Bugs item #1902378, was opened at 2008-02-26 09:43
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Category: Open Babel
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Geoff Hutchison (ghutchis)
Summary: PDB with custom connect
Initial Comment:
The PDB file I have included is a clathrate hydrate (H2 is the guest gas molecule). In this file all water hydrogens have been removed and the CONECT lines are written to connect oxygen atoms (distance between connected atoms is between 2.5 and 3.0 Å) which helps when identifying the clathrate structure.
When I open it in Avogadro, the UI “pinwheels” and I’ve never waited long enough for it to completely load. The same file without the custom connect lines opens in a reasonable amount of time.
I profiled the program while attempting to open the PDB and found most of the time was spent in
OpenBabel::operator==(OpenBabel::OBBitVec const&, OpenBabel::OBBitVec const&)
which has been called from
OpenBabel::OBRingSearch::SaveUniqueRing
OpenBabel::OBRingSearch::AddRingFromClosure
OpenBabel::OBMol::FindSSSR
OpenBabel::OBMol::PerceiveBondOrders
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=835077&aid=1902378&group_id=165310