning of hydrogen on atoms should again respect
orientation of the symbol. That is -OH and HO-, not -OH and OH-
* acknowledgments - Jakub Szypulka for a polished version of the icon
RELEASE 0.12.1
----------------------------------------
* bugfixes - entering H2O symbol should not longer result in OH2 to appear
- disconnected molecules are handled properly when importing CML
- group expansion for single node molecules fixed
- molfile import crash fixed
* enhancements - double bonds are shortened when the angle to the neighboring
bonds is small (cyclopropene, etc.)
- E/Z stereochemistry handled properly when reading SMILES
- explicit hydrogens support and more added to SMILES reading
RELEASE 0.12.0
----------------------------------------
* bugfixes - slow undo fixed (especially in case of larger drawings)
- much better handling of font size in Cairo based exports
(parts of the same text appeared sometimes in different sizes in export)
- erroneous parsing of Sc as scandium in SMILES was fixed (thanks to Reinhold Störmann for reporting it)
* enhancements - more types of groups are supported (such as -(CH2)7COOH)
- added wedge/hatch width to context menu
* changes - double bond is always centered if its between two visible atoms that are not part of a ring
RELEASE 0.12.0_pre7
----------------------------------------
* bugfixes - endless loop in cairo-based export plugins fixed
(reported on Windows)
RELEASE 0.12.0_pre6
----------------------------------------
* enhancements - new SVG export via Cairo added
- new PostScript export via Cairo added
RELEASE 0.12.0_pre5
----------------------------------------
* bugfixes - setup.py did not install file necessary for ODF plugin
RELEASE 0.12.0_pre4
----------------------------------------
* bugfixes - line width was not configurable for electron-pairs
- objects are properly deselected when the middle button is used
- OO Draw export of text does not include left and right padding anymore
* enhancements - different arrow styles support (retro, electron-transfer, equilibrium)
- ODF (OpenOffice 2.0) export plugin added
- proper export of spline arrows to OpenOffice 1.0
- more variables were added into tuning.py
* changes - reaction mode was removed - it was obsolete and buggy
- round ends for bond lines are not used when connecting atoms with visible symbols
* acknowledgments - Bernhard Radzio for help on the arrow types and splines
- René Genz for many bugreports and help
- I-Yuan Chiang for the translation into Taiwan Chinese (I forgot to
mention him when the translation was first introduced)
RELEASE 0.12.0_pre3
----------------------------------------
* bugfixes - quit properly even if text is currently edited
- plugins are now included into the translation
- cairo export now searches more precisely for proper font size of text
- some parts of the GUI were not translated (thank to René for reporting it)
- new users experienced a crash because they did not have any personal
preferences set (fixes bug 20795)
- fix error in Pmw that appeared under Python 2.5
- fix dragging of selected circles and squares (fixes bug 20766)
- fix InChI generation for drawings with stereochemistry (thanks to Bernhard for the patch)
* enhancements - splines export finally works (in SVG, Piddle and Cairo exports)
(many thanks to Bernhard Radzio for that)
* changes - triple bond between two not-hidden symbols is drawn with all lines
with the same length
- warnings from the InChI software now propagate into BKChem
* translations - German translation updated by René Genz
* acknowledgments - Bernhard Radzio for the great splines patches and more
- René Genz for German translation update and many bugreports
RELEASE 0.12.0_pre2
----------------------------------------
* bugfixes - crash with Python 2.5 because of __future__ import was fixed
- structures imported from molfiles should no longer appear outside
the boundaries of the drawing area (fixes bug 19088)
- tuning support added to SVG export (should 'fix' 19259)
- changing symbol of atom reset the z-coordinate to 0 - fixed
- error appeared when undoing a change to an atom that was part of a fragment
- background color of plus was not read from standard
* acknowledgments - to all who sent me bug reports and suggestions
RELEASE 0.12.0_pre1
----------------------------------------
* bugfixes - reading of preferences crashed on startup in some cases
- reading files containing numbers crashed in some cases
- positioning of atom numbers was tweaked
- dragging large ring systems was awfully slow in some cases
- standard_values_dialog crashed when values were added manually
- trying to read non-bkchem SVGs sometimes stalled on a comment
- forgotten pictures in documentation were added
- typo in About text was fixed
- selected rectangle did not properly respond to dragging
- undo did not work for text (not atom) in many cases
- middle mouse button caused crash in mark mode
- in some cases changing standard bond_width in standard_values_dialog
caused wrong positioning of second line in double bonds
- openoffice export of transparent lines was fixed, again
* enhancements - preferences dialog lets you decide whether to use real minus
for minuses of the hyphen. Hyphen is shorter, but is part of ASCII,
minus is the right character for minus, but is not part of ASCII.
- the same preferences are accessible on document level through the
File properties dialog
- backspace can be used to delete selected objects as well as delete.
- the text-entry used to input text has a menu with a few special
characters like minus or arrow (xml entities are used for them).
- CML export now asks whether atomic coordinates should remain in
pixels or should be rescaled to something smaller, so that bond-
lengths resemble real ones in angstroems.
- mark placement was polished
- electron pair mark has line_width as well as size
- file tuning.py was added, it enables experianced and/or brave users
to tweak some of the rendering options. More will be added in future
- running bkchem with "-v" option only prints version and exists
- the file_properties_dialog was polished a little
- fixes of typos in documentation and source-code (thanks to René Genz)
- piddle exports was finetuned (using tuning.py)
- bkchem remembers the last active directory it used.
It uses it only when it seems it is run via an desktop icon and
not from command line.
- Cairo PNG export is capable of exporting pictures with transparent
background (it can be set in a dialog that appears on export)
* acknowledgments - René Genz (bug- and typo- reports)
- many others who reported bugs and made useful suggestions
RELEASE 0.11.6
----------------------------------------
* bugfixes - checked and fixed German and Czech translation problems (fixes bug 17990)
- language dialog did not properly find available languages when BKChem started
from unusual location
- cancel in the language dialog did not have the desired effect and the
language was set anyway
- OpenOffice Draw version >=2.0.2 created thick outlines around the exported text
* translations - German translation fixed by me with help of Peter Liebetraut
- Czech translation fixed slightly by me
* acknowledgments - Michael Palmer (OpenOffice Draw fix)
- René Genz (bugreports)
- Peter Liebetraut (bugreports)
RELEASE 0.11.5
----------------------------------------
* bugfixes - fixed bug in SVG export of graphics with transparent interiors (was exported as black)
- problems dragging selections containing brackets fixed (fixes bug 15950)
* enhancements - template atoms and bonds can be now marked from the context menu
- marks are now also scaled via the Scale dialog
* translations - German translation updated by Jan Falkenhagen
* acknowledgments - Jan Falkenhagen (German translation)
- Peter Liebetraut (for interest that forced me to make this release :)
RELEASE 0.11.4
----------------------------------------
* bugfixes - bonds were not redrawn after some changes made from the context menu
- bkchem sometimes crashed on exit when undo was used before
- "atoms" like H2 are now properly parsed and understood
- direction of 3D rotation was fixed (thanks to Armando Navarro Vazquez for bugfix)
- PNG export text positioning fixed
- crash of file saving in the German localization was fixed (thanks to Stefan Duemke for bugreport)
* enhancements - Cairo PNG export plugin now allows users to set resolution for the exported picture
- size of marks is now configurable from the context menu of the atom
- atoms of molecules generated from InChI have their number set
to their number in InChI, to show it use context menu - "Show number"
- parsing of linear formula fragments was improved
* changes - bkchem now ignores subscripts and superscripts when calculating
bounding boxes for text, this changes rendering of formulas.
- automatic mark positioning was changes slightly for free electron pairs not
to appear skewed when placed on horizontally aligned molecules
* acknowledgments - Armando Navarro Vazquez for 3D rotation bugfix
- Stefan Duemke for bugreport
RELEASE 0.11.3
----------------------------------------
* bugfixes - "Paste" menu entry is activated when something is copied
- crashes of copying of molecules imported from CML were fixed
- saving of user preferences on bkchem exit was made more error-proof
- unicode names of directories are handled properly
- corrupt preference files do not render bkchem unstartable
- check of cairo PDF export availability is performed on start
* changes - due to changes in cairo, PDF support is not always available, even if
cairo is installed (depends on cairo version)
- README file was updated to include InChI information
* acknowledgments - all those who reported bugs to me
RELEASE 0.11.2
----------------------------------------
* bugfixes - on windows bkchem saves its config file and user templates to
the user directory (Documents and Settings/Username/bkchem or similar),
so no errors should be issued when non-privilidged user tries to save a template
* translations - French - updated (thanks to Edouard Saintesprit)
* acknowledgments - Piotr Wawrzyniak (bugreport and testing)
- Edouard Saintesprit (French translation)
RELEASE 0.11.1
----------------------------------------
* bugfixes - openoffice export of text was not working properly and crashed on unicode
- after expansion of groups some bonds were not drawn
- group text is no longer displayed with tags when edited
- groups are now really converted to text when second bond is added to them
- lines moved twice as fast as other objects when moved via arrow keys
- the plugin for finding files containig a fragment was somehow forgotten in the last
release
- warnings about maximum valency were not issued when an atom was the receiving side
of molecule concatenation
* enhancements - several new groups are now recongnized by BKChem such as Fmoc, MOP, TMS etc.
(thanks to Radek Liboska for providing them)
- InChI reading was tuned slightly
- BKchem now uses the standard InChI program in much cleaner way for InChI generation,
without the use of temporary files
* acknowledgments - Radek Liboska (bugreports, new groups)
- Piotr Wawrzyniak (tireless bug-hunting)
RELEASE 0.11.0
----------------------------------------
* bugfixes - one stupid bug was fixed in the coordinate generation code
that crippled InChI and SMILES reading
RELEASE 0.11.0_pre2
----------------------------------------
* enhancements - InChI reading support was very thoroughly updated and fixed
(see http://bkchem.zirael.org/inchi_en.html)
* bugfixes - OpenOffice export of colored texts was fixed
- brackets undo was fixed
- setting atom text in atom mode was buggy under special conditions
* acknowledgments - thanks to Piotr Wawrzyniak, Daniel Leidert and Jaroslav Sebestik
RELEASE 0.11.0_pre1
----------------------------------------
* enhancements - plugin to search for files containing a given molecular fragment added
(it supports free-sites, A,Q,X query groups etc., pretty much like Beilstein CrossFire)
- simple bracket mode
(draw rectangle and it will be converted to two polylines in shape of a bracket)
- dotted bonds implemented
- automatic oxidation number computation implemented
- p-orbital mark implemented
- plugins may say to which menu they should be added
(the .xml file may contain tag that says it should be placed
to the XXX menu instead of Plugins. The plugin entries are placed at the end,
separated by a separator from the rest)
- atom symbol may be set from context menu
- group may be set from context menu
* bugfixes - reading of line_color for vector graphics fixed, openoffice export update
- several openoffice export fixes
- several polyline related bugs were fixed
- minor unicode problems hopefully fixed for good
- fixed buggy reading of transparent colors from cdml in graphics
- fix crashes of export of empty paper with cairo and piddle
- fixed bug in deletion of molecule in some cases (after expand of C4H9)
- fixed bug in coords generation for alkyl chain groups expansion
- fixed bug that interpreted ch2ch2ch2ch3 as C4H9, now alkyl chains are
interpreted only for CxHy
- undo of numbering was fixed
- fixed bug in bonds saving under some obscure conditions
- crash on canceling export dialog was fixed
- fixed bug with wrong sorting of recent files
- molfile export fixed
* changes - new focusing and unfocusing code should avoid left-behind focus circles
- entries in context menu are alphabetically sorted
- setting atom symbol to something else then 'C' turns on show automatically
- when dragging an atom to another its Z-coord is changed to match the other ones
so that they can be concatenated
* acknowledgments - to all the numerous people that supplied me with bugreports and ideas
RELEASE 0.10.2
----------------------------------------
* enhancements - high quality PDF and PNG export via Cairo (pycairo) added
(it is currently available for linux only)
- line cap styles in PDF and PS piddle export are supported
so the bond-joins look much better.
