debian/0000755000000000000000000000000011664026557007202 5ustar debian/bkchem.links0000644000000000000000000000072611664026407011474 0ustar usr/share/bkchem/images/bkchem16.png usr/share/icons/hicolor/16x16/apps/bkchem.png usr/share/bkchem/images/bkchem22.png usr/share/icons/hicolor/22x22/apps/bkchem.png usr/share/bkchem/images/bkchem32.png usr/share/icons/hicolor/32x32/apps/bkchem.png usr/share/bkchem/images/bkchem48.png usr/share/icons/hicolor/48x48/apps/bkchem.png usr/share/bkchem/images/bkchem.png usr/share/pixmaps/bkchem.png usr/share/doc/bkchem/progress.log.gz usr/share/doc/bkchem/changelog.gz debian/watch0000644000000000000000000000027711176350666010240 0ustar # See uscan(1) for format version=3 opts=uversionmangle=s/_pre([^.]+)/~$1/ \ http://bkchem.zirael.org/download/ bkchem-([\d\.]+(?:_pre.*)?)\.tar\.gz # opts=uversionmangle=s/_pre(\d+)/~$1/ debian/bkchem.manpages0000644000000000000000000000002010737774663012150 0ustar debian/bkchem.1 debian/bkchem.desktop0000644000000000000000000000042510737774663012037 0ustar [Desktop Entry] Version=1.0 Name=BKchem Comment=Edit chemical structures and reactions Type=Application Exec=bkchem %U Icon=bkchem Categories=Education;Science;Chemistry; MimeType=image/svg+xml;image/svg+xml-compressed;application/x-cdml+xml;application/x-cdml+xml-compressed; debian/README.Debian0000644000000000000000000000513311146072726011237 0ustar bkchem for Debian ----------------- bkchem upstream notes --------------------- bkchem features =============== Drawing * bond-by-bond drawing * bond length and angle restrictions to assist with the drawing * ready to use templates of common rings * ability to expand common groups from abbreviated to structural form * radicals, charges... * arrows * rich text * color support * simple vector graphics (rectangles, circles, polygons etc.) Editing * unlimited undo and redo capabilities * aligning * scaling * rotation (2D, 3D) * aligning of molecules so that particular bond is horizontal/vertical * rotation of molecular fragments around bonds (conformation changes) * definition of personal preferred drawing style (bond lengths, widths, colors...) Export * full export to SVG (native data are transparently embedded into SVG file) * full export to OpenOffice Draw format * full export to Encapsulated PostScript * basic support for both CML1 and CML2 * Molfiles * generation of SMILES Import * basic support for both CML1 and CML2 * Molfiles * SMILES (subset) * INChI (subset) Other features * localization support (currently English, French, German, Czech and Polish translations are available) * native format is XML based * validity checking of drawn structures What can you expect from BKchem in future? ========================================== * Support for user written plugins * Better and more exports * Support for linear formulas (such as -CH2CH(COOCH3)2) * More arrow types What you should not expect from BKchem? ======================================= BKchem is developed for fun as a free-time activity. BKchem is free software. Therefor you should not expect: * proprietary formats export or import * features that don't make sense to the author(s) unless you implement them yourself (or convince us to implement them :o). How can you help ================ There are several ways you can help improve BKchem: * submit bug reports * translate BKchem to other languages * write exporters * write importers * submit other patches * help improve the appearance of BKchem by providing icons etc. * check or improve the documentation Any suggestions, requests, help offers or even flames are welcome. Please feel free to contact me on beda@zirael.org. There is also a public mailing list of BKchem users available. (written by Beda Kosata at http://bkchem.zirael.org) -- Daniel Leidert (dale) debian/bkchem.install0000644000000000000000000000016510737774663012035 0ustar images/bkchem.png usr/share/pixmaps debian/bkchem.xpm usr/share/pixmaps debian/bkchem.desktop usr/share/applications debian/rules0000755000000000000000000000117411664026407010257 0ustar #!