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#84: Expressions should not change the bond orders
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(Anonymous)
issuedata
Classification:
Bug
Topic:
Backend
Importance:
High
Assigned to: anhi, bertsch, oliver
Created by: anhi
Created at: 2008-01-11
progress
Deadline:
2008-01-25 04:12 PM
Hours estimated:
0
Hours needed:
0
Percent done:
0
contact
Name:
Andreas Hildebrandt
E-Mail:
anhi@bioinf.uni-sb.de
Description:
Our current implementation of SMARTS and Expression matching uses the aromaticity processor to find aromatic bonds. This is potentially dangerous, since it changes the bond orders of the molecules in an unexpected way. The simplest fix would be to add an option to the aromaticity processor deciding whether bond orders should be set. If not, we should only store the aromatic property in the bond. Then, all dependend code (AromaticBondPredicate, SMARTSMatcher, ...) needs to be changed to look for either bond order or the properties assigned to the bond.
Transcript
#2:
2008-01-13 02:39 PM (bertsch)
Why not just change the Code of 'bool SMARTSPredicate::operator () (const Atom& atom) const' to not operate on the original molecule? Copying and matching the atoms should not be too much overhead.
#1:
2008-01-11 04:16 PM (anhi)
status: "pending" ->
"accepted"
assignees: "[]" ->
"['anhi', 'bertsch', 'oliver']"
topic: "" ->
"Backend"
importance: "medium" ->
"high"
title: "" ->
"Expressions should not change the bond orders"
description: "" ->
"Our current implementation of SMARTS and Expression matching uses the aromaticity processor to find aromatic bonds. This is potentially dangerous, since it changes the bond orders of the molecules in an unexpected way. The simplest fix would be to add an option to the aromaticity processor deciding whether bond orders should be set. If not, we should only store the aromatic property in the bond. Then, all dependend code (AromaticBondPredicate, SMARTSMatcher, ...) needs to be changed to look for either bond order or the properties assigned to the bond."
PloneCollectorNG (C) 2003-2004 by ZOPYX - Software Development and Consulting Andreas Jung
