pdb2aln Improvement

[Xinqiu Yao]

There are several things to consider in pdb2aln: The input is index but output is atom selection. This caused confusion sometimes. Second, pdb2aln may cause errors if the newly added PDB sequence has gaps in the requested positions. Taking these two, we may consider revising the function to output a list containing the quivalent CA atomic indices, the corresponding xyz indices, and the alignment used to find the quivalence. Furthermore, the function name is confusing, too, which is too close to seq2aln, etc.

[Xinqiu Yao]

pdb2aln is largely changed and it returns "alignment" now. In addition, a new function, pdb2aln.ind, is added and functions similarly as old pdb2aln