MantisBT - PyRosetta
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IDProjectCategoryView StatusDate SubmittedLast Update
0000093PyRosetta[All Projects] Input Handlingpublic2012-09-04 11:362012-09-05 00:36
ReporterLabonte 
Assigned ToLabonte 
PrioritylowSeverityminorReproducibilityalways
StatusresolvedResolutionfixed 
PlatformAll platformsOSAnyOS VersionAny
Product Version[Rosetta] Trunk 
Fixed in Version[Rosetta] Trunk 
Application(s) AffectedPyRosetta
Command Line UsedN/A (See Steps To Reproduce above.)
Developer Options
Fixed in SVN Version50960
Summary0000093: Seg fault when asking for name of non-existent atom in a Residue
DescriptionCalling Residue.atom_name() with an index not in the the residue's atom list causes a long time delay followed by a seg fault.

I assume a PyAssert() will fix.
Steps To ReproduceIn [1]: from rosetta import *

In [2]: init()

In [3]: pose = pose_from_sequence("ACDEFGH")

In [5]: res = pose.residue(2)

In [6]: res.atom_name(11)
Out[6]: ' HG '

In [7]: res.atom_name(12)
Segmentation fault (core dumped)
Additional Information
Tagsexception handling, PyRosetta
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Issue History
Date ModifiedUsernameFieldChange
2012-09-04 11:36LabonteNew Issue
2012-09-04 11:36LabonteStatusnew => assigned
2012-09-04 11:36LabonteAssigned To => Labonte
2012-09-04 13:47SergeyNote Added: 0000090
2012-09-04 19:35LabonteTag Attached: exception handling
2012-09-04 19:35LabonteTag Attached: PyRosetta
2012-09-05 00:36LabonteFixed in SVN Version => 50960
2012-09-05 00:36LabonteNote Added: 0000091
2012-09-05 00:36LabonteStatusassigned => resolved
2012-09-05 00:36LabonteFixed in Version => Trunk
2012-09-05 00:36LabonteResolutionopen => fixed

Notes
(0000090)
Sergey   
2012-09-04 13:47   
Yep, - PyAssert should be a way to go here!
(0000091)
Labonte   
2012-09-05 00:36   
should be fixed -- along with several other RestidueType methods taking an atom index argument