In this example below (from Thomas), the method 'iterate' is used. The
function saves every amino acid of a structure to a separate file. First
of all, I'm not sure of how to understand the docs:
" "iterate" iterates over an expression within a temporary namespace for
each atom."
What does temporary namespace for each atom mean? Also, since 'iterate'
is used within the while-loop, are we only iterating over the single
amino acid? Its confusing me because I constantly think of iterate as
somekind of short hand notation of a for-loop, but I guess thats not it.
It would be great if somebody could explain the iterate function a bit
more to me.
Thanks for your feedback.
Martin
# *****************************************************************
# import statements
def seq(state, selection="name ca or resn hoh or resn lig"):
cmd.select("prot", selection)
while cmd.pop("_tmp", "prot"):
cmd.iterate("_tmp", "stored.x=(resn,resv)")
# Special case 1: Waters.
if stored.x[0] == 'HOH':
filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
# Special case 2: Substrate.
elif stored.x[0] == 'LIG':
filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
# Other: protein back-bone.
else:
filename = 'seq-%s%d-%s.pdb' % (one_letter[stored.x[0]].lower(),
stored.x[1], state)
cmd.save(filename, "byres _tmp")
cmd.delete('_tmp prot')
cmd.extend('seq', seq)
# -----------------------------------------------------------------
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