0000295: core::scoring::sasa::calc_per_atom_sasa_sc divides by zero with NCAAs/Ligands

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0000295

Rosetta

[All Projects] Bad Coding

public

2013-08-06 18:29

2017-08-21 18:06

Reporter

delucasl

Assigned To

amw579

Priority

high

Severity

minor

Reproducibility

always

Status

closed

Resolution

suspended

Platform

All platforms

Any

OS Version

Any

Product Version

All

Fixed in Version

Summary

0000295: core::scoring::sasa::calc_per_atom_sasa_sc divides by zero with NCAAs/Ligands

Description

if you call calc_per_atom_sasa_sc with normalize=true, the function normalizing_area is called. normalizing_area takes the name1 of the residuetype and uses the int value of the char to get a hardcoded value from a vector. The default value of the vector is 0.0, which means that a residue with a name1 other than one of the 20 canonical name1s will return 0.0, and divide the residue sasa by 0. The result of this in c++ is undefined and will result in a random number for the normalized sasa.

I suspect that the area lookup table was implemented as a vector for speed reasons, however the current behavior is extremely dangerous and would result in very difficult to diagnose bugs. The only reason I found it at all is because I was carefully reading sasa.cc for another purpose. Replacing this vector with a map, hash table, or something else would address the error.

additionally, while ligands typically have a name1 of X, this is not a requirement, and thus you cannot know that a ligand with a name1 of A is actually alanine. The failure mode of this code due to strange user input is not an error but rather a potentially subtle incorrect sasa calculation of the residue. the datastructure should almost certainly be indexed by the full name of the residuetype, as a patched residuetype can maintain the same name1 or name3 and have a very different chemical composition than the canonical AA.

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Application(s) Affected

anything using sasa

Command Line Used

score_jd2

Developer Options

Fixed in SVN Version

n/a

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Notes
(0000310) delucasl (Administrator) 2013-08-06 18:34	Changing status to minor. This is only currently used in core/scoring/methods/ProQ_Energy, which uses it in such a limited case that its unlikely that the bug occurs in practice. However, future use of this code outside of the originally intended scope will be subject to the bug

Issue History
Date Modified	Username	Field	Change
2013-08-06 18:29	delucasl	New Issue
2013-08-06 18:34	delucasl	Note Added: 0000310
2013-08-06 18:34	delucasl	Severity	major => minor
2017-08-21 18:06	amw579	Fixed in SVN Version	=> n/a
2017-08-21 18:06	amw579	Status	new => closed
2017-08-21 18:06	amw579	Assigned To	=> amw579
2017-08-21 18:06	amw579	Resolution	open => suspended