/usr/bin/make -f # -*- makefile -*- # Sample debian/rules that uses debhelper. # GNU copyright 1997 to 1999 by Joey Hess. # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 PACKAGE = bkchem DESTDIR = $(CURDIR)/debian/$(PACKAGE) %: dh --with python2 $@ --parallel override_dh_auto_install: dh_auto_install -- --strip=$(DESTDIR) --prefix=/usr --install-lib=/usr/lib/$(PACKAGE) $(RM) $(DESTDIR)/usr/lib/$(PACKAGE)/bkchem/plugins/plugins/code_to_convert_to_plugins.py $(RM) -r $(DESTDIR)/usr/share/doc/bkchem/api \ $(DESTDIR)/usr/share/doc/bkchem/INSTALL \ $(DESTDIR)/usr/share/doc/bkchem/RELEASE debian/bkchem.dirs0000644000000000000000000000003210737774663011321 0ustar usr/bin usr/share/pixmaps debian/copyright0000644000000000000000000000745411524120660011130 0ustar This package was debianized by Daniel Leidert (dale) . It was downloaded from http://bkchem.zirael.org/download_en.html. Upstream Authors: Beda Kosata Reinis Danne (current maintainer) Piddle was originally written by Andy Robinson (Robinson Analytics), Joseph J. Strout, Bill Bedford, David Ascher, Paul & Kevin Jacobs, Greg Landrum Copyright: Copyright (C) 2002-2009 Beda Kosata Piddle is copyrighted (summarized): Copyright (C) 1998-1999 Andy Robinson Copyright (C) 1998-1999 Robinson Analytics Copyright (C) 1999 Joseph J. Strout Copyright (C) 1999 Bill Bedford Copyright (C) 1999 David Ascher Copyright (C) 2000 Paul & Kevin Jacobs Copyright (C) 2000 Greg Landrum Pmw is copyrighted (summarized): Copyright (C) 1997, 1998, 1999, 2000, 2001 Telstra Corporation Limited, Australia (ACN 051 775 556) License for bkchem: GNU General Public License. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA On Debian systems, the GNU General Public License, is available as the file `/usr/share/common-licenses/GPL'. License for piddle: GNU Lesser General Public License. This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This library 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 Lesser General Public License for more details. You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA On Debian systems, the GNU Lesser General Public License, is available as the file `/usr/share/common-licenses/LGPL'. License for Pmw: Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. debian/bkchem.doc-base0000644000000000000000000000043311146040655012020 0ustar Document: bkchem Title: bkchem users guide Author: Beda Kosata Abstract: This manual describes the core functionality of bkchem and works as a user guide. Section: Science/Chemistry Format: HTML Index: /usr/share/doc/bkchem/html/index.html Files: /usr/share/doc/bkchem/html/*.html debian/source/0000755000000000000000000000000011664026557010502 5ustar debian/source/format0000644000000000000000000000001411664026407011702 0ustar 3.0 (quilt) debian/TODO0000644000000000000000000000154411524120660007657 0ustar bkchem for Debian ----------------- * Starting with the version 0.9.0-pre1 piddle sources are shipped together with bkchem. Maybe the bkchem package should be split in consideration of this fact. For the moment, this is not done. * Starting with the version 0.10.0-pre1 Pmw (http://pmw.sourceforge.net/) sources (version 1.2) are shipped together with BKChem. There is a Debian package python-pmw. Not sure what to do here. The author seemed to have the Pmw library customized (but don't trust my judgement here). I requested a name change of the fork. This may also be split out into a separate module package. * debian/rules: Test for this snippet -include /usr/share/python/python.mk [..] python setup.py install --root=debian/$(PACKAGE) --prefix=/usr --no-compile $(py_setup_install_args) -- Daniel Leidert (dale) , February 2011 debian/compat0000644000000000000000000000000211664026407010372 0ustar 7 debian/control0000644000000000000000000000230011664026407010572 0ustar Source: bkchem Section: science Priority: optional Maintainer: Debichem Team Uploaders: Michael Banck , Daniel Leidert (dale) Build-Depends: debhelper (>> 7.0.50~), python Build-Depends-Indep: python-support (>= 0.6), python-imaging, python-pmw (>= 1.2) Standards-Version: 3.9.2 Homepage: http://bkchem.zirael.org Vcs-Browser: http://svn.debian.org/wsvn/debichem/unstable/bkchem/ Vcs-Svn: svn://svn.debian.org/svn/debichem/unstable/bkchem/ DM-Upload-Allowed: yes Package: bkchem Architecture: all Depends: ${misc:Depends}, ${python:Depends}, python-imaging, python-pmw (>= 1.2) Suggests: python-cairo Description: Chemical structures editor BKchem is a free chemical drawing program, which is written in Python. . Some of the features, you can expect: * Drawing (bond-by-bond drawing; templates for common rings; expanding of common-groups; draws radicals, charges, arrows; color support ...) * Editing (unlimited undo and redo capabilities; aligning; scaling; rotation (2D, 3D) ...) * Export/Import (fully supported SVG-, OpenOffice.org-Draw-, EPS-export; basic support for CML1 and CML2 import and export) debian/patches/0000755000000000000000000000000011664026557010631 5ustar debian/patches/series0000644000000000000000000000011511664026407012035 0ustar 585233_fix_python_26_compatibility.patch 608915_fix_assertion_warnings.patch debian/patches/585233_fix_python_26_compatibility.patch0000755000000000000000000002467511664026407020145 0ustar Author: Reinis Danne Description: Fix python string exceptions Origin: upstream, http://gitorious.org/bkchem/piddle/commit/73c84c7e08dbb237f66ae78200780beade7a442c?format=patch Bug-Debian: http://bugs.debian.org/585233 Last-Update: bkchem (0.13.0-3) unstable --- a/bkchem/oasa/oasa/chem_vertex.py +++ b/bkchem/oasa/oasa/chem_vertex.py @@ -67,7 +67,7 @@ elif len( coords) == 3: self.x, self.y, self.z = coords else: - raise "wrong number of coordinates" + raise Exception("wrong number of coordinates") def _get_coords( self): return self.x, self.y, self.z --- a/bkchem/oasa/oasa/coords_generator.py +++ b/bkchem/oasa/oasa/coords_generator.py @@ -296,7 +296,7 @@ ring = self.mol.sort_vertices_in_path( ring, start_from=v) base_neighs = [a for a in v.get_neighbors() if a in base] if len( base_neighs) < 2: - raise "this should not happen" + raise Exception("this should not happen") d1 = base_neighs[0] d2 = base_neighs[1] ca1 = geometry.clockwise_angle_from_east( v.x-d1.x, v.y-d1.y) @@ -339,7 +339,7 @@ # there are more than 2 atoms common if len( ring) == len( base): out += self._process_multi_anelated_ring( ring, angle_shift=15) - #raise( "i don't how to handle this yet") + #raise Exception( "i don't how to handle this yet") else: out += self._process_multi_anelated_ring( ring) return out @@ -355,7 +355,7 @@ if not sorted_back: # the already set atoms are not in one path - we have to process it "per partes" # it should not happen with the construction method we use - raise( "i am not able to handle this, it should normaly not happen. please send me the input.") + raise Exception( "i am not able to handle this, it should normaly not happen. please send me the input.") else: v1 = sorted_back[0] v2 = sorted_back[-1] --- a/bkchem/oasa/oasa/graph/vertex.py +++ b/bkchem/oasa/oasa/graph/vertex.py @@ -65,14 +65,14 @@ if to_del: del self._neighbors[ to_del] else: - raise "cannot remove non-existing neighbor" + raise Exception("cannot remove non-existing neighbor") def remove_edge_and_neighbor( self, e): self._clean_cache() if e in self._neighbors.keys(): del self._neighbors[ e] else: - raise "cannot remove non-existing edge", e + raise Exception("cannot remove non-existing edge", e) def get_neighbors( self): --- a/bkchem/oasa/oasa/inchi.py +++ b/bkchem/oasa/oasa/inchi.py @@ -95,14 +95,14 @@ return layers structs = doc.getElementsByTagName( 'structure') if not structs: - raise "no structures found in xml string %s" % text + raise Exception("no structures found in xml string %s" % text) struct = structs[0] layers = [] for name in ('version','formula','connections','H'): try: layer = struct.getElementsByTagName( name)[0] except IndexError: - raise "no '%s' tag found in xml string" % name + raise Exception("no '%s' tag found in xml string" % name) layers.append( dom_extensions.getTextFromElement( layer)) return layers @@ -249,7 +249,7 @@ try: i = int( c) except: - raise ValueError, "unexpected character %s in the connectivity layer" % c + raise ValueError("unexpected character %s in the connectivity layer" % c) # atom if last_atom: self.structure.add_edge( last_atom-1, i-1) --- a/bkchem/oasa/oasa/molfile.py +++ b/bkchem/oasa/oasa/molfile.py @@ -107,7 +107,7 @@ def write_file( self, file): """file should be a writable file object""" if not self.structure: - raise "No structure to write" + raise Exception("No structure to write") self._write_header( file) self._write_counts_line( file) self._write_body( file) --- a/bkchem/oasa/oasa/smiles.py +++ b/bkchem/oasa/oasa/smiles.py @@ -430,7 +430,7 @@ start, end = filter( lambda x: x.get_degree() == 1, mol.vertices) except: #print filter( lambda x: x.get_degree() == 1, mol.vertices) - raise "shit" + raise Exception("shit") if start_from == end: start, end = end, start v = start @@ -567,7 +567,7 @@ the_right_branch_atom, the_right_branch) #print