Get raw alignment
get_raw_alignment is an API only function that returns a list of lists of (object,index) tuples containing the raw per-atom alignment relationships. Alignment objects can be created by passing the "object" argument to align or super.
Please note: The order of the atom tuples are not necessarily in the order in which the two (or more) selections were passed to cmd.align.
# start a python block python # get two structures cmd.fetch('2xwu 2x19', async=0) # align and get raw alignment cmd.align('/2xwu//B//CA', '/2x19//B//CA', cycles=0, transform=0, object='aln') raw_aln = cmd.get_raw_alignment('aln') # print residue pairs for idx1, idx2 in raw_aln: print '%s`%d -> %s`%d' % tuple(idx1 + idx2) #end the python block python end