Re: [Rdkit-discuss] svg export from rdkit messed up in Adobe Illustrator , but not in firefox / chrome: fixes?
I just re-tried the rdkit generated svg files in Adobe Illustrator CS5 and it works just fine. So whatever oddity there was in Adobe Illustrators handling of rdkit (and cairo) generated svg seems to be fixed. I am using the svn build of rdkit on Leopard OSX. svn release 1632 Thought I would post it to this thread for completeness sake Hari On Mon, Sep 27, 2010 at 10:25 AM, hari jayaram hari...@gmail.com wrote: I tied the hack , i.e scaling all the glyphs down. The scaled down glyphs - appear scaled down in Inkscape and other svg viewers. The adobe Illustrator glyph is still humongous and enlarged I filed a bug report at Adobe Illustrator forums and the bug report section saying svg support seems broken. For now I am editing the structures as ps objects which rdkit outputs. Thanks to your suggestion I now know what the glyphs are and a little more about svg. Hari On Fri, Sep 24, 2010 at 9:17 AM, Paul Emsley paul.ems...@bioch.ox.ac.ukwrote: As a hack, I suppose that you could add transform=scale(0.2) (or some such) to the attributes of the paths for the glyph symbols. i.e. replace path style=stroke:none; d=M 0.5 1.765625 L 0.5 -7.046875 L 5.5 -7.046875 L 5.5 1.765625 L 0.5 1.765625 Z M 1.0625 1.21875 L 4.9375 1.21875 L 4.9375 -6.484375 L 1.0625 -6.484375 L 1.0625 1.21875 Z M 1.0625 1.21875 / with path transform=scale(0.2) style=stroke:none; d=M 0.5 1.765625 L 0.5 -7.046875 L 5.5 -7.046875 L 5.5 1.765625 L 0.5 1.765625 Z M 1.0625 1.21875 L 4.9375 1.21875 L 4.9375 -6.484375 L 1.0625 -6.484375 L 1.0625 1.21875 Z M 1.0625 1.21875 / and do that for each of the glyphs. Paul. -- Nokia and ATT present the 2010 Calling All Innovators-North America contest Create new apps games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] svg export from rdkit messed up in Adobe Illustrator , but not in firefox / chrome: fixes?
I tied the hack , i.e scaling all the glyphs down. The scaled down glyphs - appear scaled down in Inkscape and other svg viewers. The adobe Illustrator glyph is still humongous and enlarged I filed a bug report at Adobe Illustrator forums and the bug report section saying svg support seems broken. For now I am editing the structures as ps objects which rdkit outputs. Thanks to your suggestion I now know what the glyphs are and a little more about svg. Hari On Fri, Sep 24, 2010 at 9:17 AM, Paul Emsley paul.ems...@bioch.ox.ac.ukwrote: As a hack, I suppose that you could add transform=scale(0.2) (or some such) to the attributes of the paths for the glyph symbols. i.e. replace path style=stroke:none; d=M 0.5 1.765625 L 0.5 -7.046875 L 5.5 -7.046875 L 5.5 1.765625 L 0.5 1.765625 Z M 1.0625 1.21875 L 4.9375 1.21875 L 4.9375 -6.484375 L 1.0625 -6.484375 L 1.0625 1.21875 Z M 1.0625 1.21875 / with path transform=scale(0.2) style=stroke:none; d=M 0.5 1.765625 L 0.5 -7.046875 L 5.5 -7.046875 L 5.5 1.765625 L 0.5 1.765625 Z M 1.0625 1.21875 L 4.9375 1.21875 L 4.9375 -6.484375 L 1.0625 -6.484375 L 1.0625 1.21875 Z M 1.0625 1.21875 / and do that for each of the glyphs. Paul. -- Nokia and ATT present the 2010 Calling All Innovators-North America contest Create new apps games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] svg export from rdkit messed up in Adobe Illustrator , but not in firefox / chrome: fixes?
As a hack, I suppose that you could add transform=scale(0.2) (or some such) to the attributes of the paths for the glyph symbols. i.e. replace path style=stroke:none; d=M 0.5 1.765625 L 0.5 -7.046875 L 5.5 -7.046875 L 5.5 1.765625 L 0.5 1.765625 Z M 1.0625 1.21875 L 4.9375 1.21875 L 4.9375 -6.484375 L 1.0625 -6.484375 L 1.0625 1.21875 Z M 1.0625 1.21875 / with path transform=scale(0.2) style=stroke:none; d=M 0.5 1.765625 L 0.5 -7.046875 L 5.5 -7.046875 L 5.5 1.765625 L 0.5 1.765625 Z M 1.0625 1.21875 L 4.9375 1.21875 L 4.9375 -6.484375 L 1.0625 -6.484375 L 1.0625 1.21875 Z M 1.0625 1.21875 / and do that for each of the glyphs. Paul. -- Nokia and ATT present the 2010 Calling All Innovators-North America contest Create new apps games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] svg export from rdkit messed up in Adobe Illustrator , but not in firefox / chrome: fixes?
Hi Greg and everyone , I do have cairo installed import cairo Works fine To generate the svg , I am using the MolToFile method from Chem.Draw from rdkit.Chem.Draw import MolToFile self.rdkitmolecule = rdkit.Chem.MolFromSmiles(self.smiles_string) def make_svg_file(self): return MolToFile(self.rdkitmolecule,%s.svg % self.compound_id) I think its Adobe Illustrator CS3 thats screwing up, since the svg works just fine in Inkscape, Chrome browser and Firefox and also validates with the w3c svg validator. I was just hoping there is a way to tweak the file to have it not blow up my font characters in Adobe Illustrator. Its sad that a commercial solution like Illustrator does not support true SVG. screenshot attached: Thanks Hari Hari On Thu, Sep 23, 2010 at 2:08 AM, Greg Landrum greg.land...@gmail.com wrote: Dear Hari, On Wed, Sep 22, 2010 at 9:23 PM, hari jayaram hari...@gmail.com wrote: Adobe illustrator reads in the SVG , however the atom alphabets are a few inches across despite the bonds showing up normally. Adobe Illustrator draws the Oxygen, Nitrogen and Carbon atoms are in font-size 60 or 80 and positioned at a random point above the molecule. The svg does validate with the w3c validator and is openable with Chrome and Firefox without any distortion ,so it seems that Adobe Illustrator is screwing up. Does anyone know how to correct the SVG file to not have this happen. I apologize that this is not strictly a rdkit question , but just asking in case others have successfully used the rdkit generated svg in a vector drawing program. I'd like to know if the SVG in question is from my code or from cairo, can you please let me know if you have cairo installed (to check start python and type import cairo) and, if so, what you did to generate the SVG? Best, -greg attachment: screenshot_svg_mol_in_adobe_illustrator.PNG-- Nokia and ATT present the 2010 Calling All Innovators-North America contest Create new apps games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
