Bugs item #2889763, was opened at 2009-10-30 19:00
Message generated for change (Tracker Item Submitted) made by fab5
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Category: Command-line Tools
Group: 2.2.x
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Fabian (fab5)
Assigned to: Nobody/Anonymous (nobody)
Summary: Building bonds from resdata-templates
Initial Comment:
Minor bug in data.cpp : OBResidueData::AssignBonds(...)
the function connects atoms of a residue according to atom names defined in
"resdata.txt" by stepping
through the atom list _vatoms and breaks when the residue information of the
atoms under investigation
are different. Residues are only compared according to the residue name and the
residue number, which
is a problem when subsequent residues in a molecule have the same number and
name, but have a different
chain identifier (see HETATM records of 1xxb.pdb : ARG residues, attached ).
Thus the code
in data.cpp AssignBonds() should include a check if the chain identifiers
match, otherwise artificial bonds
might be introduced since AssingBonds() does not check atom-atom distances:
line 680:
if (r1->GetNumString() != r2->GetNumString())
break;
if (r1->GetName() != r2->GetName())
break;
if (r1->GetChain() != r2->GetChain())
break;
cheers
F
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