mol, mol.is_connected() - raise "fuck, how comes!?" + raise Exception("fuck, how comes!?") @@ -612,7 +612,7 @@ v = (v1 in p1.vertices) and v1 or v2 return e, p1, v, p2 print mol, mol.is_connected(), ',', map( len, mol.get_connected_components()), ',', start_from - raise "fuck, how comes!?" + raise Exception("fuck, how comes!?") @staticmethod def _create_ring_join_smiles( index): --- a/bkchem/plugins/piddle/PixMapWrapper.py +++ b/bkchem/plugins/piddle/PixMapWrapper.py @@ -93,7 +93,7 @@ def __setattr__(self, attr, val): if attr == 'baseAddr': - raise 'UseErr', "don't assign to .baseAddr -- assign to .data instead" + raise Exception('UseErr', "don't assign to .baseAddr -- assign to .data instead") elif attr == 'data': self.__dict__['data'] = val self._stuff('baseAddr', id(self.data) + MacOS.string_id_to_buffer) @@ -186,7 +186,7 @@ # so convert if necessary if format != imgformat.macrgb and format != imgformat.macrgb16: # (LATER!) - raise "NotImplementedError", "conversion to macrgb or macrgb16" + raise NotImplementedError("conversion to macrgb or macrgb16") self.data = s self.bounds = (0,0,width,height) self.cmpCount = 3 @@ -207,7 +207,7 @@ return self.data # otherwise, convert to the requested format # (LATER!) - raise "NotImplementedError", "data format conversion" + raise NotImplementedError("data format conversion") def fromImage(self,im): """Initialize this PixMap from a PIL Image object.""" --- a/bkchem/plugins/piddle/pdfgen.py +++ b/bkchem/plugins/piddle/pdfgen.py @@ -707,7 +707,7 @@ image.seek(2, 1) #skip segment length x = struct.unpack('B', image.read(1)) #data precision if x[0] != 8: - raise 'PDFError', ' JPEG must have 8 bits per component' + raise Exception('PDFError', ' JPEG must have 8 bits per component') y = struct.unpack('BB', image.read(2)) height = (y[0] << 8) + y[1] y = struct.unpack('BB', image.read(2)) @@ -717,7 +717,7 @@ return width, height, color done = 1 elif x[0] in unsupportedMarkers: - raise 'PDFError', ' Unsupported JPEG marker: %0.2x' % x[0] + raise Exception('PDFError', ' Unsupported JPEG marker: %0.2x' % x[0]) elif x[0] not in noParamMarkers: #skip segments with parameters #read length and skip the data @@ -764,17 +764,17 @@ if direction in [0,90,180,270]: direction_arg = '/Di /%d' % direction else: - raise 'PDFError', ' directions allowed are 0,90,180,270' + raise Exception('PDFError', ' directions allowed are 0,90,180,270') if dimension in ['H', 'V']: dimension_arg = '/Dm /%s' % dimension else: - raise'PDFError','dimension values allowed are H and V' + raise Exception('PDFError','dimension values allowed are H and V') if motion in ['I','O']: motion_arg = '/M /%s' % motion else: - raise'PDFError','motion values allowed are I and O' + raise Exception('PDFError','motion values allowed are I and O') # this says which effects require which argument types from above @@ -790,7 +790,7 @@ try: args = PageTransitionEffects[effectname] except KeyError: - raise 'PDFError', 'Unknown Effect Name "%s"' % effectname + raise Exception('PDFError', 'Unknown Effect Name "%s"' % effectname) self._pageTransitionString = '' return --- a/bkchem/plugins/piddle/piddle.py +++ b/bkchem/plugins/piddle/piddle.py @@ -749,9 +749,9 @@ if hasattr(file, "write"): fileobj = file else: - raise 'Invalid file argument to save' + raise Exception('Invalid file argument to save') else: - raise 'Invalid file argument to save' + raise Exception('Invalid file argument to save') return fileobj --- a/bkchem/plugins/piddle/piddlePIL.py +++ b/bkchem/plugins/piddle/piddlePIL.py @@ -344,7 +344,7 @@ temppen = ImageDraw.ImageDraw(tempimg) temppen.setink( (255,255,255) ) pilfont = _pilFont(font) - if not pilfont: raise "bad font!", font + if not pilfont: raise Exception("bad font!", font) temppen.setfont( pilfont ) pos = [4, int(tempsize/2 - self.fontAscent(font)) - self.fontDescent(font)] temppen.text( pos, s ) --- a/bkchem/plugins/piddle/piddlePS.py +++ b/bkchem/plugins/piddle/piddlePS.py @@ -190,7 +190,7 @@ elif PostScriptLevel == 2 : self.drawImage = self._drawImageLevel2 else : - raise 'PostScriptLevelException' + raise Exception('PostScriptLevelException') self.code = [] --- a/bkchem/plugins/piddle/piddleWxDc.py +++ b/bkchem/plugins/piddle/piddleWxDc.py @@ -56,7 +56,7 @@ if default_color is not None: return self._getWXbrush(default_color) else: - raise "WXcanvas error: Cannot create brush." + raise Exception("WXcanvas