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Feature #1247

fix hardcoded references to atom names in analysis tools

Added by Mark Abraham over 6 years ago. Updated about 5 years ago.

Status:
New
Priority:
Normal
Assignee:
Category:
analysis tools
Target version:
Difficulty:
uncategorized
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Description

Analysis tools tend to have code that is based on assumptions about atom names, that (e.g.) get invalidated when we add CHARMM into the mix, because it names amide nitrogen HN, not H. Several past bug-fixes have fixed individual cases of this.

This kind of stuff should be re-implemented, either by calling the selection machinery with logic that is constructed in a single place, or by deprecating a specific tool in favour of calling a general tool with a specific selection.


Related issues

Related to GROMACS - Bug #953: fix for g_chi omega angle calculationClosed06/02/2012

History

#1 Updated by Mark Abraham over 6 years ago

  • Description updated (diff)

#2 Updated by Mark Abraham over 6 years ago

  • Target version changed from future to 5.0

#3 Updated by Mark Abraham over 6 years ago

  • Assignee changed from David van der Spoel to Mark Abraham

#4 Updated by Mark Abraham over 5 years ago

  • Target version changed from 5.0 to future

#5 Updated by Erik Lindahl about 5 years ago

  • Tracker changed from Bug to Feature

One could argue that the present behavior is buggy, but since it was intentionally (=stupidly) coded this way, I'm changing it to a feature since we'll need to rework things quite a bit.

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