def test_elastic_network(self):
""" test PMI setup of elastic nets """
import IMP.pmi.representation_new as r
import IMP.pmi.restraints_new.stereochemistry
import IMP.pmi.sequence_tools
mdl = IMP.Model()
# create two states, each with two copies of the protein
s = r.System(mdl)
seqs = r.Sequences(self.get_input_file_name("chainA.fasta"), name_map={"GCP2_YEAST": "Prot1"})
# build state
st1 = s.create_state()
m1 = st1.create_molecule("Prot1", sequence=seqs["Prot1"], chain_id="A")
atomic_res = m1.add_structure(self.get_input_file_name("chainA.pdb"), chain_id="A", model_num=0)
m1.add_representation(atomic_res, resolutions=[0])
hier = s.build(merge_type="backbone")
# create elastic network from some SSEs
sses = io.parse_dssp(mdl, self.get_input_file_name("chainA.dssp"), "A")
er = IMP.pmi.restraints_new.stereochemistry.ElasticNetworkRestraint(
hier, selection_dicts=sses["helix"][0], strength=10.0, dist_cutoff=5.0, atom_type=IMP.atom.AtomType("CA")
)
self.assertEqual(er.get_restraint().get_number_of_restraints(), 12)
def test_elastic_network(self):
""" test PMI setup of elastic nets """
import IMP.pmi.representation_new as r
import IMP.pmi.restraints_new.stereochemistry
import IMP.pmi.sequence_tools
mdl = IMP.Model()
# create two states, each with two copies of the protein
s = r.System(mdl)
seqs = r.Sequences(self.get_input_file_name('chainA.fasta'),
name_map={'GCP2_YEAST': 'Prot1'})
# build state
st1 = s.create_state()
m1 = st1.create_molecule("Prot1", sequence=seqs["Prot1"], chain_id='A')
atomic_res = m1.add_structure(self.get_input_file_name('chainA.pdb'),
chain_id='A',
model_num=0)
m1.add_representation(atomic_res, resolutions=[0])
hier = s.build(merge_type="backbone")
# create elastic network from some SSEs
sses = io.parse_dssp(mdl, self.get_input_file_name('chainA.dssp'), 'A')
er = IMP.pmi.restraints_new.stereochemistry.ElasticNetworkRestraint(
hier,
selection_dicts=sses['helix'][0],
strength=10.0,
dist_cutoff=5.0,
atom_type=IMP.atom.AtomType("CA"))
self.assertEqual(er.get_restraint().get_number_of_restraints(), 12)
def test_dssp_parsing(self):
"""Test reading DSSP files"""
sses = io.parse_dssp(self.get_input_file_name('chainA.dssp'),'A')
self.assertEqual(sorted(sses.keys()),sorted(['helix','beta','loop']))
self.assertEqual(len(sses['helix']),20)
self.assertEqual(len(sses['beta']),3)
self.assertEqual(len(sses['loop']),32)
def test_dssp_parsing(self):
"""Test reading DSSP files"""
sses = io.parse_dssp(self.get_input_file_name('chainA.dssp'), 'A')
self.assertEqual(sorted(sses.keys()), sorted(['helix', 'beta',
'loop']))
self.assertEqual(len(sses['helix']), 20)
self.assertEqual(len(sses['beta']), 3)
self.assertEqual(len(sses['loop']), 32)