Get raw alignment

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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.
  • Will not return atom tuples of hidden objects (see also hide_underscore_names)
  • Reimplemented in PyMOL 2.3, order of returned atom tuples can differ to previous versions


cmd.get_raw_alignment(string name)


# start a python block

# 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 (atom index)
for idx1, idx2 in raw_aln:
    print('%s`%d -> %s`%d' % tuple(idx1 + idx2))

#end the python block
python end

To print residue numbers instead of atom indices:

# continued from previous example

idx2resi = {}
cmd.iterate('aln', 'idx2resi[model, index] = resi', space={'idx2resi': idx2resi})

# print residue pairs (residue number)
for idx1, idx2 in raw_aln:
    print('%s -> %s' % (idx2resi[idx1], idx2resi[idx2]))

python end