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molconvert.bat cxsmarts:qh fails with explicit H
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Michiel

Joined: 23 Jan 2004
Posts: 136

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Link to postPosted: Wed Jun 24, 2009 4:20 pmPost subject: molconvert.bat cxsmarts:qh fails with explicit H Reply with quote

I'm trying to generate reaction CXSMARTS for a reaction that includes explicit H atoms in the form of H-I or H-H molecules.

When I try molconvert.bat cxsmarts:qh it fails. (see screenshot attached)

When I try molconvert.bat smarts:qh it succeeds.

When I try molconvert.bat cxsmarts:qs it succeeds.

The error is not restricted to reactions, it also occurs with single molecules.

The error message I get reads: error: 8 java.lang.ArrayIndexOutOfBoundsException: 8 (more detail in the screenshot).

I have also attached two MRV files:

1. the addition reaction of propene with HI, which fails to produce CXSMARTS with the 'qh' flags

2. the addition reaction of propene with I2, which produces output as expected with the 'qh' flags

 

This seems a bug to me. There is no indication in the documentation that this combination of flags is invalid or nonsensical.

 

Windows XP SP2

Java 1.6.0_14

Beans 5.22

 




 Filename: 2009-06-24_111908.jpg    Filesize: 215.49 KB    Viewed: 4758 Time(s)
 Description:  molconvert.bat screenshot
2009-06-24_111908.jpg

 Filename: propene+I2.mrv    Filesize: 1.76 KB    Downloaded: 219 Time(s)
 Description:  propene + I2 works

 Filename: propene+HI.mrv    Filesize: 1.67 KB    Downloaded: 393 Time(s)
 Description:  propene + HI fails
Volfi
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Joined: 07 Jun 2004
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Link to postPosted: Thu Jun 25, 2009 8:29 pmPost subject: Reply with quote

Hi,

It seems to be a bug, you are right.

The combination of the flags are valid.

Thank you for the report.

We fix it ASAP.

Andras

Volfi
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Link to postPosted: Sun Jun 28, 2009 10:12 pmPost subject: Reply with quote

Hi,

 

We have fixed the bug.

The next release will contain the fix.

Thank you for the report.

Andras

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