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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]])'' | ||
| + | * ''Reimplemented in PyMOL 2.3, order of returned atom tuples can differ to previous versions'' | ||
== PYMOL API == | == PYMOL API == | ||
| Line 10: | Line 13: | ||
<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 17: | Line 23: | ||
raw_aln = cmd.get_raw_alignment('aln') | raw_aln = cmd.get_raw_alignment('aln') | ||
| − | # print residue pairs | + | # 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 | ||
| + | </source> | ||
| + | |||
| + | To print residue numbers instead of atom indices: | ||
| + | |||
| + | <source lang="python"> | ||
| + | # continued from previous example | ||
| + | python | ||
| + | |||
| + | idx2resi = {} | ||
| + | cmd.iterate('aln', 'idx2resi[model, index] = resi', space={'idx2resi': idx2resi}) | ||
| + | |||
| + | # print residue pairs (residue number) | ||
for idx1, idx2 in raw_aln: | for idx1, idx2 in raw_aln: | ||
| − | print '%s | + | print('%s -> %s' % (idx2resi[idx1], idx2resi[idx2])) |
| + | |||
| + | python end | ||
</source> | </source> | ||
| Line 26: | Line 51: | ||
* [[align]] | * [[align]] | ||
* [[find_pairs]] returns a list of lists of (object,index) tuples as well | * [[find_pairs]] returns a list of lists of (object,index) tuples as well | ||
| + | * [[set_raw_alignment]] | ||
[[Category:Scripting]] | [[Category:Scripting]] | ||
[[Category:Structure_Alignment]] | [[Category:Structure_Alignment]] | ||
Latest revision as of 03:14, 7 January 2019
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
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 (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
python
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
SEE ALSO
- align
- find_pairs returns a list of lists of (object,index) tuples as well
- set_raw_alignment