public static AFPChain cpFastaToAfpChain(String first, String second, Structure structure, int cpSite) throws StructureException, CompoundNotFoundException { ProteinSequence s1 = new ProteinSequence(first); s1.setUserCollection(getAlignedUserCollection(first)); ProteinSequence s2 = new ProteinSequence(second); s2.setUserCollection(getAlignedUserCollection(second)); return cpFastaToAfpChain(s1, s2, structure, cpSite); }
/** * TODO Write comment * @param sequence1 * @param sequence2 * @param structure1 * @param structure2 * @return * @throws StructureException * @throws CompoundNotFoundException */ public static AFPChain fastaToAfpChain(String sequence1, String sequence2, Structure structure1, Structure structure2) throws StructureException, CompoundNotFoundException { ProteinSequence s1 = new ProteinSequence(sequence1); s1.setUserCollection(getAlignedUserCollection(sequence1)); ProteinSequence s2 = new ProteinSequence(sequence2); s2.setUserCollection(getAlignedUserCollection(sequence2)); return fastaToAfpChain(s1, s2, structure1, structure2); }