* bugfixes - problem of reading files with non-standard font size of atoms was fixed
- problems with dialogs when using localized interface were (hopefully) fixed
- saved SVGs did sometimes conform to the standard (stroke was set to ""), fixed
- molfile import od 3D molecules works again
- small bug in 3D rotation was fixed
* changes - import/export plugins were renamed and some info texts were added to them
- scrollregion of mail window expanded for B4 to fit easily in
* acknowledgments - Piotr Wawrzyniak (bugreports)
RELEASE 0.10.1
----------------------------------------
* bugfixes - context menu does not show "Properties" entry for marks
(there is no properties dialog for marks)
- undo of numbering via the "Misc small modes/Numbering" was fixed
- fixed crash after "maximum valency exceeded" was reported on bond order change
- atoms with visible text were inactive during dragging in draw mode
- several openoffice export fixes (marks, dash bonds and texts)
* acknowledgments - Piotr Wawrzyniak (bugreports)
RELEASE 0.10.0
----------------------------------------
* enhancements - line color is settable from context menu
- it is possible to delete fragments from the fragment dialog
- linear form support
(it is possible to select a linear fragment of a molecule and convert
it to a "linear form", that is for instance -CH2CH2CH3 from /\/,
while maintaining the independence of atoms (in contrast to groups))
- better handling of very short bonds (they are not drawn at all :)
- "recent files" functionality implemented
* bugfixes - bonds between overlapping atoms are not drawn anymore
- bug in freestyle drawing was fixed
- molfiles export swapped y-coordinate (the coordinate system is different in bkchem and in molfiles)
- SMILES generation for nested rings was fixed
- SMILES reading for aromatics given in form C1=CC=CC=C1 instead of c1ccccc1 was fixed
- adding template to the bond of ethane crashes no more
- select_all in mark mode crashes no more
- pl language was missing from the Language dialog
- redraw was not properly triggered on undo of group expansion
* changes - wheel-scrolling removed on windows - it crashes besause a Tk bug
* translations - Polish (updated)
* acknowledgments - Piotr Wawrzyniak for bugreports
- Staszek for bugreports
- Nikodem Kuznik for Polish translation
RELEASE 0.10.0_pre2
----------------------------------------
* enhancements - when editing text or atom it is possible to use keyboard shortcuts to insert formating tags
* Ctrl-s = sub, Ctrl-S = sup, Ctrl-i = i, Ctrl-b = b
* bugfixes - adding marks to atom triggered an error
- system locale overrode internal language setting when it was set to "en"
- clicking on empty canvas in reaction mode triggered an error
* acknowledgments - Piotr Wawrzyniak for bugreport
RELEASE 0.10.0_pre1
----------------------------------------
* enhancements - marks can be moved by mouse in mark_mode
- position of cursor is shown in the status bar
- wheel scrolling added
- the active paper tab is highlighted
- scaling dialog was improved
- support for fragments (continuous blocks of bond in a molecule) - right now has no builtin usage
- context menu was improved and polished
- PS (both old and new), PDF and SVG support cropping (set it in file properties or standard)
(thanks to Maciek Fialkowski for the original patch for old PS export)
- it is possible to set margins for cropping of exported drawings
- bonds are drawn only from and to the borders of visible text
- atom text selector is invisible
- support for more marks of the same type on one atom
- numbering support for atoms (use context menu or numbering mode)
* number is represented by a mark - it can be positioned in mark mode
- dragging threshold of 1px was added experimentaly to the edit_mode
- menu rewritten again to support context sensitive activation of menu items
- arrow heads are properly exported via piddle (pdf,ps)
- it is possible to choose menu language from inside of BKchem
- support for line vector graphics object
- support for user written plugins (more in doc/custom_plugins_en.html)
- transparency support in color selection, other additions
- Ctrl-click in edit mode can be used for deletion of individual atoms/bonds
(thanks to Piotr Wawrzyniak for the idea and patch)
- parsing of linear formulas (e.g. -CH2CH2COCl) used in atoms added
- group is capable of working as a single vertex of the molecule (PhCH2CCl3 is interpreted correctly)
- circle around some marks can be switched off
- marks are supported by context_menu under mark_mode - size, draw_circle
- textatom has marks again
- dotted_electronpair mark added
* it is the same as biradical but does not affect the multiplicity of the atom
- some common grups were added, such as Ac (acetyl, not actinium), Ts, Ms, Pr, Bz, Bn
(thanks to Piotr Wawrzyniak for the idea)
* changes - if both atoms of a bond are visible, the 'stroke-linecap' is set to 'butt' instead of 'round'
- drawing of hatches was tuned a little
- the size of the SVG picture is given in 'mm', fixing some rendering problems
- the CDML format was slightly changed - old files should be read properly in new BKchem
but new files will likely crash in old BKchem (when groups of text-atoms are used)
- Pmw is distributed together with BKchem as I had to fix an unicode problem there
and it seems the Pmw itself is dead
- BKchem now relies on Python 2.3 and higher (because of the new Set class)
* bugfixes - fix of occupied valency and free valency computation
* fixed the problem with marks and number of hydrogens)
- memory leak that prevented molecules and papers to be collected was fixed
- SVG export - stroke was removed from the text attributes thus rendering of text is much nicer
- fix of setting atoms valency from a context_menu
- context menu has no longer redundant separators
- there was a bug in the linux install scripts that caused api documentation
to be installed under /usr/doc/api/.., please remove it if you find it there (sorry)
- double bonds in groups as SO3H and similar are now properly centered
- SVG export of single dashed bond was fixed
- text export to svg was fixed - no redundant tspan is created
* this fixes batik rendering problems of italics subscripts
* acknowledgments - Piotr Wawrzyniak (patches and ideas)
- Maciek Fialkowski (patches and ideas)
- Martin Ballaschk (German translation)
- Tomas Novotny (bugreports and patience)
* translations - added - German
RELEASE 0.9.0
----------------------------------------
* bugfixes - the startup script used on Unix systems was updated to handle
whitespace in filenames properly
- computation of free valency of an atom was fixed (hopefully)
so the "Check chemistry" should work again
- export of text to openoffice does not fail anymore
- the "C-t" keybinding for marking a template atom/bond works
also in user template mode
- reading of INChIs for tetravalent atoms was fixed
* changes - the UI was updated
- the entry field for text input was moved back to its original position
under the mode buttons and it font size was changed
* acknowledgments - thanks to everybody who sent me a bugreport
- thanks to Piotr Wawrzyniak for the BKchem icon
RELEASE 0.9.0-pre2
----------------------------------------
* bugfixes - user template mode does not crash when clicking
on paper without any template available
* changes - PDF and PostScript (new) export do not output the squares that mark selected
bonds and atoms
- mark template atom (bond) accelerate key changed to C-t (was C-t C-1)
RELEASE 0.9.0-pre1
----------------------------------------
* bugfixes - colors of vector graphics were not read from CDML (SVG)
- reaction mode crashed when part of the reaction was removed
- a bug in undo of atoms with attached hydrogens was fixed
- vector graphics did not respond to mouse event once dragged
(until the mouse left it and reentered)
- chages are now handled correctly by molfile and other exports
- molfile export of atom charges was fixed (influences also inchi generation)
- export of wedges to openoffice was fixed (thanks to Alex Thurgood for bugreport)
- Expand groups failed on "Me"
- Expand groups had problems with positioning of double bonds (for COOH and similar)
- the paper properties setting did not have any effect in most cases
* enhancements - user template mode added - it is now possible for the user to create
her own templates (more in doc/custom_templates_en.html or on the homepage)
- File/Save As Template menu entry added
- rotation around bond added to the "transformation mode"
(it enables rapid changes of conformation of molecules)
- dash bond added
- when entering atom text with charge (such as Al3+) it gets parsed correctly
(does not work with atoms bearing a hydrogen such as ch2+ - it is ambiguous)
- bond order can be set from the context menu
- bond order can be explicitly set to 0 to allow describing of hydrogen bonds etc.
- PDF and Postscript export plugins added based on Piddle (arrows export is not complete)
- PDF and Postscript export plugins can export cropped files (depending on the
File/ File properties/ Crop SVG? setting)
- bkchem can now be started and scripted from outside
(see doc/external_import_en.html or homepage)
- Chemistry/Set display form enables you to set a string representation
of a molecule (usefull only for external tools for now)
* changes - marks are now positioned above atoms, so it is no more possible for
a mark to be hidden under an atom
- standard bond length is now 0.7 cm instead of 1 cm
- svg export of text was hacked to compensate for wrong calculation of
text size in Tkinter
- on source code install on linux systems the path to the various parts
of the program is no longer set via env variables but put into a file
XXX/lib/pythonX.Y/site-packages/bkchem/site-config.py
RELEASE 0.8.1
----------------------------------------
* bugfixes - usage of context menu under windows no longer causes hanging
- crash under windows on bkchem exit fixed
- not finished "free rotation around single bond" in transformation mode was removed
RELEASE 0.8.0
----------------------------------------
* bugfixes - unneeded import causing dependency on the XMLplus package was removed
RELEASE 0.8.0-pre2
----------------------------------------
* bugfixes - when multiple filenames were given from the command line, only the existence
of the first was properly checked
- some triple bonds were not exported correctly into SVG
- "As-is" text interpretation did not work proprly for atoms
- bond and mark positioning was reduntandly recalculated after 2D rotation
- error was triggered by closing a tab with an item focused
- after moving items via arrow keys some atoms were inactive for some time
- it is not possible to save a file under a name of already opened file anymore
- repositioning of marks is not called on all marks after deletion of something
(it was really annoying)
- when a standard value for font size was != 12 and some text had font size == 12 it
was rescaled to the standard value on rereading of the file (the font size was not saved)
- undo of marks was fixed (they were sometimes not deleted on undo)
* enhancements - some wrapper methods enable now non-ascii characters input on much wider
set of systems
- chemical meaning of all marks (except the lone electron pair) is now taken into account
- context menu bound to the right mouse key was added (thus the previous functionality
of the right key was moved to the middle key)
- INChI can be generated via an external INChI program (the capabilities are limited to
the capabilities of the Molfile export plugin)
- window geometry is saved and restored on next start (with a slight, strange shift in case of
some window managers)
- svg export of wedges was fixed for bonds with line-width != 1.0
- atom mode added to enable creation of sigle-atom molecules
- marks on selected atoms can be moved via arrow keys in mark mode (select the atom, go to the
mark mode and use the arrow keys to move the marks), it is a quick addition that will be
hopefully enhanced in the next release
- reaction mode was added (you can define the reactants, products etc. for each arrow)
- equithick hatch bonds were introduced and made default (you can change it by clicking on the
bond more than once), this is because it is recommended as sharp hatch bonds are usually
wrongly interpreted. Thanks to Michal Bozon for the patch
- CH2OH group was added
- INChI reading was updated to version 1.12Beta (older version is also supported)
- INChI reading of molecules with movable H atoms was fixed
* changes - Name mode was removed, Menu/Object/Set molecule name (ID) was introduced instead
- the keybindings were changes so that using a-zA-Z characters have the same effect
as the Space character, thus you can start to type directly without pressing Space first
- because of the previous point, all keybindings now contain a Ctrl or Alt in every part
(C-o b => C-o C-b)
- atom text could be no longer edited in the text mode, use atom mode instead
- the organization of buttons in menu was slightly changed
* acknowledgments - to Michal Bozon for the equithick patch
----------------------------------------
RELEASE 0.8.0-pre1
* bugfixes - text created by copying disappeared from the saved file (and corrupted it)
(the corrupted files are now read and the lost text is marked with ? mark)
- some double bond did not respond to shift-clicking to reposition the second line
- size of arrow-heads in SVG export was fixed for arrows thicker than 1px
- when using the "As-is" button for atom text change, the text is now always diplayed
- when focused atom was removed by undo a bug was triggered
- oasa - reading of smiles such as C1CccCC1 was corrupted
* enhancements - support for multiple files was added
- it is possible to copy objects from one file to another
- oasa - support for new format of INChI (was IChI) was added
----------------------------------------
RELEASE 0.7.1
* bugfixes - file permissions were fixed so that the "python setup.py install" works
* acknowledgments - Eugenia Loli-Queru (bugreport)
----------------------------------------
RELEASE 0.7.0
* bugfixes - double bonds were wrongly positioned on stack, thus disappearing when a molecule was
placed over some other object with full backgroung
* enhancements - \n in text entry is translated to new-line
- undo of molecule division was optimized (leading to 10-100x shorter times for large molecules)
- reading of CDML files was optimized
- some redundant informations are saved into CDML files to speed the reading up
- template addition was optimized (speedup of 10-100x for large molecules)
- deletion of parts of molecules was optimized (up to 10x speedup for larger molecules)
- new bonds are always added transoid
- addition of/to triple bonds is always in 180 deg. angle
* changes - None
* translations - updated - Czech
----------------------------------------
RELEASE 0.7.0-pre1
* bugfixes - the in the config dialog "Show hydrogens" had a wrong default value
- the ColorButton crashed (python 2.3 only?) when the config dialog was run on
objects with different colors
- the program sometimes did not quit after saying 'yes' to 'really quit?'
