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#1347 MassToFormulaTool MfRange violation
When adding an element rule (IRule) to the MassToFormulaTool, the element occurrence bounds (set via a MolecularFormulaRange that is passed as parameter to the element rule), are not fully observed by the MassToFormulaTool.
A calculation for mass 101.01 for elements C,H,N,O with a mass tolerance of 0.5 and element occurrence limits of 0-30 for all elements but Carbon, which is set to 6-7 instead, results in the sum formula C4H11N3, violating the Carbon lower bound.
Hi Stephan,
Do you have a code example so i can debug?
Hi John,
I do indeed. Please see attachment.
I didn't change the tolerance value in the code example as it does not make
a difference.
Cheers,
Stephan
From: John May [mailto:jwmay@users.sf.net]
Sent: 23 July 2014 14:58
To: [cdk:bugs]
Subject: [cdk:bugs] #1347 MassToFormulaTool MfRange violation
Hi Stephan,
Do you have a code example so i can debug?
[bugs:#1347] http://sourceforge.net/p/cdk/bugs/1347 MassToFormulaTool
MfRange violation
Status: open
Group: cdk-1.4.x
Created: Wed Jul 23, 2014 09:22 AM UTC by SBeisken
Last Updated: Wed Jul 23, 2014 09:22 AM UTC
Owner: nobody
When adding an element rule (IRule) to the MassToFormulaTool, the element
occurrence bounds (set via a MolecularFormulaRange that is passed as
parameter to the element rule), are not fully observed by the
MassToFormulaTool.
A calculation for mass 101.01 for elements C,H,N,O with a mass tolerance of
0.5 and element occurrence limits of 0-30 for all elements but Carbon, which
is set to 6-7 instead, results in the sum formula C4H11N3, violating the
Carbon lower bound.
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Related
Bugs:
#1347MassToFormulaTool has been deprecated since CDK version 1.5.10.
Please use the new MolecularFormulaGenerator class, which does not suffer from this bug.
John, I haven't updated these things recently, but this is basically what the @cdk.bug tag is for... to have the JavaDoc point to bug reports for open issues, which can include bugs that may never get fixed. That way, users can see what issues there are with some code.