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(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...") |
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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]]. | '''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 [[Align|cmd.align]].'' | + | ''Please note:'' |
| + | * ''The order of the atom tuples are not necessarily in the order in which the two (or more) selections were passed to [[Align|cmd.align]].'' | ||
| + | * ''Will not return atom tuples of hidden objects (see also [[hide_underscore_names]])'' | ||
== PYMOL API == | == PYMOL API == | ||
| Line 10: | Line 12: | ||
<source lang="python"> | <source lang="python"> | ||
| + | # start a python block | ||
| + | python | ||
| + | |||
# get two structures | # get two structures | ||
cmd.fetch('2xwu 2x19', async=0) | cmd.fetch('2xwu 2x19', async=0) | ||
| Line 20: | Line 25: | ||
for idx1, idx2 in raw_aln: | for idx1, idx2 in raw_aln: | ||
print '%s`%d -> %s`%d' % tuple(idx1 + idx2) | print '%s`%d -> %s`%d' % tuple(idx1 + idx2) | ||
| + | |||
| + | #end the python block | ||
| + | python end | ||
</source> | </source> | ||
Revision as of 13:33, 16 March 2012
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)
PYMOL API
cmd.get_raw_alignment(string name)
EXAMPLE
# 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
SEE ALSO
- align
- find_pairs returns a list of lists of (object,index) tuples as well