Bugs item #3363306, was opened at 2011-07-11 11:21
Message generated for change (Settings changed) made by hansonr
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Category: File Input/Output
Group: HEAD
>Status: Closed
Resolution: Fixed
Priority: 5
Private: No
Submitted By: NickEngland (nickengland)
Assigned to: Bob Hanson (hansonr)
Summary: CML atoms with ids of \"a1\" and \"a1_1\" cause error
Initial Comment:
XmlCmlReader.java line 394 sets isSerial to true if it reads an atom with id
"a1". If there are atoms with ids which are not serial later in the document
(eg, "a1_1") then the bonds do not load correctly.
Renaming all the ids from aX to bX cause the moelcule to load correctly.
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Comment By: Bob Hanson (hansonr)
Date: 2011-07-13 11:57
Message:
I don't think it's quite that simple. PDB files (translated to CML?) refer
to atoms for their bonding as serial numbers, not atom names. Not a problem
for a single-model file, but PDB files with multiple models have CONECT
records that are multi-model. Of course, CML is not PDB, and I can't
remember exactly why I thought that was important. This was added in
revision 12204, and although I don't remember the specifics of why, I doubt
I would have added that if there weren't a file that had the problems.
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Comment By: Bob Hanson (hansonr)
Date: 2011-07-13 11:41
Message:
fixed for 12.1.51 and 12.0.48
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Comment By: NickEngland (nickengland)
Date: 2011-07-12 09:34
Message:
Commenting out the lines:
if (!checkedSerial) {
// this is important because the atomName may not be unique
// (as in PDB files)
isSerial = (id != null && id.length() > 1 && id.startsWith("a")
&& Parser.parseInt(id.substring(1)) != Integer.MIN_VALUE);
checkedSerial = true;
}
if (isSerial)
atom.atomSerial = Parser.parseInt(id.substring(1));
fixes the issue, and all the units tests still seem to pass. AtomIds should
be unique in CML, so I am unsure what PDB files the comment is talking
about.
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