I do not think the trigger should be removed from the main SMILES parser it should however be accepted in JChemPaint (e.g. when you paste a SMILES string).

If you get the SMILES from the clipboard just run it through a regex to remove the newlines/spaces.

J

On 31 Oct 2012, at 18:17, Egon Willighagen <egonw@users.sf.net> wrote:

Point taken...

The Open SMILES specification writes, however:

"A SMILES string is terminated by a whitespace terminator character (space, tab, newline, carriage-return), or by the end of the string."

Not sure what to do here...


bugs:1272 single spaces in SMILES shouldn't trigger syntax error

Status: open Created: Wed Oct 31, 2012 06:06 PM UTC by Ralf Stephan Last Updated: Wed Oct 31, 2012 06:11 PM UTC Owner: nobody

it's the bazillionth time I cut&paste a multiline SMILES in a program to parse it: the newlines get converted to spaces and those trigger a syntax error. Then I go hunting the spaces in the overly long line. PLEASE remove this feature. My guess is that half of the people who gave up on chemistry software quit because of this silly inflexibility.


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