As I said in my last email in the thread, I wasn't adhering to the column standard.

David


On 5 February 2013 22:23, Robert Hanson <hansonr@stolaf.edu> wrote:
David,

Where's your third coordinate? Are these 2D mol files? If so, they are not identifying themselves as such in the second line. See, for example, http://c4.cabrillo.edu/404/ctfile.pdf, particularly Chapters 2 and 4. These are rigidly formatted files. For example, the atom lines must be of the following format, as described in Chapter 2:

xxxxx.xxxxyyyyy.yyyyzzzzz.zzzz aaaddcccssshhhbbbvvvHHHrrriiimmmnnneee

I think your file doesn't have that format, from the looks of it.

Bob






On Sun, Feb 3, 2013 at 4:21 PM, N David Brown <hubdave@gmail.com> wrote:

After quickly writing a MolFile generator for some fictional structures, the generated MolFile strings load acceptably in Jmol but produce several error lines containing '0 0' is not a recognized symbol.

Any idea why? Here's an example file:

unknown
NDB/matchbOx/03022013221425

 4 4 0 0 0 0 0 0 0 0 1 V2000
   0.0000 0.0000 0 C 0 0 0 0 0 0 0 0 0 0 0 0
   0.0000 1.0000 0 C 0 0 0 0 0 0 0 0 0 0 0 0
   1.0000 0.0000 0 C 0 0 0 0 0 0 0 0 0 0 0 0
   1.0000 1.0000 0 C 0 0 0 0 0 0 0 0 0 0 0 0
 1 4 1 0 0 0 0
 1 2 1 0 0 0 0
 2 3 1 0 0 0 0
 3 4 1 0 0 0 0
M END
$$$$

Even the cited benzene example here generates a '' is not a recognized symbol.

David


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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900