error: Cannot create brush.") return wxBrush(wxcolor) @@ -75,7 +75,7 @@ if default_color is not None: return self._getWXpen(width, default_color) else: - raise "WXcanvas error: Cannot create pen." + raise Exception("WXcanvas error: Cannot create pen.") return wxPen(wxcolor, width) @@ -264,7 +264,7 @@ try: import Image except ImportError: - raise "PIL not available!" + raise Exception("PIL not available!") if (x2 and y2 and x2>x1 and y2>y1): imgPil = image.resize((x2-x1,y2-y1)) --- a/bkchem/plugins/piddle/piddletest.py +++ b/bkchem/plugins/piddle/piddletest.py @@ -274,7 +274,7 @@ drawRotstring(tkcanvas) else : print "Illegal testfunc handed to tkTest" - raise "Unsupported testfunc" + raise Exception("Unsupported testfunc") tkcanvas.flush() debian/patches/608915_fix_assertion_warnings.patch0000755000000000000000000000445011664026407017273 0ustar Author: Daniel Leidert Description: Fix assertion syntax warnings Origin: Debian, http://anonscm.debian.org/viewvc/debichem?view=revision&revision=2625 Bug-Debian: http://bugs.debian.org/608915 Applied-Upstream: commit:http://gitorious.org/bkchem/piddle/commit/9c4004eaefb8b0f483d6428fcbd37a334d1dba9a?format=patch Last-Update: bkchem (0.13.0-3) unstable --- a/bkchem/plugins/piddle/pdfgen.py +++ b/bkchem/plugins/piddle/pdfgen.py @@ -639,7 +639,7 @@ #use a flate filter and Ascii Base 85 to compress raw = myimage.tostring() - assert(len(raw) == imgwidth * imgheight, "Wrong amount of data for image") + assert len(raw) == imgwidth * imgheight, "Wrong amount of data for image" compressed = zlib.compress(raw) #this bit is very fast... encoded = pdfutils._AsciiBase85Encode(compressed) #...sadly this isn't --- a/bkchem/plugins/piddle/pdfutils.py +++ b/bkchem/plugins/piddle/pdfutils.py @@ -27,7 +27,7 @@ code.append('ID') #use a flate filter and Ascii Base 85 raw = img.tostring() - assert(len(raw) == imgwidth * imgheight, "Wrong amount of data for image") + assert len(raw) == imgwidth * imgheight, "Wrong amount of data for image" compressed = zlib.compress(raw) #this bit is very fast... encoded = _AsciiBase85Encode(compressed) #...sadly this isn't --- a/bkchem/plugins/piddle/piddlePS.py +++ b/bkchem/plugins/piddle/piddlePS.py @@ -866,7 +866,7 @@ # piddlePDF again rawimage = myimage.tostring() - assert(len(rawimage) == imgwidth*imgheight, 'Wrong amount of data for image') + assert len(rawimage) == imgwidth*imgheight, 'Wrong amount of data for image' #compressed = zlib.compress(rawimage) # no zlib at moment hex_encoded = self._AsciiHexEncode(rawimage) @@ -957,7 +957,7 @@ 'image']) # after image operator just need to dump image dat to file as hexstring rawimage = myimage.tostring() - assert(len(rawimage) == imwidth*imheight, 'Wrong amount of data for image') + assert len(rawimage) == imwidth*imheight, 'Wrong amount of data for image' #compressed = zlib.compress(rawimage) # no zlib at moment hex_encoded = self._AsciiHexEncode(rawimage) debian/bkchem.sharedmimeinfo0000644000000000000000000000104410737774663013356 0ustar CDML file CDGZ file debian/bkchem.10000644000000000000000000000257511146040655010514 0ustar .TH "BKCHEM" "1" "05/18/2008" "" "User commands" .SH "NAME" bkchem \- a free chemical drawing program .SH "SYNOPSIS" .B bkchem .RB [ options ] .RI [ file ] .SH "DESCRIPTION" .PP .B bkchem is a free chemical drawing program, which was written in Python\&. The editor gives you the possibility to draw, scale, rotate, align and validate molecules and/or molecular fragments\&. You can import CML1/CML2, MDL MOL files, SMILES and INChI\&. Export is possible into SVG, OpenOffice Draw format, Encapsulated PostScript (EPS), CML1/CML2, MDL MOL files and SMILES\&. .SH "OPTIONS" .PP The following options can be used: .TP .BI "\-H " home-directory Set the new home directory to be .IR home-directory \&. .TP .BI "\-b " script Run in batch mode and execute .IR script \&. .TP .BR \-h ", " \-\-help Show usage information\&. .TP .BR \-v ", " \-\-version Show version information\&. .SH "FILES" .PP .TP .I ${HOME}/\&.bkchem/prefs.xml File to store user preferences. .SH "AUTHORS" .PP .B bkchem is written by Beda Kosata <\&beda@zirael\&.org\&>. .PP This manual page was written by Daniel Leidert <\&daniel\&.leidert@wgdd\&.de\&> for the Debian GNU/Linux system (but may be used by others). .PP Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 or (at your option) any later version published by the