def run():
filename = 'tst_multi.pdb'
f = open(filename, 'w')
f.write(pdb_lines)
f.close()
pdb_inp = pdb.input(filename)
pdb_hierarchy = pdb_inp.construct_hierarchy()
from mmtbx.conformation_dependent_library.tst_rdl import \
get_geometry_restraints_manager
geometry_restraints_manager = get_geometry_restraints_manager(filename)
pdb_hierarchy.reset_i_seq_if_necessary()
refine = [
False, # -179
True, # -44
False, # 86
True, # -22
False, # -179
]
refine += [True] * 5
refine += [False] * 14
omegalyze = [
False,
False,
False,
True,
False,
]
omegalyze += [True] * 3
omegalyze += [False] * 16
from mmtbx.conformation_dependent_library import generate_protein_threes
for i, threes in enumerate(
generate_protein_threes(
pdb_hierarchy,
geometry_restraints_manager,
cdl_class=True,
#verbose=verbose,
)):
print(i, threes)
print(' omega %5.1f' % threes.get_omega_value())
print(" cis? %-5s %s" %
(threes.cis_group(), threes.cis_group(limit=30)))
print(" trans? %-5s %s" %
(threes.trans_group(), threes.trans_group(limit=30)))
print(" rama %s" % threes.get_ramalyze_key())
print(' conf %s' % threes.is_pure_main_conf())
assert threes.cis_group() == refine[i], '%s!=%s' % (threes.cis_group(),
refine[i])
assert threes.cis_group(limit=30) == omegalyze[i]
for j in range(0, 181, 10):
i += 1
print(" %3d %-5s %-8s %-5s" % (
j,
threes._define_omega_a_la_duke_using_limit(j) == 'cis',
threes._define_omega_a_la_duke_using_limit(j, limit=30),
refine[i],
))
assert (threes._define_omega_a_la_duke_using_limit(j) == 'cis'
) == refine[i]
def id_str_for_phi_psi_2(self, ignore_altloc=False):
return '%s ~> %s' % ( id_str_for_phi_psi_2(self[1], ignore_altloc),
id_str_for_phi_psi_2(self[2], ignore_altloc))
class FiveProteinResidues(FourProteinResidues):
def get_cablam_info(self):
assert 0
if __name__=="__main__":
import sys
from iotbx import pdb
from mmtbx.conformation_dependent_library.tst_rdl import get_geometry_restraints_manager
filename=sys.argv[1]
pdb_inp = pdb.input(filename)
pdb_hierarchy = pdb_inp.construct_hierarchy()
geometry_restraints_manager = get_geometry_restraints_manager(filename)
pdb_hierarchy.reset_i_seq_if_necessary()
from mmtbx.conformation_dependent_library import generate_protein_fragments
for i in range(2,11):
for threes in generate_protein_fragments(pdb_hierarchy,
geometry_restraints_manager,
length=i,
#verbose=verbose,
):
print(threes)
try: print(' omega %5.1f' % threes.get_omega_value())
except: print(' omega is not valid') # intentional
print(' omegas %s' % threes.get_omega_values())
try: print(" cis? %-5s %s" % (threes.cis_group(), threes.cis_group(limit=30)))
except: print(' cis? is not valid') # intentional
try: print(" trans? %-5s %s" % (threes.trans_group(), threes.trans_group(limit=30)))