Iterate - Revision history

Cchem: 1 revision

2018-01-08T04:03:22Z

1 revision

Speleo3: geom etc.

2017-12-17T17:08:07Z

geom etc.

Cchem: 1 revision

2017-09-18T02:46:07Z

1 revision

Speleo3: oneletter

2017-09-15T11:17:56Z

oneletter

Cchem: 1 revision

2017-05-01T02:44:25Z

1 revision

Speleo3: pymol.stored

2017-04-03T19:24:34Z

pymol.stored

Cchem: 1 revision

2017-04-03T02:46:02Z

1 revision

Speleo3: print syntax for python 2+3

2017-03-06T17:03:39Z

print syntax for python 2+3

Bell: 2 revisions

2016-01-03T07:02:35Z

2 revisions

Speleo3: correction

2015-12-28T18:46:29Z

correction

@@ Line 39: / Line 39: @@
 *'''p''' (object): property object to access user-defined properties like '''p.abc''' (Incentive PyMOL 1.7+)
 *'''s''' (object): settings object to access settings, e.g. '''s.sphere_scale''' (Incentive PyMOL 1.7+, Open-Source PyMOL 1.8.1+)
 The '''iterate_state''' and '''alter_state''' commands in addition expose:
@@ Line 45: / Line 50: @@
 *'''y''' (float): y-coordinate
 *'''z''' (float): z-coordinate
 == Usage ==

@@ Line 14: / Line 14: @@
 *'''name''' (str): the atom name
 *'''resn''' (str): the residue name
 *'''resi''' (str): the residue identifier (residue number) as a string, including optional insertion code
 *'''resv''' (int): the residue identifier (residue number) as an integer, excluding insertion code

@@ Line 1: / Line 1: @@
-The '''iterate''' command executes a Python expression for all atoms in a selection. The local namespace exposes all atomic identifiers and properties as read-only Python variables. The global namespace by default is the '''pymol''' module namespace, and thus exposes objects like '''cmd''' and '''stored'''. The order of iteration is that of the internal atom ordering.
+The '''iterate''' command executes a Python expression for all atoms in a selection. The local namespace exposes all atomic identifiers and properties as read-only Python variables. The global namespace by default is the '''pymol''' module namespace, and thus exposes objects like '''cmd''' and '''[[pymol.stored|stored]]'''. The order of iteration is that of the internal atom ordering.
 The '''alter''' command is equivalent to '''iterate''', but provides read-write access to the exposed variables. This can for example be used to rename a chain or to assign new b-factors. If changing identifiers which would affect atom ordering, calling [[sort]] is necessary to reorder based on the new identifiers.
@@ Line 73: / Line 73: @@
 === Example: Get b-factor list ===
-The following example fills a list, '''stored.bfactors''' with the f-factors ('''b''' variable) from residue #1.
+The following example fills a list, '''[[pymol.stored|stored]].bfactors''' with the f-factors ('''b''' variable) from residue #1.
 <source lang="python">
@@ Line 162: / Line 162: @@
 The '''space''' argument can be used to pass local objects into the expression namespace, instead of evaluating the expression in the global '''pymol''' module namespace.
-The b-factor list example from above but without the global '''pymol.stored''' variable:
+The b-factor list example from above but without the global [[pymol.stored]] variable:
 <source lang="python">

@@ Line 68: / Line 68: @@
 <source lang="python">
-iterate (resi 1), print name, round(b, 2)
+iterate (resi 1), print(name + " %.2f" % b)
 </source>
@@ Line 78: / Line 78: @@
 stored.bfactors = []
 iterate (resi 1), stored.bfactors.append(b)
-print stored.bfactors
+print(stored.bfactors)
 </source>
@@ Line 122: / Line 122: @@
 stored.net_charge = 0
 iterate (all), stored.net_charge += partial_charge
-print 'Net charge:', stored.net_charge
+print('Net charge: ' + str(stored.net_charge))
 </source>
@@ Line 173: / Line 173: @@
 <source lang="python">
 def myfunc(resi,resn,name):
-     print '%s`%s/%s' % (resn ,resi, name)
+     print('%s`%s/%s' % (resn ,resi, name))
 myspace = {'myfunc': myfunc}

@@ Line 3: / Line 3: @@
 The '''alter''' command is equivalent to '''iterate''', but provides read-write access to the exposed variables. This can for example be used to rename a chain or to assign new b-factors. If changing identifiers which would affect atom ordering, calling [[sort]] is necessary to reorder based on the new identifiers.
-The '''iterate_state''' command is similar to '''iterate''', but iterates over the coordinates in the given state and selection, and exposes '''x, y, z''' in addition to the atomic identifiers and properties. The order of iteration can differ from '''iterate''', since atoms and coordinates are not necessarily stored in the same order (see also [[sort]] and [[retain_order]]).
+The '''iterate_state''' command is similar to '''iterate''', but iterates over the coordinates in the given state and selection, and exposes '''x, y, z''' in addition to the atomic identifiers and properties.
 The '''alter_state''' command is equivalent to '''iterate_state''', but allows modification of '''x, y, z''' (and atom-state level settings in Incentive PyMOL 1.7+).

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