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modprep.py

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import modeller

from modeller import automodel

from modeller.selection import Selection

import sys

def run_modeller(**kwargs):

"""

Refine protein structure using MODELLER. Only the edited regions move.

"""

default_stdout = sys.stdout

sys.stdout = open("pymodsim.log", "a")

try:

if kwargs["mode"] == "run":

modeller.log.minimal()

env = modeller.Environ()

env.io.atom_files_directory = ['.', '../atom_files']

aln = modeller.Alignment(env, file=kwargs["alnfile"])

def build(ext, randomize):

class EditedRegionsOnly(automodel.AutoModel):

def select_atoms(self):

# Linkers and cut loop ends (+ext residues each side) move; everything

# else keeps the input coordinates. loops() does not report trimmed

# termini, so the first and last ext+1 residues always move.

res = self.residues

n = len(res)

ends = [res[i] for i in range(ext + 1)] + [res[n - 1 - i] for i in range(ext + 1)]

return Selection(self.loops(aln, minlength=1, maxlength=10000,

insertion_ext=ext, deletion_ext=ext,

include_termini=True), ends)

a = EditedRegionsOnly(env, alnfile=kwargs["alnfile"],

knowns=kwargs["knowns"], sequence='refined')

a.starting_model = 1

a.ending_model = 1

a.md_level = None

if not randomize:

a.rand_method = None

a.make()

return a.outputs[0]["failure"] is None

# The random start can make the objective function NaN when few atoms are free

# (2 of 1601 GPCRdb models). Retry without randomization, then with a wider selection.

for ext, randomize in ((1, True), (1, False), (3, False)):

if build(ext, randomize):

break

print("MODELLER failed (selection +{0}, randomize={1}); retrying".format(ext, randomize))

else:

raise RuntimeError("MODELLER produced no model (see pymodsim.log)")

finally:

sys.stdout = default_stdout