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Reducing assumptions that structures are protein
Rather than checking for CA atoms, check for a generic representative (e.g. the C4' atom of nucleic acids). This paves the way for RNA structure comparisons. Mostly deprecates CA-specific functions in favor of ones named 'getRepresentativeAtom' or similar. A few functions change behavior, notably: - StructureTools.get1LetterCode returns a value for nucleotides, rather than null - StructureTools.getBackboneAtomArray returns atoms from DNA/RNA
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‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/MyTestHelper.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -90,7 +90,7 @@ public static String compareAlignment(String pdb1, String chain1, String pdb2, S
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for (int i = 0 ; i < ca2.length; i++){
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Group g = (Group)ca2[i].getGroup().clone();
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g.setChain(ca2[i].getGroup().getChain());
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ca3[i] = g.getAtom(StructureTools.CA_ATOM_NAME);
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ca3[i] = g.getAtom(ca2[i].getName());
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}
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StructureAlignment fatCat;

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