[Feature-dev] [ feature-Bugs-1316 ] ATOM-TYPE-IS-OTHER Part2

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Bugs item #1316, was opened at 2010-08-19 10:01
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Category: Application - featurize
Group: Behavior and algorithm
Status: Open
Resolution: None
Priority: 4
Submitted By: Grace Tang (gwtang)
Assigned to: Mike Wong (mikewong899)
Summary: ATOM-TYPE-IS-OTHER Part2

Initial Comment:
Non-zero values for this property are the result of 2 known bugs.

1. HIS residues are not being read in due to Amber files using HID/HIE/HIP naming conventions.  

Quick Fix: Replace all HIE with HIS in amberM2_params.dat and residue_template.dat

2. Atoms mapping to the Ca ATOM-TYPE are not be properly classified as Ca.

Quick Fix: SAtomProperties::SetType(SAtom *atom) 
This function is missing an if-else statement for incrementing atomTypeIsCa


I have implemented both fixes and my test file is now showing zero for ATOM-TYPE-IS-OTHER.  I still need to run on more test cases to confirm no more bugs are associated with this parameter.


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