0000278: AtomPairConstraint does not check existence of atoms (?)

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Project

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Date Submitted

Last Update

0000278

Rosetta

[All Projects] Input Handling

public

2013-05-31 10:03

2014-07-19 10:55

Reporter

smlewis

Assigned To

rmoretti

Priority

normal

Severity

minor

Reproducibility

always

Status

resolved

Resolution

fixed

Platform

OS Version

Product Version

3.4

Fixed in Version

Summary

0000278: AtomPairConstraint does not check existence of atoms (?)

Description

This is a bug I've run into in old versions of Rosetta (3.4 and earlier). A casual reading of trunk suggests this has been fixed but we need to check it.

AtomPairConstraint does not appear to check if atoms actually exist before attempting to apply constraints. If you pass fullatom constraints into centroid mode, where the sidechain atoms do not exist, the constraint functions look at garbage atom positions and return garbage constraint scores. Occasional crashes occur from segfaults, but usually it looks at allocated but inappropriate memory.

Here's a 3.4 example. https://www.rosettacommons.org/node/3278 [^]

I have not yet attempted to reproduce this in trunk.

Tags

No tags attached.

Application(s) Affected

docking in particular, anything with fullatom/centroid mode and constraints

Command Line Used

-cst_file file_with_atompairconstraints

Developer Options

Fixed in SVN Version

???

Attached Files

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Notes
(0000313) amw579 (Administrator) 2013-08-15 10:02	OK, do you mean that this _only_ happens when the reason the atoms don't exist is because of centroid mode? Or are you concerned that this is a general failure mode when atoms don't exist? It's definitely not true in the general case--just weeks ago I was dinged for constraining nonexistent atoms--but maybe it's somehow a specific-to-centroid-mode problem.

(0000350) rmoretti (Attentive Developer) 2014-07-19 10:54	It's definitely been fixed by 2013wk52. This has been tested with centroid poses & sidechain constraints. AtomPairConstraint used core::pose::named_atom_id_to_atom_id(), which checks for existence and raises EXCN_AtomNotFound if the atom is not found.

Issue History
Date Modified	Username	Field	Change
2013-05-31 10:03	smlewis	New Issue
2013-08-15 10:02	amw579	Note Added: 0000313
2014-07-19 10:54	rmoretti	Fixed in SVN Version	=> ???
2014-07-19 10:54	rmoretti	Note Added: 0000350
2014-07-19 10:54	rmoretti	Status	new => resolved
2014-07-19 10:54	rmoretti	Resolution	open => fixed
2014-07-19 10:54	rmoretti	Assigned To	=> rmoretti