Iterate

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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.

Contents

Details

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.

The iterate command only has access to certain properties. Those properties are:

All strings in the expression must be explicitly quoted. This operation typically takes a second per thousand atoms.

Note about Atom Coordinates

The coordinates of the atom are not accessible via iterate. To inspect the coordinates of the atoms, see Iterate_State.

USAGE

iterate (selection),expression

EXAMPLES

Example

# create the global variable between Python and PyMOL
stored.net_charge = 0
# sum up the stored charges of all the atoms
iterate (all),stored.net_charge = stored.net_charge + partial_charge

Example

# create the global variable between Python and PyMOL
stored.names = []
# get all of the names
iterate (all),stored.names.append(name)

Example

iterate resi 1, print round(b,2)

Example - b and resi

Just copy and paste this directly into command line

show_as cartoon ;
cmd.spectrum("b", "blue_white_red", "n. CA") ;
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)

Example

# set ALL b-factors to 0.
alter protName, b=0
 
# read the new bfactors from disk
f = open('fileName','r').readlines()
 
# set the alpha carbon bfactors.
alter protName and n. CA, b=f.pop(0)
 
# Spectrum color bfactors by alpha carbons.
spectrum b, selection=(protName and n. CA)

PYMOL API

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

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.

The second example from above but without the global pymol.stored variable:

myspace = {'names': []}
cmd.iterate('(all)', 'names.append(name)', 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

Iterate_State, Alter, Alter_State, Color, Coloring with different color sprectrums.

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