def process_rosetta_options(optd):
# Create the rosetta modeller - this runs all the checks required
rosetta_modeller = None
if optd['make_models'] or optd[
'make_frags']: # only need Rosetta if making models
logger.info('Using ROSETTA so checking options')
try:
rosetta_modeller = rosetta_model.RosettaModel(optd=optd)
except Exception, e:
msg = "Error setting ROSETTA options: {0}".format(e)
exit_util.exit_error(msg)
def testMultimerConstraints(self):
"""Test generation of multimer constraints"""
m = rosetta_model.RosettaModel()
m.multimer_modelling = multimer_definitions.TRIMER
m.work_dir = '.'
m.sequence_length = 4
cfile = m.create_multimer_constraints_file()
ref = """AtomPair CA 1 CA 4 FLAT_HARMONIC 6.00 3.00 5.00
AtomPair CA 1A CA 1B FLAT_HARMONIC 10.00 3.00 5.00
AtomPair CA 2A CA 2B FLAT_HARMONIC 10.00 3.00 5.00
AtomPair CA 3A CA 3B FLAT_HARMONIC 10.00 3.00 5.00
AtomPair CA 4A CA 4B FLAT_HARMONIC 10.00 3.00 5.00
AtomPair CA 1 CA 4 FLAT_HARMONIC 6.00 3.00 5.00
AtomPair CA 1A CA 1C FLAT_HARMONIC 10.00 3.00 5.00
AtomPair CA 2A CA 2C FLAT_HARMONIC 10.00 3.00 5.00
AtomPair CA 3A CA 3C FLAT_HARMONIC 10.00 3.00 5.00
AtomPair CA 4A CA 4C FLAT_HARMONIC 10.00 3.00 5.00
AtomPair CA 1 CA 4 FLAT_HARMONIC 6.00 3.00 5.00
AtomPair CA 1B CA 1C FLAT_HARMONIC 10.00 3.00 5.00
AtomPair CA 2B CA 2C FLAT_HARMONIC 10.00 3.00 5.00
AtomPair CA 3B CA 3C FLAT_HARMONIC 10.00 3.00 5.00
AtomPair CA 4B CA 4C FLAT_HARMONIC 10.00 3.00 5.00
"""
ref_windows = 'AtomPair CA 1 CA 4 FLAT_HARMONIC 6.00 3.00 5.00\r\n' \
'AtomPair CA 1A CA 1B FLAT_HARMONIC 10.00 3.00 5.00\r\n' \
'AtomPair CA 2A CA 2B FLAT_HARMONIC 10.00 3.00 5.00\r\n' \
'AtomPair CA 3A CA 3B FLAT_HARMONIC 10.00 3.00 5.00\r\n' \
'AtomPair CA 4A CA 4B FLAT_HARMONIC 10.00 3.00 5.00\r\n' \
'AtomPair CA 1 CA 4 FLAT_HARMONIC 6.00 3.00 5.00\r\n' \
'AtomPair CA 1A CA 1C FLAT_HARMONIC 10.00 3.00 5.00\r\n' \
'AtomPair CA 2A CA 2C FLAT_HARMONIC 10.00 3.00 5.00\r\n' \
'AtomPair CA 3A CA 3C FLAT_HARMONIC 10.00 3.00 5.00\r\n' \
'AtomPair CA 4A CA 4C FLAT_HARMONIC 10.00 3.00 5.00\r\n' \
'AtomPair CA 1 CA 4 FLAT_HARMONIC 6.00 3.00 5.00\r\n' \
'AtomPair CA 1B CA 1C FLAT_HARMONIC 10.00 3.00 5.00\r\n' \
'AtomPair CA 2B CA 2C FLAT_HARMONIC 10.00 3.00 5.00\r\n' \
'AtomPair CA 3B CA 3C FLAT_HARMONIC 10.00 3.00 5.00\r\n' \
'AtomPair CA 4B CA 4C FLAT_HARMONIC 10.00 3.00 5.00\r\n'
with open(cfile) as f:
fstr = f.read()
# self.assertEquals(fstr, ref, "Contents of constraints files don't match: {}".format(cfile))
if sys.platform.startswith("win"):
self.assertEquals(fstr, ref_windows)
else:
self.assertEquals(fstr, ref)
os.unlink(cfile)
def XtestMakeFragments(self):
"""See we can create fragments"""
optd = {}
optd['rosetta_dir'] = "/opt/rosetta3.4"
optd['name'] = "TOXD_"
optd['work_dir'] = os.getcwd()
optd['use_homs'] = True
optd['make_frags'] = True
optd['rosetta_db'] = None
optd['rosetta_fragments_exe'] = "/tmp/make_fragments.pl"
#optd['rosetta_fragments_exe'] = None
optd['fasta'] = os.path.join(self.ample_share + "examples",
"toxd-example", "input", "toxd_.fasta")
optd['make_models'] = False
optd['frags_3mers'] = None
optd['frags_9mers'] = None
optd['improve_template'] = None
m = rosetta_model.RosettaModel(optd=optd)
m.generate_fragments()
def XtestNoRosetta(self):
"""
Test without Rosetta
"""
os.chdir(
self.thisd
) # Need as otherwise tests that happen in other directories change os.cwd()
## Create a dummy script
script = "dummy_rosetta.sh"
with open(script, "w") as f:
content = """#!/usr/bin/env python
for i in range(10):
f = open( "rosy_{0}.pdb".format(i), "w")
f.write( "rosy_{0}.pdb".format(i) )
f.close()"""
f.write(content)
os.chmod(script, 0o777)
# Create dummy fragment files
frags3 = '3mers'
frags9 = '9mers'
with open(frags3, 'w') as f3, open(frags9, 'w') as f9:
f3.write(frags3 + "\n")
f9.write(frags9 + "\n")
# Set options
optd = {}
optd['nproc'] = 3
optd['nmodels'] = 30
optd['work_dir'] = os.getcwd()
optd['models_dir'] = "XXXmodelsXXX"
optd['rosetta_db'] = None
optd['rosetta_dir'] = "/opt/rosetta3.4"
optd['rosetta_AbinitioRelax'] = os.path.join(os.getcwd(), script)
optd['frags_3mers'] = frags3
optd['frags_9mers'] = frags9
optd['rosetta_fragments_exe'] = None
optd['use_homs'] = None
optd['make_models'] = True
optd['make_frags'] = False
optd['fasta'] = "FASTA"
optd['name'] = "TOXD_"
optd['improve_template'] = None
optd['all_atom'] = True
optd['benchmark_mode'] = False
optd['transmembrane'] = False
optd['psipred_ss2'] = None
optd['rg_reweight'] = None
optd['domain_termini_distance'] = None
optd['CC'] = None
optd['improve_template'] = None
rm = rosetta_model.RosettaModel(optd=optd)
mdir = rm.doModelling()
os.unlink(script)
os.unlink('seedlist')
os.unlink(frags3)
os.unlink(frags9)
shutil.rmtree(mdir)