(a bug in Tkinter askyesno dialog?)
* enhancements - this is the first release featuring OASA - a free chemical library I have
started to work on this year. It brings support for several chemical formats.
At this time SMILES, Molfiles and IChI (only reading). To be able to use
these features you have to have at least Python 2.3.
- Molfiles - export, import
- IChI - direct input (see the menu Chemistry)
- SMILES - direct input, ouput (see the menu Chemistry)
* changes - some of the commands were moved from 'Object' menu to 'Chemistry' menu
* translations - added - French
* acknowledgments - Alex Thurgood (French translation)
----------------------------------------
RELEASE 0.6.0
* bugfixes - hitting escape during text creation no longer produces "None" text
- addition of a molecule no longer resets the paper properties to standard values
- crash on save for files with colored texts was fixed
- backgroud color of plus in exported correctry to openoffice
- font size of a plus is saved properly
- one of the cyclopentadiene templates appeared always on the wrong side of a molecule
it was added to (by means of bond)
- permissions fixed so that templates.cdml is readable for everybody
* enhancements - bond order is cycled only within limits of free valency of neighbor atoms
- OH and similar groups ("protonated atoms") change the number of Hs on bond
addition, deletion and undo
* changes - hitting 'Space' when only single text (atom) is selected sets the default text for
edit to this particular text, the last entered text (the old way) is used only when
more items are selected
----------------------------------------
RELEASE 0.6.0-pre1
* bugfixes - non-ascii text support fixed (for some reason works only on some platforms :(
- any suggestions welcome
- menu 'Object/Swap on stack' called "sent to front" instead (typo)
- bkchem window resized sometimes itself on mode change, should be fixed
- template addition now takes atoms valency into account
* enhancements - bond order and type were separaded
- it is possible to draw wedge/hatch double bonds
- adder (unspecified stereo) and bold bond was added
- double stereo bond may be drawn in two different ways
(second bond is also stereo or line-only)
- transform mode was introduced
- aling selected bond to horizontal or vertical position
- perform inversion or mirror transformation
- horizontal and vertical mirror transforms were added
- hints on usage appear now in status bar when you change a mode
- double click in edit_mode selects the whole molecule
- cyclopentadiene template was updated to be really symmetric
- OpenOffice.org export - the output of atoms was tuned to minimize
the size of the background of the text
* changes - unmaintained PNG and Povray exports were removed
- in menu Object/Configure command was added as alternative to right click
- empty space between submodes for easier orientation
- icons are now loaded on demand - slightly faster start-up
* translations - updated - Czech
- added - Polish
* acknowledgments - Michal Bozon (the original transform mode)
- Nikodem Kuznik (Polish translation)
----------------------------------------
RELEASE 0.5.2
* bugfixes - the bugfixes that was announced for 0.5.1 was not present there.
Sorry for that, but it is for sure included in 0.5.2
- fix was added to be able to read the corrupted files from 0.5.1 and earlier
* enhancements - None
* changes - None
----------------------------------------
RELEASE 0.5.1
* bugfixes - invalid files are no longer created under Python 2.3 when marks are used
(bug was due to the introduction of boolean type in this version of python)
* enhancements - None
* changes - the progress.log format was changed and will contain only summary for
each release
-- release of 0.5.1-pre1
2004-02-10 Beda Kosata (sav4)
* bugfix - an ugly bug that caused focus circles to hang around when a delete operation was
performed with an atom (or other item) in focus.
* bugfix - annoying warnings about "leaving NONE" were fixed in arrow mode
* the points of spline arrow are no more visible. You can click the arrow to get the points
selected to see them (let me know if this does not suit you)
* in the arrow mode you can now choose if you want do create a spline arrow or a normal one.
The selected type of arrow is also applied if you modify the arrow or simply click on it.
2004-02-09 Beda Kosata (sav3)
* bugfix - a config dialog bug caused by Python 2.3 introduction of boolean type was fixed
* bugfix - an error when configuring an arrow ("config dialog has no attribute spline_changed")
was fixed
* bugfix - several redundant and baseless roundings of coordinates were removed
(thanks to Michal Bozon for the patch)
* bugfix - the cyclopentane template was updated which makes it (together with the
previous bugfix) 100% symmetric
(thanks to Michal Bozon for the patch)
* the [1]benzothieno[3,2-b][1]benzothiophene :) template was removed
* in the standard dialog it is now possible to specify if all the standard values should be
applied or only the changed ones.
2004-02-08 Beda Kosata
* bugfix - rotation mode no longer creates empty undo records when no rotation was performed
2004-02-06 Beda Kosata (sav2)
* bugfix - a typo that made the superscript button create subscript was fixed
* bugfix - wedge arrow with non-black color goes no more black after focus
* bugfix - the marks are now repositioned during rotation (after rotation for 3D rotation)
2004-02-04 Beda Kosata (sav1)
* bugfix - "Unable to parse text..." error was found and fixed. May this be caused by the
unicode usage under RedHat? (I have not seen this under Gentoo)
* code cleanup - the undo was switched to meta-info driven code which should make the code
more easily extendable
* code cleanup - the bond draw method was switched to "plugable methods" code, this should
also save much work when new bond types are added
2003-10-01 Beda Kosata
* bugfix - problem with bond width change was fixed
-- release of 0.5.0
2003-09-30 Beda Kosata
* PostScript export updated to support paper sizes and moved to a plugin (File/Export/Encapsulated PostScript)
* paper properties were added to standard so that they can be saved in personal profile
-- release of 0.5.0-pre5
2003-09-26 Beda Kosata
* it is now possible to save your personal standard (from the Options/Standard dialog)
which will be used everytime you start BKchem
* templates for common five membered heterocycles added (thanks to Petr Vodicka for them)
* templates for purine and chair conformation of cyclohexane were added
* bugfix - OpenOffice Draw export supports text color
* bugfix - in SVG export sometimes overlay of items did not correspond to their order in bkchem
* bugfix - it seems that Tkinter treats font sizes as if they were in 'px' not 'pt' as it states.
The SVG generation code was fixed to output 'px' so that the SVG export is more WYSIWYG
(please let me know if you find the SVG text significantly smaller than what you see in BKchem)
2003-09-25 Beda Kosata
* use of standard values significantly improved
* dialog for standard values added
* second bond of double and triple bonds may be drawn shorter than the main part of the bond
(the ratio is customizable via Options/Standard or in config dialog for every bond)
Thanks to Michal Bozon for the original patch.
* all button images were converted to gifs in order to preserve their transparency
2003-09-21 Beda Kosata
* if file name given to bkchem on startup does not exist create a new file with this name
2003-08-07 Beda Kosata
* support for paper sizes and marks was added to the OpenOffice export plugin
2003-08-05 Beda Kosata
* bugfix - creating text that contains only tags (e.g. '') no longer crashes
-- release of 0.5.0-pre4
2003-07-22 Beda Kosata
* the same fix as in 0.5.0-pre3 for all the plugins (the statement about full compatibility
of 0.5.0-pre3 with PyXML should be now more valid :)
-- release of 0.5.0-pre3
2003-07-21 Beda Kosata
* a nasty bug (in fact bad coding habit) that caused saving files to crash on machines with
PyXML installed was fixed. BKchem should be now fully compatible with the PyXML library.
-- release of 0.5.0-pre2
2003-07-17 Beda Kosata
* templates are scaled according to the standard bond length
2003-07-06 Beda Kosata
* bkchem now deals with abbreviated alkyl chains (CnH2n+1) as with other groups
(expansion, molecular formula etc.)
* support for b-spline arrows was added, unfortunately SVG can deal only with Bezier curves
and don't know how to transform b-spline -> Bezier; this means the export to SVG is far from perfect
* bugfix - appending a template to an atom with non-zero Z coordinate did not work properly;
code was added to detect such cases and inform the user that it is not possible
2003-07-02 Beda Kosata
* standard bond length was changed from pixels to cm, so that it is machine independent
* 'C-d n' where 'n' is number in range 2-9 appends an aliphatic chain to the focused atom
2003-06-30 Beda Kosata
* bugfix - reading negative coordinates no longer crashes (was typical for 3D rotated molecules)
2003-06-01 Beda Kosata
* bugfix - expand_group on focused group no longer causes error
-- release of 0.5.0-pre1
2003-05-25 Beda Kosata
* it is now possible to pass a file name to bkchem as a command line argument
* all positions are now stored in 'cm'
- files should now look exactly the same on different machines
2003-05-24 Beda Kosata
* sizes in SVG export were normalized;
files should look exactly the same on machines with different dpi resolution
2003-05-21 Beda Kosata
* marks (radical, electron pair etc.) were introduced - no export except SVG yet
2003-05-14 Beda Kosata
* support for paper sizes and orientation
-- release of 0.4.3
2003-03-31 Beda Kosata
* bugfix - a nasty bug that caused exports to fail on new (untitled) files was fixed
-- release of 0.4.2
2003-03-26 Beda Kosata
* bugfix - right-clicking on a selection rectangle no longer causes error
* openoffice export - vector graphics is exported
- proper stacking included
- bonds and atoms are grouped into molecules for easier manipulation
* export plugins now offer the right extension for the exported file
-- prerelease 0.4.2-pre2
2003-03-25 Beda Kosata
* openoffice export - stereo bonds, text and pluses are now also exported
-- prerelease 0.4.2-pre1
2003-03-21 Beda Kosata
* openoffice export works once again - bonds (not stereo), atoms and arrows are exported
* Import/Export menu created under File menu
2003-02-02 Beda Kosata
* bugfix - opening a file that contained atoms with text that seemed interpretable (Ph etc.)
failed because valency information for that atom are not available at read.
2002-12-23 Beda Kosata
* buttons for text tagging added - selected text can be tagged (b, i, sub, sup) during editing using buttons.
When no text is selected an empty tag is created.
-- release of version 0.4.1
2002-12-18 Beda Kosata
* bugfix - removed the openoffice plugin as it is too unfinished and buggy and causes confusion
2002-12-16 Beda Kosata
* bugfix - removed obsolete Povray export from 'Experimental exports'. It is available as a plugin.
* distribution of bkchem was automatized by means of distutils
* classic unix installation is now possible (for Unix only, of course) which makes it possible
to run bkchem from anywhere. See INSTALL for more info.
