Get raw alignment - Revision history

Cchem: 1 revision

2019-01-07T03:14:12Z

1 revision

Speleo3: 2.3

2018-12-17T12:49:45Z

2.3

Cchem: 1 revision

2018-08-20T02:21:33Z

1 revision

Speleo3: residue numbers

2018-08-13T10:29:18Z

residue numbers

Pyadmin: 3 revisions

2014-03-28T02:00:48Z

3 revisions

Speleo3: hidden objects

2012-03-16T13:33:08Z

hidden objects

New page

'''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]].''
* ''Will not return atom tuples of hidden objects (see also [[hide_underscore_names]])''

== PYMOL API ==

cmd.get_raw_alignment(string name)

== EXAMPLE ==

<source lang="python">
# 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
</source>

== SEE ALSO ==

* [[align]]
* [[find_pairs]] returns a list of lists of (object,index) tuples as well

[[Category:Scripting]]
[[Category:Structure_Alignment]]

Speleo3: 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..."

2011-08-18T15:05:17Z

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..."

New page

'''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]].''

== PYMOL API ==

cmd.get_raw_alignment(string name)

== EXAMPLE ==

<source lang="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)
</source>

== SEE ALSO ==

* [[align]]
* [[find_pairs]] returns a list of lists of (object,index) tuples as well

[[Category:Scripting]]
[[Category:Structure_Alignment]]

← Older revision	Revision as of 03:14, 7 January 2019
(No difference)

@@ Line 4: / Line 4: @@
 * ''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 ==
@@ Line 50: / Line 51: @@
 * [[align]]
 * [[find_pairs]] returns a list of lists of (object,index) tuples as well
 [[Category:Scripting]]
 [[Category:Structure_Alignment]]

← Older revision	Revision as of 02:21, 20 August 2018
(No difference)

@@ Line 22: / Line 22: @@
 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)
+     print('%s`%d -> %s`%d' % tuple(idx1 + idx2))
 #end the python block
 python end
 </source>

← Older revision	Revision as of 02:00, 28 March 2014
(No difference)