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'''iterate''' iterates over an expression with a separate name space for each atom. However, unlike the "alter" command, atomic properties can not be altered. Thus, '''iterate''' is more efficient than '''alter'''.
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.


= Details =
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.
Iterate is a powerful tool that can be used to perform operations and aggregations using atomic selections, and store the results in any global object, such as the predefined '''stored''' object (see [[#PYMOL API]] below for usage of local objects).  For example, one could iterate over all of the alpha carbons and record their B Factors, or print out all of the secondary structure classifications of all the residues. Iterates typically takes a second per thousand atoms.


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 '''iterate''' command only has access to certain properties. Those properties are:
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+).
*'''model''': the pymol object label (appearing in the selection panel on the right)
 
*'''name''': the atom name
== Exposed Variables ==
*'''resn''': the residue name
 
*'''resi''': the residue identifier (residue number) as a string, including optional insertion code
All commands in the '''iterate'''-family expose the following variables:
*'''resv''': the residue identifier (residue number) as an integer, excluding insertion code
 
*'''chain''': the chain name
*'''model''' (str): the object name (appearing in the selection panel on the right) (cannot be altered)
*'''alt''': alternate Locations
*'''name''' (str): the atom name
*'''elem''': the chemical element
*'''resn''' (str): the residue name
*'''q''': occupancy
*'''oneletter''' (str): '''resn''' translated to one letter code, like it's displayed in the sequence viewer (cannot be altered, alter '''resn''' instead) (PyMOL 1.8.7+)
*'''b''': the B Factor
*'''resi''' (str): the residue identifier (residue number) as a string, including optional insertion code
*'''segi''': segment identifier (columns 73-76 in PDB file)
*'''resv''' (int): the residue identifier (residue number) as an integer, excluding insertion code
*'''type''' (ATOM,HETATM): the atom type
*'''chain''' (str): the chain name
*'''formal_charge''': the formal charge of the atom
*'''alt''' (str): alternate location identifier
*'''partial_charge''': the partial charge of the atom
*'''elem''' (str): the chemical element
*'''q''' (float): occupancy
*'''b''' (float): the B Factor
*'''segi''' (str): segment identifier (columns 73-76 in PDB file)
*'''type''' (str: ATOM,HETATM): the atom type (PDB convention for canonical polymer residues)
*'''formal_charge''' (int): the formal charge of the atom
*'''partial_charge''' (float): the partial charge of the atom
*'''numeric_type'''
*'''numeric_type'''
*'''text_type''': automatic mol2 atom typing (Incentive PyMOL 1.4+)
*'''text_type''' (str): automatic mol2 atom typing (Incentive PyMOL 1.4+)
*'''stereo''': automatic stereochemical R/S label (Incentive PyMOL 1.4+)
*'''stereo''' (str): automatic stereochemical R/S label (Incentive PyMOL 1.4+)
*'''ID''': PDB atom id (not guaranteed to be unique!)
*'''ID''' (int): PDB atom id (not guaranteed to be unique)
*'''vdw''': Van der Waals radius
*'''rank''' (int): atom index from original file import (not guaranteed to be unique)
*'''ss''': secondary structure
*'''index''' (int): internal atom index (unique per object, sensitive to [[sort|sorting]] and [[remove|removing]] of atoms, cannot be altered)
*'''color''': color index
*'''vdw''' (float): Van der Waals radius
*'''p''': property object to access user-defined properties like '''p.abc''' (Incentive PyMOL 1.7+)
*'''ss''' (str): secondary structure
*'''color''' (int): color index
*'''reps''' (int): numeric mask of shown representations (PyMOL 1.7.4+)
*'''protons''' (int): (PyMOL 1.7.4+)
*'''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+)
*'''label''' (str): see [[label]]
*'''geom''' (int): 1=single, 2=linear, 3=planar, 4=tetrahedral (see [[set_geometry]])
*'''valence''' (int): expected number of bonds (?)
*'''flags''' (int): bitmask, see [[flag]]
*'''cartoon''' (int): see [[cartoon]]
 
The '''iterate_state''' and '''alter_state''' commands in addition expose:
 