-- release of version 0.4.0
2002-10-23 Beda Kosata
* bug that made Alt key "hang" after Alt-Tabing out of the window and back was fixed
2002-10-22 Beda Kosata
* fixed bug that caused crash after the user tried to insert a template to arrow or other non-molecular object
2002-10-20 Beda Kosata
* individual points of polygon can be deleted (but new cannot be added)
2002-10-19 Beda Kosata
* added polygon (left click to create individual points, right to finish the shape)
* added ability to adjust object visibility by changing its position on the stack
2002-10-18 Beda Kosata
* bug that caused error when trying to rotate arrow was fixed (but arrow still cannot be rotated)
2002-10-17 Beda Kosata
* fixed bug - save file dialog was not properly canceled (filename was set to 'untitled')
* fixed bug - 'really quit' dialog was not open when exiting the app via 'C-x C-c'
* fixed stupid bug in align - 'l' is left and 'r' is right now :)
* added circle
2002-10-15 Beda Kosata
* fixed bug that caused error when focused atom was deleted and then some drawing action was performed
* added square
2002-10-14 Beda Kosata
* color support added
* the title of the main window now shows the name of currently edited file
* 'common page' added to config dialog with line width and color selection
2002-10-13 Beda Kosata
* cyklopropane and cyklobutane templates added
* another small bugfix (current file name was set even if the file was not read correctly)
2002-10-09 Beda Kosata
* bug that caused crash after a template was put over a non-C atom was fixed
* bug that made Ctrl key "hang" after 'C-x C-f' was fixed
2002-10-06 Beda Kosata
* selected items can be moved using arrows
* vector graphics (rectangle and oval) introduced
-- release of version 0.3.0
2002-09-15 Beda Kosata
* group expansion - e.g. -COOH can be now expanded to complete structure (important for CML export)
* small bugfixes
* number of undo steps limited to 20 to reduce memory consumption
* rewritten and improved checking of chemical validity
* CML plugin now performs chemistry check on export and refuses to export chemically invalid data
* CML plugin now expands groups on export
* 'C-S-a' can be now used for select_all
2002-08-26 Beda Kosata
* work on export plugin for OpenOffice Draw format
2002-08-20 Beda Kosata
* fixed hard-to-find-easy-to-fix bug in undo
* on-fly warnings on exceeded valency
2002-08-05 Beda Kosata
* 3D support - import, export, 3D rotation
* checking of chemical validity of drawn molecules
* accelerator keys are now displayed in menus
2002-08-03 Beda Kosata
* minor modifications in SVG export
-- release of version 0.2.0
2002-07-20 Beda Kosata
* second line of double bond is now always automatically positioned inside a ring
2002-06-23 Beda Kosata
* code that allows convenient reading of older versions of CDML
* interactive positioning of second line in double bonds
(user can still override auto positioning by shift-click in draw mode)
* preliminary CML2 support as plugin
2002-06-15 Beda Kosata
* reduced size of CDML - only necessary data are saved
* default values are used for data absent in CDML (when possible)
* viewport transformation possible on file read
* CML import sets viewport for imported data to be always visible on screen (dimensions are usually in angstroms)
2002-06-08 Beda Kosata
* plugin framework
* CML import/export plugin started
* moved atoms are automaticaly updated (CH3 -> H3C)
2002-04-22 Beda Kosata
* "intelligent" judging of position of second line in double bond
* molecules can be named (use new mode called "name")
-- release of version 0.1.2
2002-04-16 Beda Kosata
* reduced dependency on PIL. PIL is no longer needed to display icon buttons
* binary release now possible using "Install"
2002-04-13 Beda Kosata
* bkchem now understands atoms in the chemical sense
* almost complete periodic table available (without lanthanoids and actinoids)
* information based on molecular formula available (formula, weight, composition)
-- release of version 0.1.1
2002-04-10 Beda Kosata
* freestyle submode for draw mode
* submodes (including freestyle) for arrow mode
2002-04-08 Beda Kosata
* "really quit" question
2002-04-06 Beda Kosata
* loading of CD-SVG
* full support for gzipped CDML and CD-SVG
* file reading independent of file extension
* some optimization of SVG file size
2002-04-05 Beda Kosata
* saving to SVG with embedded CDML (CD-SVG)
2002-04-04 Beda Kosata
* font family selection bkchem-0.13.0/bkchem/ 0000755 0001756 0000144 00000000000 11150507660 013076 5 ustar beda users bkchem-0.13.0/bkchem/plugin_support.py 0000644 0001756 0000144 00000010732 11146535716 016555 0 ustar beda users #--------------------------------------------------------------------------
# This file is part of BKchem - a chemical drawing program
# Copyright (C) 2004 Beda Kosata
# 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.
# Complete text of GNU GPL can be found in the file gpl.txt in the
# main directory of the program
#--------------------------------------------------------------------------
import xml.dom.minidom as dom
import dom_extensions as dom_ext
import os_support
import os
import debug
from singleton_store import Store
class plugin_manager( object):
def __init__( self):
self.plugins = {}
self.descriptions = {}
def get_available_plugins( self):
dir2 = os_support.get_dirs( 'plugin')
dir1 = os_support.get_bkchem_private_dir()
dir1 = os.path.join( dir1, 'plugins')
dirs = dir2 + [dir1]
for dir in dirs:
if not os.path.isdir( dir):
continue
for name in os.listdir( dir):
base, ext = os.path.splitext( name)
if ext == ".xml":
#try:
self.read_plugin_file( dir, name)
#except:
# debug.log( "could not load plugin file", name)
return self.plugins.keys()
def read_plugin_file( self, dir, name):
doc = dom.parse( os.path.join( dir, name))
root = doc.childNodes[0]
plugin_type = root.getAttribute( 'type') or 'script'
sources = dom_ext.simpleXPathSearch( doc, "/plugin/source")
if sources:
source = sources[0]
files = dom_ext.simpleXPathSearch( source, "file")
names = dom_ext.simpleXPathSearch( source, "menu-text")
descs = dom_ext.simpleXPathSearch( source, "/plugin/meta/description")
menus = dom_ext.simpleXPathSearch( source, "menu")
if files and names:
file = dom_ext.getAllTextFromElement( files[0])
if not os.path.isabs( file):
file = os.path.normpath( os.path.join( dir, file))
name = self._select_correct_text( names)
if menus:
menu = dom_ext.getAllTextFromElement( menus[0])
else:
menu = ""
plugin = plugin_handler( name, file, type=plugin_type,
desc=self._select_correct_text( descs),
menu=menu)
self.plugins[ name] = plugin
def run_plugin( self, name):
handler = self.plugins[ name]
if handler.type == "script":
filename = handler.filename
the_globals = {'App': Store.app}
execfile( filename, the_globals)
else:
raise ValueError, "Wrong type of plugin %s" % name
def get_names( self, type=""):
if not type:
return self.plugins.keys()
else:
return [k for k, v in self.plugins.iteritems() if v.type == type]
def get_description( self, name):
handler = self.get_plugin_handler( name)
if handler:
return handler.desc
return ''
def get_menu( self, name):
handler = self.get_plugin_handler( name)
if handler:
return handler.menu
return ''
def get_plugin_handler( self, name):
return self.plugins.get( name, None)
def _select_correct_text( self, texts):
"""returns the right text according to the lang attribute"""
if not texts:
return ''
for text in texts:
lang = text.getAttribute( "lang") or "en"
if lang == Store.lang:
return dom_ext.getAllTextFromElement( text)
# if nothing found, return the first one
return dom_ext.getAllTextFromElement( texts[0])
class plugin_handler:
"""this class stores information about plugin"""
def __init__( self, name, filename, type="script", desc="", menu=""):
self.name = name
self.type = type
self.desc = desc
self.filename = filename
self.menu = menu
def get_module_name( self):
"""returns name of module suitable for loading of this plugin via import"""
return os.path.splitext( os.path.split( self.filename)[1])[0]
def get_directory_name( self):
"""returns directory where the plugin resides"""
return os.path.split( self.filename)[0]
bkchem-0.13.0/bkchem/temp_manager.py 0000644 0001756 0000144 00000013066 11146536707 016126 0 ustar beda users #--------------------------------------------------------------------------
# This file is part of BKchem - a chemical drawing program
# Copyright (C) 2002-2004 Beda Kosata
# 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.
# Complete text of GNU GPL can be found in the file gpl.txt in the
# main directory of the program
#--------------------------------------------------------------------------
#
#
#
#--------------------------------------------------------------------------
"""template manager resides here"""
import math
from oasa.oasa.transform import transform
from molecule import molecule
import xml.dom.minidom as dom
from warnings import warn
import config
import os.path
import os_support
import xml.sax
import misc
from singleton_store import Store, Screen
class template_manager:
templates = []
def __init__( self):
self.templates = []
self._prepared_templates = []
def add_template_from_CDML( self, file):
if not os.path.isfile( file):
file = os_support.get_path( file, "template")
if not file:
warn( "template file %s does not exist - ignoring" % file)
return
try:
doc = dom.parse( file).getElementsByTagName( 'cdml')[0]
except xml.sax.SAXException:
warn( "template file %s cannot be parsed - ignoring" % file)
return
# when loading old versions of CDML try to convert them, but do nothing when they cannot be converted
import CDML_versions
CDML_versions.transform_dom_to_version( doc, config.current_CDML_version)
Store.app.paper.onread_id_sandbox_activate()
added = []
for tmp in doc.getElementsByTagName('molecule'):
self.templates.append( tmp)
m = molecule( Store.app.paper, package=tmp)
self._prepared_templates.append( m)
added.append( m)
Store.app.paper.onread_id_sandbox_finish( apply_to=[]) # just switch the id_managers, no id mangling
def get_template( self, n):
return self.templates[n]
def get_templates_valency( self, name):
return self._prepared_templates[ name].next_to_t_atom.occupied_valency -1
def get_template_names( self):
return [o.name for o in self._prepared_templates]
def get_transformed_template( self, n, coords, type='empty', paper=None):
"""type is type of connection - 'bond', 'atom1'(for single atom), 'atom2'(for atom with more than 1 bond), 'empty'"""
pap = paper or Store.app.paper
pap.onread_id_sandbox_activate() # must be here to mangle the ids
current = molecule( pap, package=self.templates[n])
pap.onread_id_sandbox_finish( apply_to= [current]) # id mangling
current.name = ''
self._scale_ratio = 1
trans = transform()
# type empty - just draws the template - no conection
if type == 'empty':
xt1, yt1 = current.t_atom.get_xy()
xt2, yt2 = current.next_to_t_atom.get_xy()
x1, y1 = coords
bond_length = Screen.any_to_px( Store.app.paper.standard.bond_length)
current.delete_items( [current.t_atom], redraw=0, delete_single_atom=0)
trans.set_move( -xt2, -yt2)
trans.set_scaling( bond_length / math.sqrt( (xt1-xt2)**2 + (yt1-yt2)**2))
trans.set_move( x1, y1)
#type atom
elif type == 'atom1' or type == 'atom2':
xt1, yt1 = current.t_atom.get_xy()
xt2, yt2 = current.next_to_t_atom.get_xy()
x1, y1, x2, y2 = coords
trans.set_move( -xt2, -yt2)
trans.set_scaling( math.sqrt( (x1-x2)**2 + (y1-y2)**2) / math.sqrt( (xt1-xt2)**2 + (yt1-yt2)**2))
trans.set_rotation( math.atan2( xt1-xt2, yt1-yt2) - math.atan2( x1-x2, y1-y2))
trans.set_move( x2, y2)
#type bond
elif type == 'bond':
if not (current.t_bond_first and current.t_bond_second):
warn( "this template is not capable to be added to bond - sorry.")
return None
current.delete_items( [current.t_atom], redraw=0, delete_single_atom=0)
xt1, yt1 = current.t_bond_first.get_xy()
xt2, yt2 = current.t_bond_second.get_xy()
x1, y1, x2, y2 = coords
self._scale_ratio = math.sqrt( (x1-x2)**2 + (y1-y2)**2) / math.sqrt( (xt1-xt2)**2 + (yt1-yt2)**2) # further needed for bond.bond_width transformation
trans.set_move( -xt1, -yt1)
trans.set_rotation( math.atan2( xt1-xt2, yt1-yt2) - math.atan2( x1-x2, y1-y2))
trans.set_scaling( self._scale_ratio)
trans.set_move( x1, y1)
self.transform_template( current, trans)
#remove obsolete info from template
if type == 'atom1':
current.delete_items( [current.t_atom], redraw=0, delete_single_atom=0)
elif type == 'atom2':
current.t_atom.x = x1
current.t_atom.y = y1
current.t_atom = None
current.t_bond_first = None
current.t_bond_second = None
#return ready template
return current
def transform_template( self, temp, trans):
for a in temp.atoms:
a.x, a.y = trans.transform_xy( a.x, a.y)
a.scale_font( self._scale_ratio)
for b in temp.bonds:
if b.order != 1:
b.bond_width *= self._scale_ratio
# update template according to current default values
Store.app.paper.apply_current_standard( [temp], template_mode=1)
# return the ready template
return temp
bkchem-0.13.0/bkchem/os_support.py 0000644 0001756 0000144 00000011762 11146535716 015704 0 ustar beda users #--------------------------------------------------------------------------
