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Bug #3113

Use of read_tps_conf is depecrated

Added by Paul Bauer about 2 months ago. Updated about 2 months ago.

Status:
New
Priority:
Low
Assignee:
Category:
analysis tools
Affected version - extra info:
and all other recent versions
Affected version:
Difficulty:
uncategorized
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Description

When using legacy tools, structure files are often read in using the old call to read_tps_conf.
This routine depends on an internal conversion of the global topology to the legacy topology and reassigning of chain IDs.
But as structure files are read in as one molecule in case of them being not a TPR, all atoms are given the same chain ID during reassignment.

To avoid this causing issues with selections, the tools should not use the legacy function but one of the modern alternatives.


Related issues

Related to GROMACS - Bug #3070: make_ndx not recognizing different chainsClosed

Associated revisions

Revision 63c30db7 (diff)
Added by Paul Bauer about 2 months ago

Fix chain ID handling in make_ndx

The tool was still using the oldest possible way to read in structure
files, leading to issues with the chain IDs being overwritten and
replaced with the default id.

Fixes #3070
Refs #3113

Change-Id: I25112103a043d0266fe64c7619fe8e4abc56ffa5

History

#1 Updated by Paul Bauer about 2 months ago

  • Related to Bug #3070: make_ndx not recognizing different chains added

#2 Updated by Mark Abraham about 2 months ago

In particular, tools that write indexed output like PDB chain IDs are likely broken because of the lack of test coverage and invalid refactoring that took place.

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