def setup(self, cmd_args, **options):
#trim off basepairs on the end do not need them in the simulation
ss = ssfactory.factory.get_structure(
cmd_args.cseq[3:-3] + "+" + cmd_args.fseq[3:-3],
cmd_args.css[3:-3] + "+" + cmd_args.fss[3:-3],
to_RNA=1
)
#update secondary structure to include tertiary contact motifs
m1 = rm.manager.get_motif(name='GAAA_tetraloop')
m2 = rm.manager.get_motif(name='GGAA_tetraloop')
ss.add_motif(m1.secondary_structure, m1.name)
ss.add_motif(m2.secondary_structure, m2.name)
m2 = rm.manager.get_motif(name='GGAA_tetraloop')
last_end_id = None
for i, end in enumerate(m2.ends):
if end.name() == "A1-A6":
last_end_id = m2.end_ids[i]
break
last_end = ss.motif('GGAA_tetraloop').get_end_by_id(last_end_id)
conn = ss.motif_topology_from_end(ss.ends[1], last_end=last_end)
mtt = motif_tree_topology.MotifTreeTopology(conn)
mt = motif_tree.motif_tree_from_topology(mtt, sterics=0)
mset = motif_state_ensemble_tree.MotifStateEnsembleTree(mt=mt)
ni = -1
ei = -1
for n in mt:
if n.data.name == 'GGAA_tetraloop':
ni = n.index
bp = n.data.get_basepair(name="A1-A6")[0]
ei = n.data.ends.index(bp)
if cmd_args.pdbs:
mt.write_pdbs("good")
mst = mset.to_mst()
n1 = mst.get_node(ni)
n2 = mst.get_node(mt.last_node().index-1)
end_state_1 = n1.data.cur_state.end_states[ei]
end_state_2 = n2.data.cur_state.end_states[1]
scorer = thermo_fluc_sampler.FrameScorer()
score = scorer.score(end_state_1, end_state_2)
print "distance + rotation diff = ",score
exit()
self.simulator = thermo_fluc_sampler.ThermoFlucSimulation()
self.simulator.setup(mset, ni, mt.last_node().index-1, ei, 1)
self.simulator.run()
def new_build():
seq1 = 'CTAGGATATGGGGGGUUUUUGGGAACAAAAACCCCCCTAAGTCCTAG'
seq2 = 'CTAGGAATCTGGAAGTACCGAGGAAACTCGGTACTTCCTGTGTCCTAG'
db1 = '(((((((..((((((((((((....))))))))))))...)))))))'
db2 = '((((((....((((((((((((....))))))))))))....))))))'
ss = ssfactory.factory.get_structure(seq1 +"+" + seq2, db1 + "+" + db2, to_RNA=1)
m1 = rm.manager.get_motif(name='GAAA_tetraloop')
m2 = rm.manager.get_motif(name='GGAA_tetraloop')
ss.add_motif(m1.secondary_structure, m1.name)
ss.add_motif(m2.secondary_structure, m2.name)
ss_m = ss.motif('GGAA_tetraloop')
last_end = None
for i, end in enumerate(ss_m.ends):
if ss_m.end_ids[i] == 'GGGAAC_LUUUUR_CCUGUGUC_LLULUULL_GAAUCUGG_RRUURURR':
last_end = end
break
conn = ss.motif_topology_from_end(ss.ends[1], last_end=last_end)
mtt = motif_tree_topology.MotifTreeTopology(conn)
mt = motif_tree.motif_tree_from_topology(mtt, sterics=0)
mt.write_pdbs()