# This file is part of BKchem - a chemical drawing program
# Copyright (C) 2002-2004 Beda Kosata
# 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.
# Complete text of GNU GPL can be found in the file gpl.txt in the
# main directory of the program
#--------------------------------------------------------------------------
import os
import sys
env_vars = {'template': 'BKCHEM_TEMPLATE_PATH',
'pixmap': 'BKCHEM_PIXMAP_PATH',
'image': 'BKCHEM_IMAGE_PATH',
'plugin': 'BKCHEM_PLUGIN_PATH'}
std_dirs = {'template': '../templates',
'pixmap': '../pixmaps',
'image': '../images',
'plugin': '../plugins'}
class os_support_store:
private_dir_override = None
try:
import site_config
except:
site_config = None
def get_path( filename, file_category):
dir = None
dirs = get_dirs( file_category)
for dir in dirs:
path = os.path.join( dir, filename)
if os.path.isfile( path):
break
if dir:
path = os.path.join( dir, filename)
if os.path.isfile( path):
return path
return None
def get_config_filename( name, level="global", mode="r"):
dir = None
if level == "global":
if os.name in ('posix', 'nt'):
dir = (site_config and site_config.BKCHEM_MODULE_PATH) or os.getenv( 'BKCHEM_MODULE_PATH') or os.path.join('..','.bkchem')
elif level == "local":
if os.name in ('posix', 'nt'):
dir = (site_config and site_config.BKCHEM_MODULE_PATH) or os.getenv( 'BKCHEM_MODULE_PATH') or None
if level == "personal":
if os.name in ('posix', 'nt'):
dir = get_personal_config_directory()
if dir:
if mode == "w":
if not os.path.isdir( dir):
try:
os.mkdir( dir)
except:
return None
if os.access( dir, os.W_OK):
return os.path.join( dir, name)
else:
return None
elif mode == "r":
path = os.path.join( dir, name)
if os.access( path, os.R_OK):
return path
else:
return None
return None
def get_dirs( file_category):
if os.name in ('posix', 'nt'):
if os.getenv( env_vars[ file_category]):
dirs = [os.getenv( env_vars[ file_category])]
elif site_config:
dirs = [site_config.__dict__[ env_vars[ file_category]]]
else:
dirs = []
dirs.extend( (os.path.join( get_bkchem_run_dir(), std_dirs[ file_category]),))
else:
dirs = std_dirs[ file_category]
return dirs
def get_local_templates():
dir = get_local_templates_path()
if os.path.isdir( dir):
return [os.path.join( dir, d) for d in os.listdir( dir) if os.path.splitext( d)[1] in ('.cdml', '.cdgz', '.svg', '.svgz')]
return []
def get_personal_config_directory():
return get_bkchem_private_dir()
def create_personal_config_directory( path=""):
if not path:
dir = get_personal_config_directory()
else:
dir = os.path.join( get_personal_config_directory(), path)
if dir:
if not os.path.isdir( dir):
try:
os.mkdir( dir)
except:
return None
if os.access( dir, os.W_OK):
return dir
else:
return None
return None
def get_local_templates_path():
return os.path.join( get_personal_config_directory(), 'templates')
def get_module_path():
dir = (site_config and site_config.BKCHEM_MODULE_PATH) or os.getenv( 'BKCHEM_MODULE_PATH') or './'
return dir
def get_opened_config_file( name, level="global", mode="r"):
fname = get_config_filename( name, level=level, mode=mode)
if fname:
f = file( fname, mode=mode)
return f
def set_bkchem_private_dir( dir):
if os.path.exists( dir):
os_support_store.private_dir_override = dir
def get_bkchem_private_dir():
# this allows users to override the private dir
if os_support_store.private_dir_override and os.path.exists( os_support_store.private_dir_override):
return os_support_store.private_dir_override
dir = ""
if os.name == "nt":
try:
import _winreg as reg
dir = reg.QueryValueEx( reg.OpenKey( reg.HKEY_CURRENT_USER, "Volatile Environment"), "APPDATA")[0]
dir = os.path.join( dir, "bkchem")
except EnvironmentError:
pass
if not dir:
dir = os.getenv( 'HOME') or '../'
dir = os.path.join( dir, ".bkchem/")
return dir
def get_bkchem_run_dir():
"""returns directory from which bkchem is run"""
path = sys.path[0]
if not os.path.isdir( path):
# this happens on windows when running from bkchem.exe
path = os.path.split( path)[0]
return path
bkchem-0.13.0/bkchem/special_parents.py 0000644 0001756 0000144 00000046772 11147203220 016633 0 ustar beda users #--------------------------------------------------------------------------
# This file is part of BKchem - a chemical drawing program
# Copyright (C) 2005 Beda Kosata
# 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.
# Complete text of GNU GPL can be found in the file gpl.txt in the
# main directory of the program
#--------------------------------------------------------------------------
import misc
import marks
from oasa import geometry
from math import sin, cos, sqrt, pi
import types
import oasa
from parents import meta_enabled, area_colored, point_drawable, text_like, child_with_paper
from singleton_store import Store, Screen
from ftext import ftext
import xml.dom.minidom as dom
import tkFont
import debug
from tuning import Tuning
import operator
class vertex_common( object):
"""implements some properties and methods common for all vertices
(children of oasa.chem_vertex), such as numbering and mark support"""
meta__undo_properties = ('number', 'show_number')
meta__undo_copy = ('marks',)
meta__undo_children_to_record = ('marks',)
meta__allowed_marks = () # when empty all marks are allowed
def __init__( self):
self.marks = set()
# numbering
self._show_number = True
self._number = None
# number
def _set_number( self, number):
if number:
self._number = unicode( number)
else:
self._number = number # we do not want to convert None to unicode :)
if self._number != None and self.show_number:
numbers = self.get_marks_by_type( "atom_number")
if not numbers:
self.create_mark( "atom_number", draw=self.drawn)
elif self.drawn:
numbers[0].redraw()
def _get_number( self):
if hasattr( self, "_number"):
return self._number
else:
return None
number = property( _get_number, _set_number, None, "the number associated with the atom")
# show_number
def _set_show_number( self, show_number):
self._show_number = show_number
if self._show_number and self.number:
numbers = self.get_marks_by_type( "atom_number")
if not numbers:
self.create_mark( "atom_number", draw=self.drawn)
elif not self._show_number and self.number:
numbers = self.get_marks_by_type( "atom_number")
if numbers:
self.remove_mark( numbers[0])
def _get_show_number( self):
return self._show_number
show_number = property( _get_show_number, _set_show_number, None, "should the number (if present) be displayed")
def _mark_to_name_and_class( self, mark):
if type( mark) in (types.ClassType, types.TypeType):
return mark.__name__, mark
else:
return mark, marks.__dict__[ mark]
def set_mark( self, mark='radical', angle='auto', draw=1, angle_resolution=1):
"""sets the mark and takes care of charge and multiplicity changes;
mark may be either the class or mark name"""
mark_name, _ = self._mark_to_name_and_class( mark)
if not self.meta__allowed_marks or mark_name in self.meta__allowed_marks:
m = self.create_mark( mark=mark, angle=angle, angle_resolution=angle_resolution)
self._set_mark_helper( mark, sign=1)
return m
else:
raise ValueError, "not a allowed mark for this type - %s" % mark
def remove_mark( self, mark):
"""mark is either mark instance of type, in case of instance, the instance is removed,
in case of type a random mark of this type (if present is removed).
Returns the removed mark or None"""
if type( mark) == types.StringType:
ms = [m for m in self.marks if m.__class__.__name__ == mark]
if ms:
m = ms[0]
else:
return None
elif isinstance( mark, marks.mark):
if mark in self.marks:
m = mark
else:
raise ValueError, "trying to remove a mark that does not belong to this atom"
else:
raise TypeError, "mark is on unknown type " + str( mark)
m.delete()
self.marks.remove( m)
self._set_mark_helper( m.__class__, sign=-1)
return m
def _set_mark_helper( self, mark, sign=1):
mark_name, _ = self._mark_to_name_and_class( mark)
if mark_name == "atom_number":
if not self.get_marks_by_type( "atom_number"):
self.show_number = False
def create_mark( self, mark='radical', angle='auto', draw=1, angle_resolution=1):
"""creates the mark, does not care about the chemical meaning of this"""
# decide where to put the mark
mark_name, mark_class = self._mark_to_name_and_class( mark)
if angle == 'auto':
x, y = self.find_place_for_mark( mark, resolution=angle_resolution)
else:
if not self.show:
dist = 5 + round( mark_class.standard_size / 2)
else:
bbox = self.bbox()
x2 = self.x + round( cos( angle) *1000)
y2 = self.y + round( sin( angle) *1000)
x1, y1 = geometry.intersection_of_line_and_rect( (self.x,self.y,x2,y2), bbox, round_edges=0)
dist = geometry.point_distance( self.x, self.y, x1, y1) + round( mark_class.standard_size / 2)
x = self.x + round( cos( angle) *dist)
y = self.y + round( sin( angle) *dist)
#ang = angle
m = mark_class( self, x, y, auto=(angle=='auto'))
if draw:
m.draw()
self.marks.add( m)
return m
def get_marks_by_type( self, mark_type):
return [m for m in self.marks if m.__class__.__name__ == mark_type]
def reposition_marks( self):
ms = set( [m for m in self.marks if m.auto])
self.marks -= ms
for m in ms:
x, y = self.find_place_for_mark( m.__class__.__name__)
m.move_to( x, y)
self.marks.add( m)
def find_place_for_mark( self, mark, resolution=30):
"""resolution says if the angles should be somehow 'rounded', it is given in degrees;
see geometry.point_on_circle for a similar thing"""
mark_name, mark_class = self._mark_to_name_and_class( mark)
# deal with marks centered
if mark_class.meta__mark_positioning == 'atom':
return self.x, self.y
# deal with statically positioned marks
if mark_class.meta__mark_positioning == 'righttop':
bbox = self.bbox()
return bbox[2]+2, bbox[1]
# deal with marks in linear_form
if self.is_part_of_linear_fragment():
if mark_name == "atom_number":
bbox = self.bbox()
return int( self.x-0.5*self.font_size), bbox[1]-2
if not self.show:
dist = 5 + round( mark_class.standard_size / 2)
else:
dist = 0.75*self.font_size + round( mark_class.standard_size / 2)
atms = self.get_neighbors()
x, y = self.get_xy()
# special cases
if not atms:
# single atom molecule
if self.show_hydrogens and self.pos == "center-first":
return x -dist, y-3
else:
return x +dist, y-3
# normal case
coords = [(a.x,a.y) for a in atms]
# we have to take marks into account
[coords.append( (m.x, m.y)) for m in self.marks]
# hydrogen positioning is also important
if self.show_hydrogens and self.show:
if self.pos == 'center-last':
coords.append( (x-10,y))
else:
coords.append( (x+10,y))
# now we can compare the angles
angles = [geometry.clockwise_angle_from_east( x1-x, y1-y) for x1,y1 in coords]
angles.append( 2*pi + min( angles))
angles.sort()
angles.reverse()
diffs = misc.list_difference( angles)
i = diffs.index( max( diffs))
angle = (angles[i] +angles[i+1]) / 2
# we calculate the distance here again as it is anisotropic (depends on direction)
bbox = list( misc.normalize_coords( self.bbox()))
x0, y0 = geometry.point_on_circle( x, y, 500, direction=(cos(angle), sin( angle)), resolution=resolution)
x1, y1 = geometry.intersection_of_line_and_rect( (x,y,x0,y0), bbox, round_edges=0)
dist = geometry.point_distance( x, y, x1, y1) + round( mark_class.standard_size / 2)
# //
retx, rety = geometry.point_on_circle( x, y, dist, direction=(cos(angle), sin( angle)), resolution=resolution)
# in visible text x,y are not on the center, therefore we compensate for it
# if self.show:
# y -= 0.166 * self.font_size
return retx, rety
class drawable_chem_vertex( oasa.chem_vertex, meta_enabled, area_colored, point_drawable, text_like, child_with_paper, vertex_common):
"""this is a common ancestor for all children of oasa.chem_vertex in bkchem. It adds some
basic functionality to the chem_vertex so that it is not needed to add it every child;
all the methods are tuned for always shown texts; atoms need to override something"""
# these values will be automaticaly read from paper.standard on __init__
meta__used_standard_values = ['line_color','area_color','font_size','font_family','show_hydrogens']
# undo meta infos
meta__undo_fake = ('xml_ftext',)
meta__undo_simple = ()
meta__undo_properties = area_colored.meta__undo_properties + \
point_drawable.meta__undo_properties + \
text_like.meta__undo_properties + \
vertex_common.meta__undo_properties + \
( 'z', 'molecule', 'pos', 'charge')
meta__undo_copy = vertex_common.meta__undo_copy + ('_neighbors',)
meta__undo_children_to_record = vertex_common.meta__undo_children_to_record
def __init__( self, standard=None, xy=(), molecule=None):
meta_enabled.__init__( self, standard=standard)
vertex_common.__init__( self)
self.molecule = molecule
point_drawable.__init__( self)
oasa.chem_vertex.__init__( self)
if xy:
self.x, self.y = xy
self.z = 0
# hidden
self._reposition_on_redraw = 0
# presentation attrs
self.selector = None
self._selected = 0 #used to keep track whether this is selected or not
self.item = None
self.ftext = None
self.pos = None
self.focus_item = None
## ---------------------------------------- PROPERTIES ------------------------------
# molecule
def _get_molecule( self):
return self._molecule
def _set_molecule( self, mol):
self._molecule = mol
molecule = property( _get_molecule, _set_molecule)
# x
def _get_x( self):
return self._x
def _set_x( self, x):
self._x = Screen.any_to_px( x)
x = property( _get_x, _set_x)
# y
def _get_y( self):
return self._y
def _set_y( self, y):
self._y = Screen.any_to_px( y)
y = property( _get_y, _set_y)
# z
def _get_z( self):
return self._z or 0
def _set_z( self, z):
self._z = z
z = property( _get_z, _set_z)
# pos
def _get_pos( self):
return self._pos
def _set_pos( self, pos):
self._pos = pos
self.dirty = 1
pos = property( _get_pos, _set_pos)
# parent
def _get_parent( self):
return self.molecule
def _set_parent( self, par):
self.molecule = par
parent = property( _get_parent, _set_parent, None,
"returns self.molecule")
# drawn
def _get_drawn( self):
"""is the atoms drawn? on the paper or just virtual"""
if self.item:
return 1
return 0
drawn = property( _get_drawn, None, None, "tells if the atom is already drawn")
# font_size (override of text_like.font_size)
def _get_font_size( self):
return self._font_size
def _set_font_size( self, font_size):
self._font_size = font_size
self.dirty = 1
font_size = property( _get_font_size, _set_font_size)
# xml_ftext (override text_like.xml_ftext)
def _get_xml_ftext( self):
return self.symbol
xml_ftext = property( _get_xml_ftext, None, None, "the text used for rendering using the ftext class")
## // -------------------- END OF PROPERTIES --------------------------
def copy_settings( self, other):
"""copies settings of self to other, does not check if other is capable of receiving it"""
meta_enabled.copy_settings( self, other)
area_colored.copy_settings( self, other)
point_drawable.copy_settings( self, other)
text_like.copy_settings( self, other)
child_with_paper.copy_settings( self, other)
other.z = self.z
#other.pos = self.pos
def decide_pos( self):
"""decides whether the first or the last letter in the text should be positioned on the
coords of the vertex"""
if self.is_part_of_linear_fragment():
self.pos = 'center-first'
return
atms = self.get_neighbors()
p = 0
for a in atms:
if a.x < self.x:
p -= 1
elif a.x > self.x:
p += 1
if p > 0:
self.pos = 'center-last'
else:
self.pos = 'center-first'
def draw( self, redraw=False):
"draws vertex with respect to its properties"
if self.item:
warn( "drawing vertex that is probably drawn", UserWarning, 2)
x, y = self.x, self.y
self.update_font()
if not self.pos:
self.decide_pos()
# we use self.text to force undo when it is changed (e.g. when atom is added to OH so it changes to O)
name = '%s' % self.xml_ftext
self.ftext = ftext( self.paper, (self.x, self.y), name, font=self.font, pos=self.pos, fill=self.line_color)
self.ftext.draw()
# should we want a complete bbox? (yes only for atoms in linear form)
if len( [x for x in self.molecule.get_fragments_with_vertex( self) if x.type=="linear_form" and x.properties.get('bond_length',0)>20]):
complete = True
else:
complete = False
x1, y1, x2, y2 = self.ftext.bbox( complete=complete)
self.item = self.paper.create_rectangle( x1, y1, x2, y2, fill='', outline='', tags=('atom'))
## shrink the selector according to the font size and properties
hack_y = self.font.metrics()['descent'] - 1
self.selector = self.paper.create_rectangle( x1, y1, x2, y2-hack_y, fill=self.area_color, outline='',tags='helper_a')
if not redraw:
[m.draw() for m in self.marks]
self.ftext.lift()
self.paper.lift( self.item)
self.paper.register_id( self.item, self)
self._reposition_on_redraw = 0
def redraw( self, suppress_reposition=0):
if self._reposition_on_redraw and not suppress_reposition:
self.reposition_marks()
self._reposition_on_redraw = 0
self.update_font()
