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RE: [Jmol-users] Support of V3000 Mol format
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From: <her...@te...> - 2006-03-23 09:11:38
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Answers below ! Herv=E9 -----Original Message----- From: jmo...@li... [mailto:jmo...@li...] On Behalf Of Miguel Sent: jeudi 23 mars 2006 01:43 To: jmo...@li... Subject: RE: [Jmol-users] Support of V3000 Mol format Herve wrote: > But my users require support from information coming from MDL products > i.e. mol description in V2000 AND V3000. No way for me to force them = to > get only V2000. Just for my own edification ... Q: Are they all 2D files, or are some of the 3D files? [Herv=E9 Azoulay] Well ... I don't think I can answer this one. What I = can tell you is that all the molecules described in the file I sent you are correctly displayed in 3D by the MDL plug-in Q: When Chime reads a 2D file does it display it using the RasMol 3D engine? Or do they have a separate 2D renderer built into Chime? [Herv=E9 Azoulay] Don=92t know .... > File containing more than one molecule > The sample file contains more than one molecule because it's an "SD = file". > SD file is basically a grouping of mol descriptions in a file with = some > extra information (the information you want btw ...). All the = molecules > are separated with a specific string: $$$$. Ok ... it's basic but it = seems > to be widely used in industry as a way to exchange mol description. Yes. I have the MDL ctfile specification. [Herv=E9 Azoulay] OK this is where I took all the knowledge I have ... > What does Chime do? > MDL provides a number of products dealing with chemistry. They provide > chemical entity recognition component and a name to structure = component. > The name to structure sent back either a mol description or a chime > string. A chime string is an MDL encrypted, compressed version of a = mol > description (MDL proprietary algorithm). Chime strings are also = properly > displayed by the MDL chime plug-in. I understand that 'Chime string' is an encryptedversion of a 'mol description' But I am not clear what a 'mol description' is. Q: Are you using the term 'mol description' to refer to the molecular model file format? In this case .mol/V2000/V3000 ? [Herv=E9 Azoulay] yes > But chime strings does not seem to be > standard. By dealing with mol descriptions, much more things can be = done: > SD file generation for post processing ... and display with another > component ...like JMOL! > > Hope this clarifies ... I am still somewhat confused :-( Let's try a different approach. You sent me a file that contains 8 molecular models. They contain different molecules, not different conformations of the same molecule. When Jmol opens this file it should: 1. read and display only the first molecular model [Herv=E9 Azoulay] yes. I've sent you an SD file but basically I would = like to display only one molecule at a time. 2. read all of the atoms in all of the molecular models into the same = Jmol model and display them all at the same time ... essentially merging all = of the files together. [Herv=E9 Azoulay] No, see my previous answer 3. read the molecular models independently into individual Jmol 'models' [Herv=E9 Azoulay] No, see my previous answer 4. do something else Q: Which of the 4 choices above best describes your desire? [Herv=E9 Azoulay] The first one :-)! Don't worry about SD file. If I can = open a mol file whether it's V2000 or V3000 I'm the king of the world :-) ! Miguel ------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting = language that extends applications into web and mobile media. Attend the live = webcast and join the prime developer group breaking into this new coding = territory! http://sel.as-us.falkag.net/sel?cmd______________________________________= ___ ______ Jmol-users mailing list Jmo...@li... https://lists.sourceforge.net/lists/listinfo/jmol-users |