*'''x''' (float): x-coordinate
*'''y''' (float): y-coordinate
*'''z''' (float): z-coordinate
*'''state''' (int): (PyMOL 1.7.0+)
 
== Usage ==
 
iterate (selection), expression
 
iterate_state state, (selection), expression
 
alter (selection), expression
 
alter_state state, (selection), expression
 
=== Arguments ===
 
* '''state''' = int: object state, -1 for current state, 0 for all states
* '''selection''' = str: atom selection
* '''expression''' = str: expression in Python language
 
== Examples ==
 
=== Example: Print b-factors ===
 
The following prints the atom names ('''name''' variable) and b-factors ('''b''' variable) for residue #1.


'''Important''': All strings in the expression must be explicitly quoted.
<source lang="python">
iterate (resi 1), print(name + " %.2f" % b)
</source>


===Note about Atom Coordinates===
=== Example: Get b-factor list ===


The coordinates of the atom are not accessible via '''iterate'''. To inspect the coordinates of the atoms, see [[Iterate_State]].
The following example fills a list, '''[[pymol.stored|stored]].bfactors''' with the f-factors ('''b''' variable) from residue #1.
 
<source lang="python">
stored.bfactors = []
iterate (resi 1), stored.bfactors.append(b)
print(stored.bfactors)
</source>


===USAGE===
=== Example: Get coordinates ===
iterate (selection),expression


===EXAMPLES===
====Example====
*The following example calculates the net charge on an object.
<source lang="python">
<source lang="python">
# create the global variable between Python and PyMOL
stored.coords = []
stored.net_charge = 0
iterate_state 1, (all), stored.coords.append([x,y,z])
# sum up the stored charges of all the atoms
iterate (all),stored.net_charge = stored.net_charge + partial_charge
</source>
</source>


====Example====
=== Example: Modify coordinates ===
*The following example fills an array, '''stored.names''' with the names of all the atoms.
 
This example shifts the selection by 10 Angstrom along the model x-axis.
 
<source lang="python">
<source lang="python">
# create the global variable between Python and PyMOL
alter_state 1, (all), x += 10.0
stored.names = []
rebuild
# get all of the names
iterate (all),stored.names.append(name)
</source>
</source>


====Example====
=== Example: Rename chain ===
*The following prints the b-factors for all atoms around residue #1.
 
This renames chain '''A''' to '''C'''. Note the difference between the selection syntax (first argument) and the Python syntax with the quoted string (second argument). The [[sort]] call is necessary if let's say there is also a chain B, and you expect chain B to appear before chain C (formerly A) in the sequence viewer.
 
<source lang="python">
<source lang="python">
iterate resi 1, print round(b,2)
alter chain A, chain="C"
sort
</source>
</source>
====Example - b and resi ====
 
Just copy and paste this directly into command line
=== Example: Sequence numbering offset ===
 
Assume the residue numbering in a PDB file starts at 100, then the following updates the residue numbers to start at 1.
 
<source lang="python">
<source lang="python">
show_as cartoon ;
alter (chain A), resv -= 99
cmd.spectrum("b", "blue_white_red", "n. CA") ;
sort
m1 = [] ;
iterate (all and n. CA),m1.append((b,resi,chain)) ;
zero = [] ;
[zero.append(i) for i,val in enumerate(m1) if val[0]==0] ;
m2 = [i for j,i in enumerate(m1) if j not in zero] ;
for j,i,k in m2: print j,i,k
bmax,resimax,chainmax =  max(m2, key=lambda p: p[0]) ;
bmin,resimin,chainmin =  min(m2, key=lambda p: p[0]) ;
cmd.ramp_new("R2", "* n. CA", range=[0, bmin, bmax], color="[blue, white, red ]") ;
for b,resi,chain in m2: cmd.label("chain %s and resi %s and n. CA"%(chain,resi), "b=%3.2f"%b)
</source>
</source>


====Example====
=== Example: Net Charge ===
*The following example shows a common task in PyMOL, changing the B-factor column to display some other property.  Let's assume you have a file with a list of numbers, one per line, for each alpha carbon in the protein.  Furthermore, assume you want to map these values to the alpha carbons in the protein.
 
