[Open Babel] [ openbabel-Bugs-1364583 ] Hydrogens

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[Open Babel] [ openbabel-Bugs-1364583 ] Hydrogens

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Bugs item #1364583, was opened at 2005-11-23 12:09
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https://sourceforge.net/tracker/?func=detail&atid=428740&aid=1364583&group_id=40728

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Category: Command-line Tools
Group: 2.0 alpha/beta
Status: Open
Resolution: None
Priority: 5
Submitted By: drc (chris_swa)
Assigned to: Nobody/Anonymous (nobody)
Summary: Hydrogens

Initial Comment:
I tried the following search.

/usr/local/bin/babel /Users/user/Desktop/outputfile.fs -osmi /Users/
user/Desktop/outputfile.smi -s'C[NH2]'
192 candidates from fingerprint search phase
Bus error


I think the problem is that the original file used to generate the .fs did not
have explicit hydrogens. When I add hydrogens there is no error.

This probably raises a wider issue, when searching using a SMILES/
SMARTS that contain an explicit hydrogen the search will fail silently for
files that do not contain explicit hdrogens. Is this correct? If so should I
add a comment to the user docs that you ought to add hydrogens before
any searching?

Chris


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