Last modified: 2014-07-07 06:10:47 UTC

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Bug 67075 - indigo-depict badly fails when molecules contain the "any" bond because it's query language and does not belong into a molecule


Summary:	indigo-depict badly fails when molecules contain the "any" bond because it's ...

Status:	RESOLVED WORKSFORME

Product:	MediaWiki extensions
Classification:	Unclassified
Component:	MolHandler (Other open bugs)
Version:	unspecified
Hardware:	All All

Importance:	Normal normal (vote)
Target Milestone:	---
Assigned To:	Rainer Rillke @commons.wikimedia

URL:
Whiteboard:
Keywords:

Depends on:
Blocks:
	Show dependency tree / graph

Reported:	2014-06-25 11:07 UTC by Rainer Rillke @commons.wikimedia
Modified:	2014-07-07 06:10 UTC (History)
CC List:	4 users (show)

See Also:
Web browser:	---
Mobile Platform:	---
Assignee Huggle Beta Tester:	---

Attachments
complex.mol - note the bond type "8" and MRV_COORDINATE_BOND_TYPE (2.37 KB, text/plain) 2014-06-25 11:12 UTC, Rainer Rillke @commons.wikimedia	Details
complex.mol - what marvin rendering (1.71 KB, image/png) 2014-06-25 11:14 UTC, Rainer Rillke @commons.wikimedia	Details
Add an attachment (proposed patch, testcase, etc.)

Description Rainer Rillke @commons.wikimedia 2014-06-25 11:07:43 UTC

However, Marvin & Co use this bond type for the "coordinate" bond in complexes etc. AND put them into mol files. MolHandler should probably replace them just before conversion to SVG when using indigo-depict.

Comment 1 Rainer Rillke @commons.wikimedia 2014-06-25 11:12:15 UTC

Created attachment 15734 [details]
complex.mol - note the bond type "8" and MRV_COORDINATE_BOND_TYPE

Comment 2 Rainer Rillke @commons.wikimedia 2014-06-25 11:14:08 UTC

Created attachment 15735 [details]
complex.mol - what marvin rendering

Comment 3 Gilles Dubuc 2014-07-01 11:35:10 UTC

Doesn't that sort of bug belong on the GGA side of things? Or are you planning to patch your own fork of indigo-depict?

Comment 4 Rainer Rillke @commons.wikimedia 2014-07-01 11:41:16 UTC

(In reply to Gilles Dubuc from comment #3)
> are you planning to patch your own fork of indigo-depict

Not really but we might want to return meaningful error messages and be aware of the issue. I'll try to report it upstream.

Comment 5 Rainer Rillke @commons.wikimedia 2014-07-07 06:10:47 UTC

D'oh, there is a command line switch:

-query
   Treat the input as a query molecule or reaction (disabled by default)

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