Free Software Foundation\&. debian/bkchem.menu0000644000000000000000000000024610737774663011333 0ustar ?package(bkchem):\ needs="X11"\ section="Applications/Science/Chemistry"\ title="BKchem"\ icon="/usr/share/pixmaps/bkchem.xpm" \ command="/usr/bin/bkchem" debian/bkchem.xpm0000644000000000000000000001314710737774663011177 0ustar /* XPM */ static char *bkchem[] = { /* columns rows colors chars-per-pixel */ "32 32 216 2", " c black", ". c #000001", "X c #000002", "o c #000200", "O c #010301", "+ c #020000", "@ c #000105", "# c #000007", "$ c #000400", "% c #000500", "& c #000600", "* c #000700", "= c #070000", "- c #00000A", "; c #03060F", ": c #030902", "> c #030E02", ", c #050E04", "< c #030B0D", "1 c #080201", "2 c #000312", "3 c #020410", "4 c #030610", "5 c #040712", "6 c #010E11", "7 c #000F12", "8 c #040813", "9 c #051104", "0 c #091605", "q c #0A1807", "w c #031114", "e c #021417", "r c #041012", "t c #00171D", "y c #071B1F", "u c #0C1719", "i c #160302", "p c #1B0100", "a c #1A0403", "s c #1B0403", "d c #1A0404", "f c #1C0100", "g c #1C1313", "h c #070C21", "j c #050D2F", "k c #080E23", "l c #0E142B", "z c #0C1433", "x c #0E173B", "c c #0E193E", "v c #0E2C09", "b c #132C0E", "n c #152513", "m c #14310F", "M c #0B2C32", "N c #0C3037", "B c #0D343B", "V c #142427", "C c #210403", "Z c #290201", "A c #2D0807", "S c #360A09", "D c #360B0A", "F c #321413", "G c #20351B", "H c #2D2F2F", "J c #203A3F", "K c #323333", "L c #0F1A41", "P c #0F3B43", "I c #162660", "U c #192A6A", "Y c #192B6E", "T c #1A2E74", "R c #1C2F77", "E c #1E327E", "W c #253059", "Q c #313854", "! c #293A76", "~ c #1E4A15", "^ c #24591A", "/ c #294125", "( c #384A34", ") c #2A671F", "_ c #36702B", "` c #15515C", "' c #16535F", "] c #1A6471", "[ c #1C6E7E", "{ c #254D55", "} c #374A4E", "| c #3C4256", " . c #325C64", ".. c #470D0B", "X. c #490D0B", "o. c #4D1412", "O. c #491A18", "+. c #5A110F", "@. c #5C120F", "#. c #582221", "$. c #50302F", "%. c #6C1412", "&. c #741613", "*. c #771815", "=. c #622F2D", "-. c #44673D", ";. c #4C4F5B", ":. c #5C5D62", ">. c #575E78", ",. c #52684E", "<. c #5F667E", "1. c #547076", "2. c #656F63", "3. c #606A6B", "4. c #6E717C", "5. c #70776F", "6. c #233A93", "7. c #1D7282", "8. c #2945AD", "9. c #2A47B3", "0. c #2D4BBF", "q. c #217D8E", "w. c #2B7380", "e. c #2E4DC3", "r. c #3654C6", "t. c #3755C6", "y. c #4C5884", "u. c #517E86", "i. c #4963BF", "p. c #566FCE", "a. c #3C922C", "s. c #439933", "d. c #4B9C3C", "f. c #5EAF4F", "g. c #5FA053", "h. c #6FB761", "j. c #258C9F", "k. c #2EACC4", "l. c #30B6CF", "z. c #30B7D0", "x. c #36CDE9", "c. c #3ECFEA", "v. c #3FCFEA", "b. c #6C8285", "n. c #708F95", "m. c #4DBACF", "M. c #5CD5EC", "N. c #9C1E1A", "B. c #A0302C", "V. c #874D4B", "C. c #875F5E", "Z. c #937574", "A. c #A06664", "S. c #B16A68", "D. c #CA2621", "F. c #D92924", "G. c #E6302A", "H. c #F2312C", "J. c #FF332D", "K. c #D36461", "L. c #F24F4A", "P. c #FF4C42", "I. c #FF534E", "U. c #FF7468", "Y. c #86C37B", "T. c #FA817D", "R. c #879A83", "E. c #919798", "W. c #9B9D9D", "Q. c #8FB986", "!. c #99A896", "~. c #BE9897", "^. c #A0B79B", "/. c #A9B7A6", "(. c #8093DB", "). c #8E9FDE", "_. c #A0A9CA", "`. c #B0BCE9", "'. c #9DCE94", "]. c #B3DAAC", "[. c #88E2F3", "{. c #92E3F2", "}. c #9CFFFF", "|. c #BEDDE3", " X c #BAEEF7", ".X c #C69997", "XX c #C29998", "oX c #FF8682", "OX c #FF8784", "+X c #FFBAB7", "@X c #FFBAB9", "#X c #FFBEBC", "$X c #C6C9D2", "%X c #C7DCC3", "&X c #C9D1EF", "*X c #CAE4C5", "=X c #DBEFD8", "-X c #C9F1F8", ";X c #DBE0E1", ":X c #E1E3E3", ">X c #E2EAEB", ",X c #E8EBF7", ".,X&Xp.e.9.L eX", "eX 2.%X].Y.f.s.^ eX eXeXeXeXeXeXeXeXeX | _.(.t.e.6.h eX", "eXeXn -.g.d.a.) q t 7 eXeXeXeXeXeXeXeXeXeX2 Q ! 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Increased required dh version. * debian/rules: Rewritten for dh 7. * debian/README.source: Dropped (obsolete). * debian/source/format: Added for format 3.0 (quilt). * debian/patches/585233_fix_python_26_compatibility.dpatch: Renamed to debian/patches/585233_fix_python_26_compatibility.patch. * debian/patches/608915_fix_assertion_warnings.dpatch: Renamed to debian/patches/608915_fix_assertion_warnings.patch. * debian/patches/00list: Renamed to debian/patches/series and adjusted. -- Daniel Leidert (dale) Sat, 26 Nov 2011 01:04:45 +0100 bkchem (0.13.0-3) unstable; urgency=low * debian/control (Standards-Version): Bumped to 3.9.1. (Vcs-Browser): Point