# at first we delete everything...
self.paper.unregister_id( self.item)
self.paper.delete( self.item)
if self.selector:
self.paper.delete( self. selector)
if self.ftext:
self.ftext.delete()
self.item = None # to ensure that warning in draw() is not triggered when redrawing
# ...then we draw it again
self.draw( redraw=True)
[m.redraw() for m in self.marks]
if self._selected:
self.select()
else:
self.unselect()
if not self.dirty:
pass
#print "redrawing non-dirty atom"
self.dirty = 0
def focus( self):
self.paper.itemconfig( self.selector, fill='grey')
def unfocus( self):
self.paper.itemconfig( self.selector, fill=self.area_color)
def select( self):
self.paper.itemconfig( self.selector, outline='black')
self._selected = 1
def unselect( self):
self.paper.itemconfig( self.selector, outline='')
self._selected = 0
def move( self, dx, dy, dont_move_marks=False):
"""moves object with his selector (when present)"""
# saving old dirty value
# d = self.dirty
self.x += dx
self.y += dy
if self.drawn:
self.paper.move( self.item, dx, dy)
if self.selector:
self.paper.move( self.selector, dx, dy)
if self.ftext:
self.ftext.move( dx, dy)
if not dont_move_marks:
for m in self.marks:
m.move( dx, dy)
# restoring dirty value because move does not dirty the atom
# self.dirty = d
def move_to( self, x, y, dont_move_marks=False):
dx = x - self.x
dy = y - self.y
self.move( dx, dy, dont_move_marks=dont_move_marks)
def get_xy( self):
return self.x, self.y
def get_xyz( self, real=0):
"""returns atoms coordinates, default are screen coordinates, real!=0
changes it to real coordinates (these two are usually different for imported molecules)"""
if real:
x, y = self.paper.screen_to_real_coords( (self.x, self.y))
z = self.z *self.paper.screen_to_real_ratio()
return x, y, z
else:
return self.x, self.y, self.z
def delete( self):
if self.focus_item:
self.unfocus()
if self.selector:
self.unselect()
self.paper.delete( self.selector)
self.selector = None
self._selected = 0
if self.item:
self.paper.unregister_id( self.item)
self.paper.delete( self.item)
self.item = None
if self.ftext:
self.ftext.delete()
[m.delete() for m in self.marks]
self.marks = set()
return self
def toggle_center( self, mode = 0):
"""toggles the centering of text between 'center-first' and 'center-last'(mode=0)
or sets it strictly - mode=-1, mode=1"""
if not mode:
if self.pos == 'center-last':
self.pos = 'center-first'
else:
self.pos = 'center-last'
elif mode == -1:
self.pos = 'center-first'
else:
self.pos = 'center-last'
self.redraw()
def update_font( self):
self.font = tkFont.Font( family=self.font_family, size=self.font_size)
def scale_font( self, ratio):
"""scales font of atom. does not redraw !!"""
self.font_size = int( round( self.font_size * ratio))
self.update_font()
def lift( self):
# marks
[m.lift() for m in self.marks]
if self.ftext:
self.ftext.lift()
if self.item:
self.paper.lift( self.item)
def lift_selector( self):
if self.selector:
self.paper.lift( self.selector)
def transform( self, tr):
x, y, z = tr.transform_xyz( self.x, self.y, self.z)
self.move_to( x, y, dont_move_marks=1)
self.z = z
for m in self.marks:
m.transform( tr)
def bbox( self, substract_font_descent=False):
"""returns the bounding box of the object as a list of [x1,y1,x2,y2]"""
if self.item:
box = self.paper.bbox( self.item)
if substract_font_descent and self.show:
hack_y = self.font.metrics()['descent']
x1, y1, x2, y2 = map( operator.add, box, Tuning.Screen.drawable_chem_vertex_bbox_mod_after_descent_removal)
box = x1, y1, x2, y2-hack_y
#if Store.app.in_batch_mode:
# # in batch mode the bboxes work really strangely and this fixes it somehow
# length = self.font.measure( self.text)
# return [box[0],box[1],box[0]+length,box[3]]
#else:
return box
else:
# we have to calculate it, the atoms was not drawn yet
length = self.font.measure( self.text)
if self.pos == 'center-first':
dx = self.font.measure( self.text[0]) / 2
descent = self.font.metrics()['descent']
ascent = self.font.metrics()['ascent']
return (self.x + length - dx, self.y + descent, self.x - dx, self.y - ascent)
else:
dx = self.font.measure( self.text[-1]) / 2
return (self.x + dx, self.y + descent, self.x - length + dx, self.y - ascent)
def is_part_of_linear_fragment( self):
"""returns boolean, useful to trigger special drawing of linear forms"""
if not self.molecule:
return False
if [f for f in self.molecule.get_fragments_with_vertex( self) if f.type == "linear_form"]:
return True
else:
return False
bkchem-0.13.0/bkchem/splash.py 0000644 0001756 0000144 00000003444 11146535716 014757 0 ustar beda users #--------------------------------------------------------------------------
# This file is part of BKchem - a chemical drawing program
# Copyright (C) 2002-2004 Beda Kosata
# 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.
# Complete text of GNU GPL can be found in the file gpl.txt in the
# main directory of the program
#--------------------------------------------------------------------------
#
#
#
#--------------------------------------------------------------------------
"""the Splash class resides here"""
import Tkinter
import messages
import os_support
class Splash( Tkinter.Toplevel):
def __init__( self):
Tkinter.Toplevel.__init__( self)
self.title(_('BKchem is starting...'))
# splash image
splash_image_path = 'logo.ppm'
try:
self.splash_image = Tkinter.PhotoImage( file = os_support.get_path( splash_image_path, 'image'))
except:
self.splash_image = None
text = Tkinter.Label( self,
font=('Helvetica', 12, 'normal'),
relief = 'raised',
borderwidth = 2,
padx=50, pady=50,
image = self.splash_image,
text = messages.splash_text
)
text.pack(fill = 'both', expand = 1)
bkchem-0.13.0/bkchem/debug.py 0000644 0001756 0000144 00000003174 11146535716 014553 0 ustar beda users #--------------------------------------------------------------------------
# This file is part of BKchem - a chemical drawing program
# Copyright (C) 2004 Beda Kosata
# 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.
# Complete text of GNU GPL can be found in the file gpl.txt in the
# main directory of the program
#--------------------------------------------------------------------------
import config
import sys
import inspect
def log( *args, **kw):
"""it takes an optional keyword arguments 'output' (output file-like)
and 'levels' (stack levels to report)"""
if 'output' in kw:
out = kw['output']
else:
out = None
if 'levels' in kw:
levels = kw['levels']
else:
levels = []
if config.debug:
frames = inspect.getouterframes( inspect.currentframe(), 1)
try:
for i in levels:
if i < len( frames):
frame = frames[i][0]
print " %s:%d -> %s()" % (frame.f_globals.get('__file__'), frame.f_lineno, frame.f_code.co_name)
finally:
del frames
try:
del frame
except:
pass
for arg in args:
print >> out, arg,
print >> out
bkchem-0.13.0/bkchem/classes.py 0000644 0001756 0000144 00000051173 11146535716 015124 0 ustar beda users #--------------------------------------------------------------------------
# This file is part of BKchem - a chemical drawing program
# Copyright (C) 2002-2007 Beda Kosata
# 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.
# Complete text of GNU GPL can be found in the file gpl.txt in the
# main directory of the program
#--------------------------------------------------------------------------
"""set of basic classes such as standard, plus, text etc.
