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[Joelib-help] Aromaticity in SD files
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From: Joerg K. W. <we...@in...> - 2003-11-18 16:31:47
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Hi Wayne, ah, o.k., but that's not a bug that's a feature! These bonds are aromatic and you will find this also in the SD-FILE definition of MDL. That why you should use JOELib or OpenBabel, because they have a really great chemical expert system behind 'simple' file conversion. Only if you know aromatic atoms/bonds you can create e.g. a MOL2 file !!! 1. If you don't want that, you should use your own SDF writer resolving the aromaticity flags into a conjugated system using single and double bonds. Just modify joelib.io.types.MDLSD to joelib.io.types.MyMDLSD and tell joelib the new defintion at joelib.properties joelib.filetypes.1.name = SDF joelib.filetypes.1.representation = joelib.io.types.MyMDLSD 2. The unelegant way would be to supress the aromaticity typer, by saying: 'aromaticity was already assigned' ! Which will cause a lot of problems, e.g. if you will try to find aromatic rings or much more serious assigning correct atom types for general file conversions ... Regards, Joerg > Thanks Joerg. I'll follow your suggestions, in particular I'll grab the > latest release. You can see the exact problem I had in the atom > connection section of the sd file, I've grabbed just a few lines to > illustrate : > > Input file : > 4 5 2 0 0 0 0 > 4 9 1 0 0 0 0 > 5 6 1 0 0 0 0 > 5 19 1 0 0 0 0 > 6 7 2 0 0 0 0 > > Output file : > 4 5 4 0 0 0 0 > 4 9 4 0 0 0 0 > 5 6 4 0 0 0 0 > 5 19 1 0 0 0 0 > 6 7 4 0 0 0 0 > > See all the 4's? > > I'll try grabbing the latest release and see if that works--I had bad > timing, you must have put up the new release a day or two after I > downloaded JOELib. I'll use one of the mailing lists if I still have a > problem. > > Thanks > Wayne > > >>-----Original Message----- >>From: Joerg K. Wegner [mailto:we...@in...] >>Sent: Tuesday, November 18, 2003 2:47 AM >>To: Wayne Volkmuth >>Subject: Re: JOELib question >> >>Hi Wayne, >> >>1. New release was submitted yesterday with improved PDF writer. >> >>2. I don't get it. What is the exact problem ? >>I've simply replaced "out.sdf" by "out.pdf" and here is the result. > > I've > >>shortly compared this to the original 55.sdf and can't see any > > problems. > >>Your code works as it should or did you expect another result ? >> >>3.1. Please explain problems in more detail and contact me again. >>You can also use the helping mailing or developer mailing list for >>further responses to avoid e-mail redundancies. >>3.2. You are still using a simple writer, if you want handle special >>cases like corrupted input SDF entries (e.g. missing bond definitions) >>or somethings else you should use the complex reader/writer mechanism >>explained in joelib.test.ConvertSkip >> >>BTW, image output properties can be set in joelib.properties, look for >>Renderer2DModel and Mol2Image and PDF options ! >> >>Regards, Joerg >> >> >>>I downloaded JOELib a few days ago and got stuck with simply reading > > in > >>>an sd file then writing it back out. I've attached the short > > program I > >>>wrote, along with test input and output. I'm getting ring > > structures > >>>that have four bonds shared between the atoms, I'm not sure what I'm >>>doing wrong. I'd appreciate it if you are able to tell me what I > > should > >>>be doing. >>> >>> >>> >>>Thanks >>> >>>Wayne >>> >>> > > ------------------------------------------------------------------------ > >>------------------------- >> >>>This email may contain material that is confidential and privileged > > and > >>>is for the sole use of the intended recipient. Any review, reliance > > or > >>>distribution by others or forwarding without express permission is >>>strictly prohibited. If you are not the intended recipient, please >>>contact the sender and delete all copies. >>> >> >> >>-- >>Dipl. Chem. Joerg K. Wegner >>Center of Bioinformatics Tuebingen (ZBIT) >>Department of Computer Architecture >>Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany >>Phone: (+49/0) 7071 29 78970 >>Fax: (+49/0) 7071 29 5091 >>E-Mail: mailto:we...@in... >>WWW: http://www-ra.informatik.uni-tuebingen.de >>-- >>Never mistake motion for action. >> E. Hemingway > > > > --------------------------------------------------------------------------------------------------------------------- > This email may contain material that is confidential and privileged and is for the sole use of the intended recipient. Any review, reliance or distribution by others or forwarding without express permission is strictly prohibited. If you are not the intended recipient, please contact the sender and delete all copies. > > -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. E. Hemingway |
