Re: [Rdkit-discuss] rdkit.Chem.Draw.spingCanvas.py (and py27 aggdraw / cairo help?)
Hi Greg, Greg wrote: The attached .pyd is 32-bit aggdraw build for python2.7 on windows. I tested it very briefly and it seems to work; let me know if you have problems with it. It works a treat - very much appreciated! My molecules have never looked better : ) __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies Oakdene Court 613 Reading Road Winnersh, Berkshire RG41 5UA. Tel: +44 118 977 3133 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the Company address and registration details link at the bottom of the page.. __ -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] rdkit.Chem.Draw.spingCanvas.py (and py27 aggdraw / cairo help?)
Hi James, On Thu, Jun 9, 2011 at 8:22 PM, James Davidson j.david...@vernalis.com wrote: [...] File C:\Python26\RDKit_2011_03_2\rdkit\Chem\Draw\__init__.py, line 54, in MolToImage canvas = Canvas(img) File C:\Python26\RDKit_2011_03_2\rdkit\Chem\Draw\cairoCanvas.py, line 38, in __init__ imgd = image.tostring(raw,BGRA) File C:\Python26\lib\site-packages\PIL\Image.py, line 516, in tostring e = _getencoder(self.mode, encoder_name, args) File C:\Python26\lib\site-packages\PIL\Image.py, line 389, in _getencoder return apply(encoder, (mode,) + args + extra) type 'exceptions.SystemError': unknown raw mode I don't know exactly about the other problems, but this one should be related to the version of the installed PIL. If I remember correctly, BGRA raw mode requires PIL 1.1.7. Regards, Riccardo -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] rdkit.Chem.Draw.spingCanvas.py (and py27 aggdraw / cairo help?)
Dear Greg, Riccardo, et al. Riccardo wrote: I don't know exactly about the other problems, but this one should be related to the version of the installed PIL. If I remember correctly, BGRA raw mode requires PIL 1.1.7. @Riccardo - Thanks for the advice, Riccardo. I think I was already on 1.1.7 - but maybe an alpha release(?) Anyway, I have now standardised across Python 2.6 and 2.7 with the latest PIL installers from http://www.pythonware.com/products/pil/. Greg wrote: I will try to do an aggdraw build for 2.7. If I succeed, I'll post something. @Greg - Thanks for the kind offer. I for one would be very pleased to be using aggdraw again (as I think the image quality seems the best). I am pleased to say, however, that it is less critical now that I have worked through my cairo issues! : ) Previously I was getting: Python 2.7.1 (r271:86832, Nov 27 2010, 18:30:46) [MSC v.1500 32 bit (Intel)] on win32 Type copyright, credits or license() for more information. from rdkit import Chem from rdkit.Chem import AllChem, Draw mol = Chem.MolFromSmiles(c1c1) AllChem.Compute2DCoords(mol) im = Draw.MolToImage(mol) !!!PYTHONW.EXE CRASH!!! Finally, after a morning of going round in circles (and following red-herring Dependency Walker trails(!)), things are running well; with RDKit now happily calling cairo! I thought it might be useful for others to list the versions of software / DLLs that I finally found to work: Windows XP Pro. SP3 (32-bit) Python 2.7.1 (http://www.python.org/ftp/python/2.7.1/python-2.7.1.msi) PIL 1.1.7 (installer - http://effbot.org/downloads/PIL-1.1.7.win32-py2.7.exe) Pycairo-1.8.10.win32-py2.7 (installer - http://ftp.gnome.org/pub/GNOME/binaries/win32/pycairo/1.8/pycairo-1.8.10 .win32-py2.7.exe) Libcairo-2.dll (get from the following archive: http://wxpython.org/cairo/cairo_1.8.6-1_win32.zip) libpng12-0.dll (get from the following archive: http://wxpython.org/cairo/libpng_1.2.34-1_win32.zip) Zlib1.dll (get from the following archive: http://wxpython.org/cairo/zlib123-dll.zip) I then put the 3 DLLs into the C:\Python27\Lib\site-packages\cairo\ folder, and made sure that this is on the system path. The use of the wxPython DLLs seemed to be the key to sorting things out (I certainly tried a few other versions!) - thanks to Alex Matan's blog-post for the instructions (http://electromagnetictelegraph.com/install-cairo-wxpyton-pycairo-pytho n-windows) The setup under 2.6 was exactly the same - except I used the corresponding 2.6 installer for PIL, and used the Pycairo-1.8.4.win32-py26 from the wxPython site (http://wxpython.org/cairo/pycairo-1.8.4.win32-py2.6.exe) as detailed in Alex's blog. I can add these instructions to to the wiki if you like(?) Kind regards James __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies Oakdene Court 613 Reading Road Winnersh, Berkshire RG41 5UA. Tel: +44 118 977 3133 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the Company address and registration details link at the bottom of the page.. __ -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] rdkit.Chem.Draw.spingCanvas.py (and py27 aggdraw / cairo help?)
