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Feature #1328

Names for selection positions

Added by Teemu Murtola about 6 years ago. Updated about 3 years ago.

Status:
Accepted
Priority:
Normal
Assignee:
-
Category:
selections
Target version:
-
Difficulty:
uncategorized
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Description

The selection engine would benefit from an additional feature: the selected positions should get user-friendly names. This would have several uses:
  • If/when a mechanism of writing a (pdb/gro) trajectory out of the selected positions is implemented, the atom/residue names in the output need to come from somewhere.
  • Some tools may want to use these in output, e.g., in the form of plot legends. For example, g_bond has a legend like "CA RES1 - O RES2".
  • Tool code would need less access to the actual atom data; it would even be possible to write them such that a custom vdwradii.dat etc. could be used to assign properties to these selected positions, even if they would not map to individual atoms.

Should be relatively straightforward to implement once it is clear what the names should consist of. Probably they need to be split to (at least) three parts: "atom" name, "residue" name, and "residue" number to accommodate the above uses. The last probably naturally maps to SelectionPosition::refId() or SelectionPosition::mappedId(), but the names are less clear. We should decide on the rules of how these names are set for different types of selections (e.g., res_com, mol_cog), and also fallbacks and/or user control for cases where it's difficult to have a generic solution (e.g., com of molecule 1 to 10); suggestions are welcome.

History

#1 Updated by Teemu Murtola over 5 years ago

  • Project changed from Next-generation analysis tools to GROMACS
  • Category set to selections
  • Status changed from New to Accepted
  • Target version set to 5.x

#2 Updated by Mark Abraham about 3 years ago

  • Target version deleted (5.x)

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