Iterate

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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
  • 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+)

The iterate_state and alter_state commands in addition expose:

  • x (float): x-coordinate
  • y (float): y-coordinate
  • z (float): z-coordinate

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, round(b, 2)

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:', 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