Hi guys.. Im finding that two structures that are the same give me non-zero
RMSD alignments.... There could be a bug in my code, but this is an
initial notice that I'm pretty sure about.... Any thoughts on the
performance of CEAlign in ideal cases ?
Atom[] ca1 = GPdbUtils.getAtoms(s1, type);
Atom[] ca2 = GPdbUtils.getAtoms(s2, type);
System.out.println("Aligning two sets of atoms, " + ca1.length
+","+ca2.length);
// get default parameters
CeParameters params = new CeParameters();
// set the maximum gap size to unlimited
// params.setMaxGapSize(-1);
StructureAlignment algorithm = StructureAlignmentFactory
.getAlgorithm(CeMain.algorithmName);
// The results are stored in an AFPChain object
AFPChain afpChain = algorithm.align(ca1, ca2, params);
afpChain.setName1("A");
afpChain.setName2("B");
return (float) afpChain.getChainRmsd();
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