also imports atom, bond and molecule from historical reasons :)"""
from __future__ import division
from __future__ import generators
from math import atan2, sin, cos, pi, sqrt
import misc
from warnings import warn
from ftext import ftext
import dom_extensions
import xml.dom.minidom as dom
import operator
import tkFont
from parents import meta_enabled, container, with_line, text_like, line_colored
from parents import area_colored, point_drawable, interactive, drawable, top_level
from parents import child, with_font
from reaction import reaction
from singleton_store import Screen
### NOTE: now that all classes are children of meta_enabled, so the read_standard_values method
### is called during their __init__ (in fact meta_enabled.__init__), therefor these values are
### not set in __init__ itself
##-------------------- STANDARD CLASS ------------------------------
class standard:
def __init__( self):
# common
self.line_width = '1px'
self.font_size = 12
self.font_family = 'helvetica'
self.line_color = "#000"
self.area_color = '' ##ffffff'
# bond
self.bond_length = '0.7cm'
self.bond_width = '6px'
self.wedge_width = '5px'
self.double_length_ratio = 0.75
# atom
self.show_hydrogens = 0
# arrow
self.arrow_length = '1.6cm'
# paper
self.paper_type = 'A4'
self.paper_orientation = 'portrait'
self.paper_crop_svg = 0
self.paper_crop_margin = 10
def __eq__( self, other):
for (k,v) in self.__dict__.iteritems():
if str( v) != str( other.__dict__[ k]):
return 0
return 1
def __ne__( self, other):
return not self.__eq__( other)
def get_package( self, doc):
"""returns a DOM element describing the object in CDML,
doc is the parent document which is used for element creation
(the returned element is not inserted into the document)"""
ret = doc.createElement( 'standard')
dom_extensions.setAttributes( ret, (('line_width', str( self.line_width)),
('font_size', str( self.font_size)),
('font_family', str( self.font_family)),
('line_color', self.line_color),
('area_color', self.area_color),
('paper_type', self.paper_type),
('paper_orientation', self.paper_orientation),
('paper_crop_svg', str( self.paper_crop_svg)),
('paper_crop_margin', str( self.paper_crop_margin))))
dom_extensions.elementUnder( ret, 'bond', (('length', str( self.bond_length)),
('width', str( self.bond_width)),
('wedge-width', str( self.wedge_width)),
('double-ratio', str( self.double_length_ratio))))
dom_extensions.elementUnder( ret, 'arrow', (('length', str( self.arrow_length)),))
dom_extensions.elementUnder( ret, 'atom', (('show_hydrogens', str( int( self.show_hydrogens))),))
return ret
def read_package( self, p):
for attr in ('line_width', 'font_size', 'font_family', 'line_color','area_color',
'paper_crop_svg','paper_orientation','paper_type','paper_crop_margin'):
if p.getAttribute( attr):
self.__dict__[ attr] = p.getAttribute( attr)
self.font_size = int( self.font_size)
self.paper_crop_svg = int( self.paper_crop_svg)
self.paper_crop_margin = int( self.paper_crop_margin)
b = dom_extensions.getFirstChildNamed( p, 'bond')
if b:
self.bond_length = b.getAttribute( 'length') or self.bond_length
self.bond_width = b.getAttribute( 'width') or self.bond_width
self.double_length_ratio = b.getAttribute( 'double-ratio') or self.double_length_ratio
self.double_length_ratio = float( self.double_length_ratio)
self.wedge_width = b.getAttribute( 'wedge-width') or self.wedge_width
a = dom_extensions.getFirstChildNamed( p, 'arrow')
if a:
self.arrow_length = a.getAttribute( 'length')
a = dom_extensions.getFirstChildNamed( p, 'atom')
if a:
show_hydrogens = a.getAttribute('show_hydrogens')
if show_hydrogens == "False":
show_hydrogens = 0
elif show_hydrogens == "True":
show_hydrogens = 1
self.show_hydrogens = int( show_hydrogens)
## -------------------- POINT CLASS ------------------------------
class point( point_drawable, interactive, child):
# note that all children of simple_parent have default meta infos set
# therefor it is not necessary to provide them for all new classes if they
# don't differ (are not non-empty)
object_type = 'point'
# undo related metas
meta__undo_properties = point_drawable.meta__undo_properties
def __init__( self, paper, xy=(), arrow=None, package=None, type='invisible'):
point_drawable.__init__( self)
if xy:
self.x, self.y = xy
self.paper = paper
self.item = None
self.focus_item = None
self.selector = None
self.type = type
if arrow:
self.arrow = arrow
if package:
self.read_package( package)
def draw( self):
if self.item:
self.redraw()
else:
if self.type == 'invisible':
self.item = self.paper.create_line( self.x, self.y, self.x, self.y, tags='point', fill='')
elif self.type == 'circle':
self.item = self.paper.create_oval( self.x-2, self.y-2, self.x+2, self.y+2, fill='grey', outline='grey', tags='point')
else:
warn( 'unknown point type')
return
self.paper.register_id( self.item, self)
def redraw( self):
if not self.item:
self.draw()
else:
self.paper.delete( self.item)
self.item = None
self.draw()
if self.selector:
self.paper.coords( self.selector, self.x-2, self.y-2, self.x+2, self.y+2)
def move( self, dx, dy):
self.x += dx
self.y += dy
self.paper.move( self.item, dx, dy)
if self.selector:
self.paper.move( self.selector, dx, dy)
def move_to( self, x, y):
if not self.item:
self.x = x
self.y = y
self.draw()
else:
dx = x -self.x
dy = y -self.y
self.move( dx, dy)
def focus( self):
self.focus_item = self.paper.create_oval( self.x-4, self.y-4, self.x+4, self.y+4)
if self.item:
self.paper.lift( self.item)
def unfocus( self):
if self.focus_item:
self.paper.delete( self.focus_item)
self.focus_item = None
def select( self):
if not self.selector:
self.selector = self.paper.create_rectangle( self.x-2, self.y-2, self.x+2, self.y+2)
self.paper.lower( self.selector)
def unselect( self):
if self.selector:
self.paper.delete( self.selector)
self.selector = None
def get_xy( self):
return self.x, self.y
def delete( self):
self.unselect()
self.unfocus()
if self.item:
self.paper.unregister_id( self.item)
self.paper.delete( self.item)
self.item = None
def read_package( self, package):
"""reads the dom element package and sets internal state according to it"""
x, y, z = Screen.read_xml_point( package)
self.x, self.y = self.paper.real_to_screen_coords( (x,y))
#self.z = int( package.getAttribute( 'z') )
def get_package( self, doc):
"""returns a DOM element describing the object in CDML,
doc is the parent document which is used for element creation
(the returned element is not inserted into the document)"""
pnt = doc.createElement('point')
x, y = map( Screen.px_to_text_with_unit, self.paper.screen_to_real_coords( (self.x, self.y)))
dom_extensions.setAttributes( pnt, (('x', x),
('y', y)))
return pnt
def lift( self):
if self.selector:
self.paper.lift( self.selector)
if self.item:
self.paper.lift( self.item)
def change_type( self, type):
self.type = type
self.redraw()
def transform( self, tr):
x, y = tr.transform_xy( self.x, self.y)
self.move_to( x, y)
# parent
def _get_parent( self):
return self.arrow
def _set_parent( self, par):
self.arrow = par
parent = property( _get_parent, _set_parent, None,
"returns self.molecule")
##-------------------- PLUS CLASS ------------------------------
class plus(meta_enabled, interactive, point_drawable, with_font, area_colored, top_level):
# note that all children of simple_parent have default meta infos set
# therefor it is not necessary to provide them for all new classes if they
# don't differ (are not non-empty)
object_type = 'plus'
# these values will be automaticaly read from paper.standard on __init__
meta__used_standard_values = ['line_color','area_color','font_family']
# undo related metas
meta__undo_properties = point_drawable.meta__undo_properties +\
with_font.meta__undo_properties +\
area_colored.meta__undo_properties
def __init__( self, paper, xy=(), package=None):
area_colored.__init__( self)
point_drawable.__init__( self)
with_font.__init__( self)
meta_enabled.__init__( self, standard=paper.standard)
self.paper = paper
self.x = self.y = None
self.focus_item = None
self.selector = None
self._selected = 0
self.font_size = 14
if xy:
self.x, self.y = xy
if package:
self.read_package( package)
# standard values
self.update_font()
def draw( self):
self.update_font()
self.item = self.paper.create_text( self.x, self.y, text='+', tags='plus', font = self.font, fill=self.line_color)
self.paper.register_id( self.item, self)
self.selector = self.paper.create_rectangle( self.paper.bbox( self.item), fill=self.area_color, outline=self.area_color)
self.paper.lift( self.item)
def redraw( self):
self.update_font()
self.paper.coords( self.item, self.x, self.y)
self.paper.itemconfig( self.item, font = self.font, fill=self.line_color)
if self.selector:
self.paper.coords( self.selector, self.paper.bbox( self.item))
self.paper.itemconfig( self.selector, fill=self.area_color, outline=self.area_color)
def focus( self):
if self.selector:
self.paper.itemconfig( self.selector, fill='grey')
def unfocus( self):
if self.selector:
self.paper.itemconfig( self.selector, fill=self.area_color)
def get_id( self):
return self.item
def select( self):
if self.selector:
self.paper.itemconfig( self.selector, outline='black')
self._selected = 1
def unselect( self):
if self.selector:
self.paper.itemconfig( self.selector, outline=self.area_color)
self._selected = 0
def move( self, dx, dy):
self.x += dx
self.y += dy
if hasattr( self, 'item') and self.item:
self.paper.move( self.item, dx, dy)
if self.selector:
self.paper.move( self.selector, dx, dy)
def move_to( self, x, y):
dx = x - self.x
dy = y - self.y
self.move( dx, dy)
def read_package( self, package):
"""reads the dom element package and sets internal state according to it"""
if package.getAttribute( 'id'):
self.id = package.getAttribute( 'id')
pnt = package.getElementsByTagName( 'point')[0]
self.x, self.y, z = Screen.read_xml_point( pnt)
if package.getAttribute( 'font_size'):
self.font_size = int( package.getAttribute( 'font_size'))
if package.getAttribute( 'color'):
self.line_color = package.getAttribute( 'color')
if package.getAttribute( 'background-color'):
self.area_color = package.getAttribute( 'background-color')
def get_package( self, doc):
"""returns a DOM element describing the object in CDML,
doc is the parent document which is used for element creation
(the returned element is not inserted into the document)"""
pls = doc.createElement('plus')
pls.setAttribute( 'id', self.id)
x, y = Screen.px_to_text_with_unit( (self.x, self.y))
dom_extensions.elementUnder( pls, 'point', (('x', x),
('y', y)))
pls.setAttribute('font_size', str( self.font_size))
if self.line_color != '#000':
pls.setAttribute( 'color', self.line_color)
if self.area_color != '#ffffff':
pls.setAttribute( 'background-color', self.area_color)
return pls
def delete( self):
self.paper.delete( self.selector)
self.paper.unregister_id( self.item)
self.paper.delete( self.item)
def get_xy( self):
return self.x, self.y
def bbox( self):
"""returns the bounding box of the object as a list of [x1,y1,x2,y2]"""
if hasattr( self, 'item') and self.item:
return self.paper.bbox( self.item)
else:
dx = self.font.measure( '+') / 2
return self.x + dx, self.y + 0.7*self.font_size, self.x - dx, self.y - 0.3*self.font_size
def scale_font( self, ratio):
"""scales font of plus. does not redraw !!"""
self.font_size = int( round( self.font_size * ratio))
self.update_font()
def update_font( self):
self.font = tkFont.Font( family=self.font_family, size=self.font_size)
def lift( self):
if self.selector:
self.paper.lift( self.selector)
if self.item:
self.paper.lift( self.item)
##--------------------TEXT CLASS--------------------
class text( meta_enabled, interactive, point_drawable, text_like, area_colored, top_level):
# note that all children of simple_parent have default meta infos set
# therefor it is not necessary to provide them for all new classes if they
# don't differ (are not non-empty)
object_type = 'text'
# these values will be automaticaly read from paper.standard on __init__
meta__used_standard_values = ['line_color','area_color','font_size','font_family']
# undo related metas
meta__undo_properties = point_drawable.meta__undo_properties +\
text_like.meta__undo_properties +\
area_colored.meta__undo_properties +\
("xml_ftext",)
def __init__( self, paper, xy=(), text='', package=None):
text_like.__init__( self)
point_drawable.__init__( self)
area_colored.__init__( self)
meta_enabled.__init__( self, standard=paper.standard)
self.paper = paper
self.selector = None
self._selected = 0
self.ftext = None
if xy:
self.set_xy( xy[0], xy[1])
self.xml_ftext = text
self.item = None
if package:
self.read_package( package)
self.focus_item = None
# public methods
def set_xy( self, x, y):
self.x = round( x, 2)
self.y = round( y, 2)
def draw( self):
"draws text"
self.update_font()
name = '%s' % self.xml_ftext
self.ftext = ftext( self.paper, (self.x, self.y), name, font=self.font, fill=self.line_color)
self.ftext.draw()
x1, y1, x2, y2 = self.ftext.bbox()
self.item = self.paper.create_rectangle( x1, y1, x2, y2, fill='', outline='', tags=('text'))
self.selector = self.paper.create_rectangle( x1, y1, x2, y2, fill=self.area_color, outline='', tags='helper_a')
self.ftext.lift()
self.paper.lift( self.item)
self.paper.register_id( self.item, self)
def redraw( self):
self.paper.unregister_id( self.item)
self.paper.delete( self.item)
if self.selector:
self.paper.delete( self.selector)
if self.ftext:
self.ftext.delete()
self.draw()
if self._selected:
self.select()
def focus( self):
if self.selector:
self.paper.itemconfig( self.selector, fill='gray')
def unfocus( self):
if self.selector:
self.paper.itemconfig( self.selector, fill=self.area_color)
def select( self):
if self.selector:
self.paper.itemconfig( self.selector, outline='black')
self._selected = 1
def unselect( self):
if self.selector:
self.paper.itemconfig( self.selector, outline=self.area_color)
self._selected = 0
def move( self, dx, dy):
"""moves object with his selector (when present)"""
self.x += dx
self.y += dy
self.paper.move( self.item, dx, dy)
if self.selector:
self.paper.move( self.selector, dx, dy)
if self.ftext:
self.ftext.move( dx, dy)
def move_to( self, x, y):
dx = x - self.x
dy = y - self.y
self.set_xy( x, y)
self.paper.move( self.item, dx, dy)
if self.selector:
self.paper.move( self.selector, dx, dy)
if self.ftext:
self.ftext.move_to( x, y)
def get_x( self):
return self.x
def get_y( self):
return self.y
def get_xy( self):
return self.x, self.y
def delete( self):
if self.focus_item:
self.unfocus()
if self.selector:
self.paper.delete( self.selector)
self.selector = None
if self.item:
self.paper.unregister_id( self.item)
self.paper.delete( self.item)
if self.ftext:
self.ftext.delete()
return self
def read_package( self, package):
"""reads the dom element package and sets internal state according to it"""
if package.getAttribute( 'id'):
self.id = package.getAttribute( 'id')
pos = package.getElementsByTagName( 'point')[0]
x, y, z = Screen.read_xml_point( pos)
self.set_xy( x, y)
ft = package.getElementsByTagName('ftext')
try:
self.xml_ftext = reduce( operator.add, [e.toxml() for e in ft[0].childNodes], '')
except IndexError:
self.xml_ftext = "?"
