Get raw alignment

From PyMOLWiki
Revision as of 11:05, 18 August 2011 by Speleo3 (talk | contribs) (Created page with "'''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 b...")
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigation Jump to search

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.

PYMOL API

cmd.get_raw_alignment(string name)

EXAMPLE

# 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)

SEE ALSO