Dear All, I am in the process of upgrading to python 2.7 under Windows, and part of this has included moving to the RDKit_2011_03_2 (py27) build. I had previously done most work with earlier versions of RDKit under python 2.6, but have found a problem with calling Draw.MolToImage() with the latest RDKit binary for both py26 and py27: Traceback (innermost last): File C:\Python26\lib\site-packages\Pmw\Pmw_1_3\lib\PmwBase.py, line 1747, in __call__ return apply(self.func, args) File C:\Python26\lib\site-packages\pmg_tk\startup\VerMOL.py, line 1188, in lambda command=lambda s=self:s.draw_ligand(self.modelling_chainlist.listbox, self.ligcanvas, self.smiles, '3D',200,200, 'modelling_lig_image')) File C:\Python26\lib\site-packages\pmg_tk\startup\VerMOL.py, line 2871, in draw_ligand im = Draw.MolToImage(mol, size=(x,y)) File C:\Python26\RDKit_2011_03_2\rdkit\Chem\Draw\__init__.py, line 71, in MolToImage drawer.AddMol(mol,**kwargs) File C:\Python26\RDKit_2011_03_2\rdkit\Chem\Draw\MolDrawing.py, line 361, in AddMol color=color,width=width,color2=color2) File C:\Python26\RDKit_2011_03_2\rdkit\Chem\Draw\MolDrawing.py, line 190, in _drawBond dash=self.dash) File C:\Python26\RDKit_2011_03_2\rdkit\Chem\Draw\MolDrawing.py, line 169, in _drawWedgedBond self.canvas.addCanvasDashedWedge(poly[0],poly[1],poly[2],color=color) File C:\Python26\RDKit_2011_03_2\rdkit\Chem\Draw\spingCanvas.py, line 104, in addCanvasDashedWedge pts1 = _getLinePoints(p1,p2,dash) type 'exceptions.NameError': global name '_getLinePoints' is not defined Not a big problem to sort - I think spingCanvas.addCanvasDashedWedge() should read: pts1 = self._getLinePoints(p1,p2,dash) pts2 = self._getLinePoints(p1,p3,dash) on lines 104, 105 instead of: pts1 = _getLinePoints(p1,p2,dash) pts2 = _getLinePoints(p1,p3,dash) Anyway, this is only a problem if spingCanvas is being called - which I think only happens as a last resort if aggdraw or cairo aren't found. So on that note, the reason I was calling spingCanvas was that I don't have a build of aggdraw for python 2.7, and I have found that when cairo/pycairo are available to python 2.7 I get a pythonw.exe Application Error at the point of calling Draw.MolToImage(). Under python 2.6 I thought I would see what would happen if I removed aggdraw to force cairo into play (different version of PIL, different version of cairo - not an ideal comparison!): File C:\Python26\RDKit_2011_03_2\rdkit\Chem\Draw\__init__.py, line 54, in MolToImage canvas = Canvas(img) File C:\Python26\RDKit_2011_03_2\rdkit\Chem\Draw\cairoCanvas.py, line 38, in __init__ imgd = image.tostring(raw,BGRA) File C:\Python26\lib\site-packages\PIL\Image.py, line 516, in tostring e = _getencoder(self.mode, encoder_name, args) File C:\Python26\lib\site-packages\PIL\Image.py, line 389, in _getencoder return apply(encoder, (mode,) + args + extra) type 'exceptions.SystemError': unknown raw mode If it helps, I can follow-up with more details on exact versions of DLLs, etc; but for now wondered if: (a) anybody had a version of aggdraw for windows, built with python 2.7? (b) or any recommendations for reliable PIL / cairo / pycairo combinations for python 2.7 / windows? Kind regards James __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies Oakdene Court 613 Reading Road Winnersh, Berkshire RG41 5UA. Tel: +44 118 977 3133 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the Company address and registration details link at the bottom of the page.. __-- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking.
