From: SourceForge.net <no...@so...> - 2004-08-03 11:44:58
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Feature Requests item #1002202, was opened at 2004-08-02 21:45 Message generated for change (Comment added) made by nicove You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1002202&group_id=23629 Category: New IO Format Group: v10 Status: Open Priority: 5 Submitted By: Nico (nicove) Assigned to: Nobody/Anonymous (nobody) Summary: Tinker format Initial Comment: Is it possible to add the reading of the Tinker format ? The home site of Tinker is http://dasher.wustl.edu/tinker/ If it can help, I'm willing to help as developper to add this feature. Description : SAMPLE.XYZ The .xyz file is the basic TINKER Cartesian coordinates file type. It contains a title line followed by one line for each atom in the structure. Each line contains: the sequential number within the structure, an atomic symbol or name, X-, Y-, and Z-coordinates, the force field atom type number of the atom, and a list of the atoms connected to the current atom. Except for programs whose basic operation is in torsional space, all TINKER calculations are done from some version of the .xyz format. ---------------------------------------------------------------------- >Comment By: Nico (nicove) Date: 2004-08-03 13:44 Message: Logged In: YES user_id=1096197 I will try to get more information on the file format in the forums of folding@home. I let you know when I have info. If I get the answers, I don't mind working on the reader myself. BTW, I got some other files as examples. I put them in a zip. ---------------------------------------------------------------------- Comment By: Egon Willighagen (egonw) Date: 2004-08-03 12:52 Message: Logged In: YES user_id=25678 Miguel, file formats is something I can do. The rendering stuff is still out of my league, so let me take take over this request, ok? BTW, these test files are not yet in cvs, are they? I'll add them... ---------------------------------------------------------------------- Comment By: Miguel (migueljmol) Date: 2004-08-03 11:04 Message: Logged In: YES user_id=1050060 Hmmm ... each of these files has a problem ... p269_h2o has 216 atoms. The top line has the atom count of 216. This is consistent with the last line of the file. The problem with this file is ... it is not clear to me what the mechanism should be to determine what the element type is. That is, I do not know how to determine the element type from the atom names. I suggest that we try to find some examples which have element symbols with more than one character. Hopefully they will use a lower case second letter ... in order to be able to distinguish between CA (alpha carbon) and Ca (calcium) ... HG and He, etc. There are different problems with p639_L939_K12M_nat: The top line says that there are 392 atoms in the file. But, in fact, there are 393. Each of the lines is terminated by two Carriage Return characters \r and one newline character \n. In order to be cross-platform, Jmol/java needs to recognize \r as a valid end-of-line sequence (for MacOS). Therefore, the sequences \r\r\n will be recognized as as new end-of-line sequences \r and \r\n And again we have an atom naming problem ... although this one seems slightly different. This file has atom names like CH and CH2. I suppose that these are carbons ... but is there something special that would be done about the implied hydrogens? I will give you my honest feedback ... I now have concerns about supporting this file format. File formats are a nightmare. And if the Tinker developers were so sloppy in defining their format then we will have a large number of problems. At this point I am not saying no, but be advised that I am nervous :-) Miguel ---------------------------------------------------------------------- Comment By: Nico (nicove) Date: 2004-08-02 23:38 Message: Logged In: YES user_id=1096197 I will have a look at ModelResolver.java and XyzReader.java to see how I can develop the tinker reader. Thanks for your answer ---------------------------------------------------------------------- Comment By: Nico (nicove) Date: 2004-08-02 23:37 Message: Logged In: YES user_id=1096197 I put two files (200 and 400 atoms). They're the only files I have just now. Tomorrow I should be able to send other files. About your questions, I don't exactly know. I participate in a distributed computing project about protein folding (http://folding.stanford.edu) and I would like to see the proteins with jmol. ---------------------------------------------------------------------- Comment By: Miguel (michaelthoward) Date: 2004-08-02 22:56 Message: Logged In: YES user_id=608250 I think it would be straightforward to add support for this file format. It is a unfortunate that they chose .xyz as the file name extension, since this extension was taken by SGI xmol long ago. The good news is that this won't really hurt Jmol. This text description hardly qualifies as a "file format specification". Q: Is there a better description available? Q: What is meant by "atomic symbol or name" ? Q: What is a "force field atom type number" ? Please send me two files ... one with only a few atoms and one with many atoms. mi...@jm... If you want to work on this yourself, then you should check out the Jmol source from anonymous cvs. Look at src/org/jmol/adapter/smarter ... ModelResolver.java & XyzReader.java Miguel ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1002202&group_id=23629 |