The following example calculates the net charge of an object.
 
<source lang="python">
<source lang="python">
# set ALL b-factors to 0.
stored.net_charge = 0
alter protName, b=0
iterate (all), stored.net_charge += partial_charge
print('Net charge: ' + str(stored.net_charge))
</source>


# read the new bfactors from disk
=== Example: Color transfer ===
f = open('fileName','r').readlines()


# set the alpha carbon bfactors.
Copy (transfer) the color from one object to another
alter protName and n. CA, b=f.pop(0)


# Spectrum color bfactors by alpha carbons.
<source lang="python">
spectrum b, selection=(protName and n. CA)
stored.colors = {}
iterate obj1, stored.colors[chain,resi,name] = color
alter obj2, color = stored.colors.get((chain,resi,name), color)
recolor
</source>
</source>


=== PYMOL API ===
== PYMOL API ==


<source lang="python">
<source lang="python">
cmd.iterate(string selection, string expression, int quiet=1, dict space=None)
cmd.iterate(str selection, str expression, int quiet=1, dict space=None)
 
cmd.iterate_state(int state, str selection, str expression, int quiet=1, dict space=None)
 
cmd.alter(str selection, str expression, int quiet=1, dict space=None)
 
cmd.alter_state(int state, str selection, str expression, int quiet=1, dict space=None)
</source>
</source>


When calling iterate, iterate_state, alter or alter_state from a python script, you can use the 'space' argument to pass local objects into the expression namespace.
=== Arguments ===


The second example from above but without the global pymol.stored variable:
* '''state''' = int: state-index if positive number or any of these:
** '''state''' = 0: all states
** '''state''' = -1: current state
* '''selection''' = str: atom selection
* '''expression''' = str: expression in valid [http://en.wikipedia.org/wiki/Python_syntax_and_semantics python syntax]
* '''space''' = dict: namespace dictionary {default: pymol namespace}
* '''atomic''' = 0/1: provide atomic properties as variables if 1, or only x/y/z if 0 (in older PyMOL versions, atomic=0 gives some speed improvement) {default: 1}
 
=== "space" argument ===
 
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:


<source lang="python">
<source lang="python">
myspace = {'names': []}
myspace = {'bfactors': []}
cmd.iterate('(all)', 'names.append(name)', space=myspace)
cmd.iterate('(all)', 'bfactors.append(b)', space=myspace)
</source>
</source>


Line 114: Line 180:
<source lang="python">
<source lang="python">
def myfunc(resi,resn,name):
def myfunc(resi,resn,name):
     print '%s`%s/%s' % (resn ,resi, name)
     print('%s`%s/%s' % (resn ,resi, name))


myspace = {'myfunc': myfunc}
myspace = {'myfunc': myfunc}
Line 120: Line 186:
</source>
</source>


===SEE ALSO===
== See Also ==
[[Iterate_State]], [[Alter]], [[Alter_State]], [[Color]], [[Color#Color_by_Spectrum_Example|Coloring with different color sprectrums]].
 
* [[sort]]
* [[Get_Model|get_model]]


[[Category:Commands|Iterate]]
[[Category:Commands|Iterate]]

Latest revision as of 12:08, 17 December 2017

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 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 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+).

Exposed Variables

All commands in the iterate-family expose the following variables:

