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);
}