HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>();
int resNum = -10000;
int index = 0;
+ char insCode = ' ';
do
{
Atom tmp = maxChain.atoms.elementAt(index);
- if (resNum != tmp.resNumber && tmp.alignmentMapping != -1)
+ if ((resNum != tmp.resNumber || insCode != tmp.insCode)
+ && tmp.alignmentMapping != -1)
{
resNum = tmp.resNumber;
+ insCode = tmp.insCode;
if (tmp.alignmentMapping >= -1)
{
- // TODO (JAL-1836) address root cause: negative residue no in PDB
- // file
mapping.put(tmp.alignmentMapping + 1, new int[] { tmp.resNumber,
tmp.atomIndex });
}