  • model (str): the object name (appearing in the selection panel on the right) (cannot be altered)
  • name (str): the atom name
  • resn (str): the residue name
  • oneletter (str): resn translated to one letter code, like it's displayed in the sequence viewer (cannot be altered, alter resn instead) (PyMOL 1.8.7+)
  • 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
  • chain (str): the chain name
  • alt (str): alternate location identifier
  • elem (str): the chemical element
  • q (float): occupancy
  • b (float): the B Factor
  • segi (str): segment identifier (columns 73-76 in PDB file)
  • type (str: ATOM,HETATM): the atom type (PDB convention for canonical polymer residues)
  • formal_charge (int): the formal charge of the atom
  • partial_charge (float): the partial charge of the atom
  • numeric_type
  • text_type (str): automatic mol2 atom typing (Incentive PyMOL 1.4+)
  • stereo (str): automatic stereochemical R/S label (Incentive PyMOL 1.4+)
  • ID (int): PDB atom id (not guaranteed to be unique)
  • rank (int): atom index from original file import (not guaranteed to be unique)
  • index (int): internal atom index (unique per object, sensitive to sorting and removing of atoms, cannot be altered)
  • vdw (float): Van der Waals radius
  • ss (str): secondary structure
  • color (int): color index
  • reps (int): numeric mask of shown representations (PyMOL 1.7.4+)
  • protons (int): (PyMOL 1.7.4+)
  • 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+)
  • label (str): see label
  • geom (int): 1=single, 2=linear, 3=planar, 4=tetrahedral (see set_geometry)
  • valence (int): expected number of bonds (?)
  • flags (int): bitmask, see flag
  • cartoon (int): see cartoon

The iterate_state and alter_state commands in addition expose:

  • x (float): x-coordinate
  • y (float): y-coordinate
  • z (float): z-coordinate
  • state (int): (PyMOL 1.7.0+)

Usage

iterate (selection), expression

iterate_state state, (selection), expression

alter (selection), expression

alter_state state, (selection), expression

Arguments

  • state = int: object state, -1 for current state, 0 for all states
  • selection = str: atom selection
  • expression = str: expression in Python language

Examples

Example: Print b-factors

The following prints the atom names (name variable) and b-factors (b variable) for residue #1. 

iterate (resi 1), print(name + " %.2f" % b)

Example: Get b-factor list

The following example fills a list, stored.bfactors with the f-factors (b variable) from residue #1. 

stored.bfactors = []
iterate (resi 1), stored.bfactors.append(b)
print(stored.bfactors)

Example: Get coordinates

stored.coords = []
iterate_state 1, (all), stored.coords.append([x,y,z])

Example: Modify coordinates

This example shifts the selection by 10 Angstrom along the model x-axis. 

alter_state 1, (all), x += 10.0
rebuild

Example: Rename chain

This renames chain A to C. Note the difference between the selection syntax (first argument) and the Python syntax with the quoted string (second argument). The sort call is necessary if let's say there is also a chain B, and you expect chain B to appear before chain C (formerly A) in the sequence viewer. 

alter chain A, chain="C"
sort

Example: Sequence numbering offset

Assume the residue numbering in a PDB file starts at 100, then the following updates the residue numbers to start at 1. 

alter (chain A), resv -= 99
sort

Example: Net Charge

The following example calculates the net charge of an object. 

stored.net_charge = 0
iterate (all), stored.net_charge += partial_charge
print('Net charge: ' + str(stored.net_charge))

Example: Color transfer

Copy (transfer) the color from one object to another 

stored.colors = {}
iterate obj1, stored.colors[chain,resi,name] = color
alter obj2, color = stored.colors.get((chain,resi,name), color)
recolor

PYMOL API

cmd.iterate(str selection, str expression, int quiet=1, dict space=None)

cmd.iterate_state(int state, str selection, str expression, int quiet=1, dict space=None)

cmd.alter(str selection, str expression, int quiet=1, dict space=None)

cmd.alter_state(int state, str selection, str expression, int quiet=1, dict space=None)

Arguments

  • state = int: state-index if positive number or any of these:
    • state = 0: all states
    • state = -1: current state
  • selection = str: atom selection
  • expression = str: expression in valid python syntax
  • space = dict: namespace dictionary {default: pymol namespace}
  • atomic = 0/1: provide atomic properties as variables if 1, or only x/y/z if 0 (in older PyMOL versions, atomic=0 gives some speed improvement) {default: 1}

"space" argument

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: 

myspace = {'bfactors': []}
cmd.iterate('(all)', 'bfactors.append(b)', space=myspace)

User defined functions can also be included in the namespace: 

def myfunc(resi,resn,name):
    print('%s`%s/%s' % (resn ,resi, name))

myspace = {'myfunc': myfunc}
cmd.iterate('(all)', 'myfunc(resi,resn,name)', space=myspace)

See Also

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