fnt = package.getElementsByTagName('font')
if fnt:
fnt = fnt[0]
self.font_size = int( fnt.getAttribute( 'size'))
self.font_family = fnt.getAttribute( 'family')
if fnt.getAttribute( 'color'):
self.line_color = fnt.getAttribute( 'color')
if package.getAttribute( 'background-color'):
self.area_color = package.getAttribute( 'background-color')
def get_package( self, doc):
"""returns a DOM element describing the object in CDML,
doc is the parent document which is used for element creation
(the returned element is not inserted into the document)"""
a = doc.createElement('text')
a.setAttribute( 'id', self.id)
if self.area_color != '':
a.setAttribute( 'background-color', self.area_color)
if self.font_size != self.paper.standard.font_size \
or self.font_family != self.paper.standard.font_family \
or self.line_color != self.paper.standard.line_color:
font = dom_extensions.elementUnder( a, 'font', attributes=(('size', str( self.font_size)), ('family', self.font_family)))
if self.line_color != self.paper.standard.line_color:
font.setAttribute( 'color', self.line_color)
x, y = Screen.px_to_text_with_unit( (self.x, self.y))
dom_extensions.elementUnder( a, 'point', attributes=(('x', x),('y', y)))
a.appendChild( self.get_parsed_text())
return a
# xml_ftext
def _get_xml_ftext( self):
return self._ftext
def _set_xml_ftext( self, text):
try:
t = unicode( text)
except UnicodeDecodeError:
t = text.decode( 'utf-8')
self._ftext = t.encode('utf-8')
xml_ftext = property( _get_xml_ftext, _set_xml_ftext, None, "the text used for rendering using the ftext class")
def bbox( self):
"""returns the bounding box of the object as a list of [x1,y1,x2,y2]"""
return self.ftext.bbox()
def update_font( self):
#if 'font_family' in self.__dict__ and 'font_size' in self.__dict__:
self.font = tkFont.Font( family=self.font_family, size=self.font_size)
def scale_font( self, ratio):
"""scales font of text. does not redraw !!"""
self.font_size = int( round( self.font_size * ratio))
self.update_font()
def lift( self):
if self.selector:
self.paper.lift( self.selector)
if self.ftext:
self.ftext.lift()
if self.item:
self.paper.lift( self.item)
def get_parsed_text( self):
return dom.parseString( "%s" % self.xml_ftext).childNodes[0]
bkchem-0.13.0/bkchem/export.py 0000644 0001756 0000144 00000004156 11146535716 015007 0 ustar beda users #--------------------------------------------------------------------------
# This file is part of BKchem - a chemical drawing program
# Copyright (C) 2002-2004 Beda Kosata
# 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.
# Complete text of GNU GPL can be found in the file gpl.txt in the
# main directory of the program
#--------------------------------------------------------------------------
"""support for exporters resides here"""
import xml_writer
import dom_extensions
def export_CD_SVG( paper, filename, gzipped=0):
"""exports to CD-SVG, returns 1 on success, 0 otherwise; optionally compresses with gzip"""
if gzipped:
import gzip as module
else:
import __builtin__ as module
try:
inp = module.open( filename, "w")
except IOError, x:
return 0
exporter = xml_writer.SVG_writer( paper)
exporter.construct_dom_tree( paper.top_levels)
doc = exporter.document
cdml = paper.get_package().childNodes[0]
doc.childNodes[0].appendChild( cdml)
dom_extensions.safe_indent( doc.childNodes[0], dont_indent=("text","ftext","user-data"))
inp.write( unicode(doc.toxml()).encode('utf-8'))
inp.close()
return 1
def export_CDML( paper, filename, gzipped=0):
"""exports to CDML, returns 1 on success, 0 otherwise; optionally compresses with gzip"""
if gzipped:
import gzip as module
else:
import __builtin__ as module
try:
inp = module.open( filename, "w")
except IOError, x:
return 0
doc = paper.get_package()
dom_extensions.safe_indent( doc.childNodes[0], dont_indent=("text","ftext","user-data"))
inp.write( unicode(doc.toxml()).encode('utf-8'))
inp.close()
return 1
bkchem-0.13.0/bkchem/__init__.py 0000644 0001756 0000144 00000000260 11146535716 015215 0 ustar beda users ## import sys
## import os
## path = os.path.abspath('./bkchem')
## if path not in sys.path:
## sys.path.append( path)
## import bkchem
## sys.modules['bkchem'] = bkchem
bkchem-0.13.0/bkchem/PmwBlt.py 0000644 0001756 0000144 00000054642 11146535716 014700 0 ustar beda users # Python interface to some of the commands of the 2.4 version of the
# BLT extension to tcl.
import string
import types
import Tkinter
# Supported commands:
_busyCommand = '::blt::busy'
_vectorCommand = '::blt::vector'
_graphCommand = '::blt::graph'
_testCommand = '::blt::*'
_chartCommand = '::blt::stripchart'
_tabsetCommand = '::blt::tabset'
_haveBlt = None
_haveBltBusy = None
def _checkForBlt(window):
global _haveBlt
global _haveBltBusy
# Blt may be a package which has not yet been loaded. Try to load it.
try:
window.tk.call('package', 'require', 'BLT')
except Tkinter.TclError:
# Another way to try to dynamically load blt:
try:
window.tk.call('load', '', 'Blt')
except Tkinter.TclError:
pass
_haveBlt= (window.tk.call('info', 'commands', _testCommand) != '')
_haveBltBusy = (window.tk.call('info', 'commands', _busyCommand) != '')
def haveblt(window):
if _haveBlt is None:
_checkForBlt(window)
return _haveBlt
def havebltbusy(window):
if _haveBlt is None:
_checkForBlt(window)
return _haveBltBusy
def _loadBlt(window):
if _haveBlt is None:
if window is None:
window = Tkinter._default_root
if window is None:
window = Tkinter.Tk()
_checkForBlt(window)
def busy_hold(window, cursor = None):
_loadBlt(window)
if cursor is None:
window.tk.call(_busyCommand, 'hold', window._w)
else:
window.tk.call(_busyCommand, 'hold', window._w, '-cursor', cursor)
def busy_release(window):
_loadBlt(window)
window.tk.call(_busyCommand, 'release', window._w)
def busy_forget(window):
_loadBlt(window)
window.tk.call(_busyCommand, 'forget', window._w)
#=============================================================================
# Interface to the blt vector command which makes it look like the
# builtin python list type.
# The -variable, -command, -watchunset creation options are not supported.
# The dup, merge, notify, offset, populate, seq and variable methods
# and the +, -, * and / operations are not supported.
# Blt vector functions:
def vector_expr(expression):
tk = Tkinter._default_root.tk
strList = tk.splitlist(tk.call(_vectorCommand, 'expr', expression))
return tuple(map(string.atof, strList))
def vector_names(pattern = None):
tk = Tkinter._default_root.tk
return tk.splitlist(tk.call(_vectorCommand, 'names', pattern))
class Vector:
_varnum = 0
def __init__(self, size=None, master=None):
# can be either an integer size, or a string "first:last".
_loadBlt(master)
if master:
self._master = master
else:
self._master = Tkinter._default_root
self.tk = self._master.tk
self._name = 'PY_VEC' + str(Vector._varnum)
Vector._varnum = Vector._varnum + 1
if size is None:
self.tk.call(_vectorCommand, 'create', self._name)
else:
self.tk.call(_vectorCommand, 'create', '%s(%s)' % (self._name, size))
def __del__(self):
self.tk.call(_vectorCommand, 'destroy', self._name)
def __str__(self):
return self._name
def __repr__(self):
return '[' + string.join(map(str, self), ', ') + ']'
def __cmp__(self, list):
return cmp(self[:], list)
def __len__(self):
return self.tk.getint(self.tk.call(self._name, 'length'))
def __getitem__(self, key):
oldkey = key
if key < 0:
key = key + len(self)
try:
return self.tk.getdouble(self.tk.globalgetvar(self._name, str(key)))
except Tkinter.TclError:
raise IndexError, oldkey
def __setitem__(self, key, value):
if key < 0:
key = key + len(self)
return self.tk.globalsetvar(self._name, str(key), float(value))
def __delitem__(self, key):
if key < 0:
key = key + len(self)
return self.tk.globalunsetvar(self._name, str(key))
def __getslice__(self, start, end):
length = len(self)
if start < 0:
start = 0
if end > length:
end = length
if start >= end:
return []
end = end - 1 # Blt vector slices include end point.
text = self.tk.globalgetvar(self._name, str(start) + ':' + str(end))
return map(self.tk.getdouble, self.tk.splitlist(text))
def __setslice__(self, start, end, list):
if start > end:
end = start
self.set(self[:start] + list + self[end:])
def __delslice__(self, start, end):
if start < end:
self.set(self[:start] + self[end:])
def __add__(self, list):
return self[:] + list
def __radd__(self, list):
return list + self[:]
def __mul__(self, n):
return self[:] * n
__rmul__ = __mul__
# Python builtin list methods:
def append(self, *args):
self.tk.call(self._name, 'append', args)
def count(self, obj):
return self[:].count(obj)
def index(self, value):
return self[:].index(value)
def insert(self, index, value):
self[index:index] = [value]
def remove(self, value):
del self[self.index(value)]
def reverse(self):
s = self[:]
s.reverse()
self.set(s)
def sort(self, *args):
s = self[:]
s.sort()
self.set(s)
# Blt vector instance methods:
# append - same as list method above
def clear(self):
self.tk.call(self._name, 'clear')
def delete(self, *args):
self.tk.call((self._name, 'delete') + args)
def expr(self, expression):
self.tk.call(self._name, 'expr', expression)
def length(self, newSize=None):
return self.tk.getint(self.tk.call(self._name, 'length', newSize))
def range(self, first, last=None):
# Note that, unlike self[first:last], this includes the last
# item in the returned range.
text = self.tk.call(self._name, 'range', first, last)
return map(self.tk.getdouble, self.tk.splitlist(text))
def search(self, start, end=None):
return self._master._getints(self.tk.call(
self._name, 'search', start, end))
def set(self, list):
if type(list) != types.TupleType:
list = tuple(list)
self.tk.call(self._name, 'set', list)
# The blt vector sort method has different semantics to the python
# list sort method. Call these blt_sort:
def blt_sort(self, *args):
self.tk.call((self._name, 'sort') + args)
def blt_sort_reverse(self, *args):
self.tk.call((self._name, 'sort', '-reverse') + args)
# Special blt vector indexes:
def min(self):
return self.tk.getdouble(self.tk.globalgetvar(self._name, 'min'))
def max(self):
return self.tk.getdouble(self.tk.globalgetvar(self._name, 'max'))
# Method borrowed from Tkinter.Var class:
def get(self):
return self[:]
#=============================================================================
# This is a general purpose configure routine which can handle the
# configuration of widgets, items within widgets, etc. Supports the
# forms configure() and configure('font') for querying and
# configure(font = 'fixed', text = 'hello') for setting.
def _doConfigure(widget, subcommand, option, kw):
if not option and not kw:
# Return a description of all options.
ret = {}
options = widget.tk.splitlist(widget.tk.call(subcommand))
for optionString in options:
optionInfo = widget.tk.splitlist(optionString)
option = optionInfo[0][1:]
ret[option] = (option,) + optionInfo[1:]
return ret
if option:
# Return a description of the option given by