Mantis Bug Tracker

View Issue Details Jump to Notes ] Issue History ] Print ]
IDProjectCategoryView StatusDate SubmittedLast Update
0000240Rosetta[All Projects] Incorrect Resultspublic2013-04-02 16:212013-04-03 12:29
Assigned Topbradley 
PlatformAll platformsOSAnyOS VersionAny
Product VersionTrunk 
Fixed in VersionTrunk 
Summary0000240: abs() method used on Real values in core::scoring
DescriptionThis may not be an error, but I'd like someone who knows more to double check it, just in case, because it looks very wrong to me and is throwing a ton of warnings.

In core/scoring/dna/, a lot of asserts are using the int abs(int) method but passing Reals. Rather than just cast everything to an int, I wanted to make sure that this is the intended behavior, because there is also a float abs(float) (in a different namespace, cmath) that could be used.

For an example, see l. 1246:

assert( abs( params[1] - asin( dot( MBT.col_z(), cross( M2.col_y(), M1.col_y() ) ) ) ) + abs( params[1] - asin( dot( MBT.col_z(), cross( M2.col_x(), M1.col_x() ) ) ) ) < 1e-2 );

where params is a vector1<Real>.

Not all of the issues are in asserts either -- l. 1303:

Real dot = std::abs( ( atoms[4]-atoms[3] ).normalized() ) );

where n12 is an xyzVector. This looks very bad to me; or am I missing something?

No one listed him- or herself as author on this file, but whoever you are, could you fix all the abs() calls in this file, whether by casting or by using cmath::abs()? Thanks!
Additional Information [^]
TagsNo tags attached.
Application(s) AffectedDNA & RNA applications?
Command Line UsedN/A
Developer Options
Fixed in SVN Version54660
Attached Files

- Relationships

-  Notes
rmoretti (Attentive Developer)
2013-04-02 16:41

Note: For those who have trouble finding it, the file is core/scoring/dna/

My guess would be this is a potential bug due to unawaredness that the abs function doesn't have sane polymophism.

svn praise (aka svn blame) and the svn server places most to the initial commits of the code by Phil Bradley some 6 years ago. Given that he's still actively working on code that likely uses these functions, I'd recommend shooting him an email directly.
Labonte (Developer)
2013-04-02 17:37

Thanks, Rocco!
pbradley (Developer)
2013-04-03 12:29

Thanks for the tip! Switched to std::fabs and included <cmath> in revision 54660

- Issue History
Date Modified Username Field Change
2013-04-02 16:21 Labonte New Issue
2013-04-02 16:41 rmoretti Note Added: 0000242
2013-04-02 17:37 Labonte Note Added: 0000244
2013-04-02 17:38 Labonte Description Updated View Revisions
2013-04-02 17:39 Labonte Priority low => normal
2013-04-02 17:39 Labonte Severity minor => major
2013-04-03 09:32 delucasl Assigned To => pbradley
2013-04-03 09:32 delucasl Status new => assigned
2013-04-03 12:29 pbradley Fixed in SVN Version => 54660
2013-04-03 12:29 pbradley Note Added: 0000247
2013-04-03 12:29 pbradley Status assigned => resolved
2013-04-03 12:29 pbradley Resolution open => fixed
2013-04-03 12:29 pbradley Fixed in Version => Trunk

Copyright © 2000 - 2012 MantisBT Group
Powered by Mantis Bugtracker