Bugs item #3018188, was opened at 2010-06-18 15:53
Message generated for change (Tracker Item Submitted) made by fab5
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Category: Command-line Tools
Group: 2.3.x
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Fabian (fab5)
Assigned to: Nobody/Anonymous (nobody)
Summary: mol2formats.cpp : ReadMolecule() efficiency
Initial Comment:
Hi,
Just a small efficiency issue when reading very large mol2-files
(formats/mol2format.cpp) in
bool MOL2Format::ReadMolecule(OBBase* pOb, OBConversion* pConv).
The assignment of neighbor bond information to atoms is using an unnecessary
amount of time and could
be split up into two loops (clearing and assigning). While stepping through the
bond list, adding said
bond directly to the "Begin" and "End" atom would make the function more
efficient instead of always searching
for the correct atom in the entire bond list (which can take a couple of
seconds for very large
molecules). However the order of the neighbor bonds for a particular atom might
be different than
before (does this matter?).
Hope this helps
Fabian
PS> I didn't check the other file formats if the same applies there too.
Original version starting on line 291 :
for (patom = mol.BeginAtom(apos); patom; patom = mol.NextAtom(apos))
{
patom->ClearBond();
for (pbond = mol.BeginBond(bpos); pbond; pbond = mol.NextBond(bpos))
{
if (patom == pbond->GetBeginAtom() || patom == pbond->GetEndAtom())
{
patom->AddBond(pbond);
}
}
}
New version:
for (patom = mol.BeginAtom(apos); patom; patom = mol.NextAtom(apos))
{
patom->ClearBond();
}
for (pbond = mol.BeginBond(bpos); pbond; pbond = mol.NextBond(bpos))
{
patom = pbond->GetBeginAtom();
patom->AddBond(pbond);
patom = pbond->GetEndAtom();
patom->AddBond(pbond);
}
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