to real location. * debian/copyright: Update. Added missing bits for Pmw. * debian/TODO: Updated. * debian/patches/585233_fix_python_26_compatibility.dpatch: Adjusted. - Fix remaining instances of string exception left (closes: #585233). * debian/patches/608915_fix_assertion_warnings.dpatch: Added. - Fix syntax warnings about asserts always being true (closes: #608915). * debian/patches/00list: Adjusted. -- Daniel Leidert (dale) Tue, 08 Feb 2011 02:51:48 +0100 bkchem (0.13.0-2) unstable; urgency=low * debian/control (Standards-Version): Bumped to 3.9.0. (Build-Depends): Added dpatch. Replaced python-all-dev by python and fix build-depends-on-python-dev-with-no-arch-any. (Vcs-Svn): Fixed vcs-field-uses-not-recommended-uri-format. (Depends): Fixed debhelper-but-no-misc-depends. (Description): Removed implementation language. * debian/rules: Added dpatch infrastructure. (binary-indep): Removed deprecated dh_desktop. (.PHONY): Dropped configure target. * debian/watch: Slightly improved. * debian/README.source: Added because of patch system. * debian/patches/585233_fix_python_26_compatibility.dpatch: Added. - Fix string exceptions no more allowed in Python 2.6 (closes: #585233). * debian/patches/00list: Added accordingly. -- Daniel Leidert (dale) Fri, 23 Jul 2010 23:45:25 +0200 bkchem (0.13.0-1) unstable; urgency=low * New upstream release 0.13.0. * debian/control (Vcs-Svn): Fixed. -- Daniel Leidert (dale) Mon, 23 Feb 2009 22:43:18 +0100 bkchem (0.12.6-1) unstable; urgency=low * New upstream release 0.12.6. -- Daniel Leidert (dale) Wed, 18 Feb 2009 01:13:32 +0100 bkchem (0.12.5-2) unstable; urgency=low * Upload to unstable. * debian/README.Debian: Fixed two typos. Thanks to lintian. -- Daniel Leidert (dale) Sun, 15 Feb 2009 19:37:35 +0100 bkchem (0.12.5-1) experimental; urgency=low * New upstream release 0.12.5. -- Daniel Leidert (dale) Mon, 01 Dec 2008 00:47:01 +0100 bkchem (0.12.4-1) experimental; urgency=low * New upstream release 0.12.4. -- Daniel Leidert (dale) Sun, 02 Nov 2008 11:43:18 +0100 bkchem (0.12.3-1) experimental; urgency=low * New upstream release 0.12.3. * debian/bkchem.1: Rewritten in pure GROFF. * debian/bkchem.1.xml: Therefor removed. * debian/bkchem.doc-base (Title, Abstract): Improved wording. * debian/bkchem.links: Added tocreate links in the hicolor theme. * debian/control (Build-Depends): Removed dpatch, docbook-xsl and xsltproc. Split packages into Build-Depends and Build-Depends-Indep. (Standards-Version): Bumped to 3.8.0 (no other changes). (Vcs-Svn): Set to experimental location. * debian/rules: Removed dpatch stuff. Removed code related to debian/bkchem.1 creation. (install): Install into /usr/lib/bkchem and strip DESTDIR. So we can install without patching upstream build system. Further remove API documentation and some files, that were removed by patch in earlier package versions. * debian/patches/: Removed. We can use the build system without patching. -- Daniel Leidert (dale) Mon, 13 Oct 2008 13:19:24 +0200 bkchem (0.12.2-1) unstable; urgency=low * New upstream release 0.12.2. -- Daniel Leidert (dale) Sat, 07 Jun 2008 18:35:55 +0200 bkchem (0.12.1-1) unstable; urgency=low * New upstream version 0.12.1. * debian/bkchem.1: Added. * debian/bkchem.1.xml: Updated. * debian/bkchem.doc-base (Section): Fixed accordingly to latest doc-base policy version 0.8.10. * debian/control: Added DM-Upload-Allowed for DM status. (Architecture): This is an architecture-independent package. (Uploaders): Removed LI as he retired from the team. Thanks for your work! * debian/copyright: Updated. * debian/rules: Removed several spaces. (build): Added target to create man-page. (install): Don't hardcode python version when removing files. (binary-indep, binary-arch): This is an architecture-independent package. -- Daniel Leidert (dale) Sun, 18 May 2008 03:17:10 +0200 bkchem (0.12.0-1) unstable; urgency=low * First official build for Debian unstable (closes: #310165). * New upstream release 0.12.0. - debian/patches/03_oasa_future.dpatch: removed. - debian/patches/00list: updated. -- LI Daobing Sun, 16 Dec 2007 15:04:26 +0800 bkchem (0.11.6-1) unstable; urgency=low * New upstream release 0.11.6. [ Daniel Leidert ] * debian/bkchem.install: Install the official icon to pixmaps path. * debian/bkchem.menu: Adjusted icon path. (section): Menu section transition. * debian/bkchem_icon.xpm: Removed. * debian/control: Homepage field transition. Added Vcs-* fields. (Maintainer): Set the team as maintainer. * debian/copyright: Adjusted copyright. Fixed a typo. * debian/watch: Added. [ Michael Banck ] * debian/bkchem.install: Do not install the removed reportbug override. * debian/control (Uploaders): Added myself. * debian/README.Debian: Removed unofficial notice. * debian/reportbug/control: Removed. [ LI Daobing ] * debian/control: add me to uploaders. * debian/control: bump standards version to 3.7.3. * port to python-support. - debian/control: update - debian/rules: update - debian/compat: bump compat level to 5 - debian/patches/02_fix_build_issues.dpatch: update * debian/bkchem.doc-base: remove blank line to satisfy lintian. * menu file like xpm file as icon - debian/bkchem.xpm: added, convert from bkchem.png and resize to 32x32 - debian/bkchem.install: install debian/bkchem.xpm - debian/bkchem.menu: updated * debian/bkchem.dirs: don't install usr/share/bug/bkchem. * debian/patches/03_oasa_future.dpatch: python2.5 raise Syntax Error if 'from __future__' is not in the begin. * debian/patches/04_bkchem_bkchem.dpatch: add current dir to sys.path * debian/patches/02_fix_build_issues.dpatch: + use sys.version instead of hard coded version + use `exec' in /usr/bin/bkchem * add desktop file support: + debian/bkchem.desktop: added + debian/bkchem.install: updated + debian/rules: add dh_desktop * add mime support: + debain/bkchem.sharedmimeinfo: added + debian/rules: add dh_installmime + debian/bkchem.desktop: add mime part -- LI Daobing Sun, 16 Dec 2007 14:50:27 +0800 bkchem (0.11.4-0dl1) unstable; urgency=low * New upstream release 0.11.4. -- Daniel Leidert (dale) Mon, 6 Mar 2006 00:05:35 +0100 bkchem (0.11.3-0dl1) unstable; urgency=low * New upstream release 0.11.3. * debian/README.Debian: Updated. * debian/TODO: Updated. Replaces TODO.Debian. * debian/rules: Build the manpage during build target. * debian/control: Ditto. Added necessary build-dependencies. * This package also fixes the problem, that bkchem was installed to /usr/share/python-support. -- Daniel Leidert (dale) Thu, 16 Feb 2006 00:56:27 +0100 bkchem (0.11.2-0dl1) unstable; urgency=low * New upstream release 0.11.2. * debian/rules: scratch.py was removed from upstream. * debian/README.Debian: python2.3-cairo is part of Debian since a while. -- Daniel Leidert (dale) Wed, 11 Jan 2006 21:44:01 +0100 bkchem (0.11.1-0dl1) unstable; urgency=low * New upstream release 0.11.1. * debian/README.Debian: Removed contrib-comment. * debian/rules: Also remove scratch.py from package. -- Daniel Leidert (dale) Thu, 29 Dec 2005 13:32:07 +0100 bkchem (0.11.0-0dl1) unstable; urgency=low * New upstream release 0.11.0. * Moved package to main (no longer needs python2.3-profiler) - thanks to LI Daobing for pointing this out. * Fixed debian/copyright - updated local license link and FSF address. -- Daniel Leidert (dale) Thu, 29 Sep 2005 20:15:45 +0200 bkchem (0.10.2-0dl0) unstable; urgency=low * New upstream release 0.10.2. * Added suggestion to install python2.3-cairo. -- Daniel Leidert (dale) Sat, 16 Jul 2005 16:25:00 +0200 bkchem (0.10.1-0dl0) unstable; urgency=low * New upstream release 0.10.1. * Removed 01_xml_dtd.dpatch - doc.xml is not longer distributed. -- Daniel Leidert (dale) Tue, 5 Jul 2005 01:09:29 +0200 bkchem (0.10.0-0dl1) unstable; urgency=low * Fixed: 02_fix_build_issues.dpatch - add fix for plugin path. -- Daniel Leidert (dale) Sun, 26 Jun 2005 02:24:13 +0200 bkchem (0.10.0-0dl0) unstable; urgency=low * New upstream release 0.10.0. * Fixed: 02_fix_build_issues.dpatch - setup.py has changed and the patch was fixed. * Fixed: doc-base entry now contains the right section and a better abstract. * Fixed: copyright should be complete now (missed Piddle notes). * Updated: manpage now considers -b option. * Updated: standards version now is 3.6.2.1. * Added: icon for menu entry. -- Daniel Leidert (dale) Sun, 26 Jun 2005 00:49:52 +0200 bkchem (0.9.0-0dl0) unstable; urgency=low * New upstream release 0.9.0. * Package building now uses dpatch. * Package moved into contrib. -- Daniel Leidert (dale) Sat, 30 Apr 2005 17:31:38 +0200 bkchem (0.8.0-0dl0) unstable; urgency=low * New upstream release. -- Daniel Leidert (dale) Tue, 14 Sep 2004 04:51:48 +0200 bkchem (0.7.1-0dl0) unstable; urgency=low * Initial Release. -- Daniel Leidert (dale) Thu, 19 Aug 2004 13:02:27 +0200