def main():
pdb_inp = pdb.input(lines=pdb_1ehz, source_info='model_1ehz')
pdb_hierarchy = pdb_inp.construct_hierarchy()
geometry_restraints_manager = get_geometry_restraints_manager(raw_records=pdb_1ehz)
pdb_hierarchy.reset_i_seq_if_necessary()
from mmtbx.conformation_dependent_library import generate_dna_rna_fragments
for k in range(2,3):
for j, threes in enumerate(generate_dna_rna_fragments(
pdb_hierarchy,
geometry_restraints_manager,
length=k,
#verbose=True,
)):
print k,j,threes
print threes.get_base_types()
print threes.get_ntc_angles()
return get_ca_dihedrals(self)
class FiveProteinResidues(FourProteinResidues):
def get_cablam_info(self):
assert 0
if __name__ == "__main__":
import sys
from iotbx import pdb
from test_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, 6):
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()
bond.distance_ideal = averages[key]/averages.n[key]
elif len(key)==3:
rkey = (key[2],key[1],key[0])
averages.n[rkey]=averages.n[key]
for angle in self.geometry.angle_proxies:
if angle.i_seqs in averages.n:
key = angle.i_seqs
if key not in averages:
assert 0
angle.angle_ideal = averages[key]/averages.n[key]
if __name__=="__main__":
import sys
from iotbx import pdb
from test_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_threes
for threes in generate_protein_threes(pdb_hierarchy,
geometry_restraints_manager,
#verbose=verbose,
):
print threes
print " cis? %s" % threes.cis_group()
print " rama %s" % threes.get_ramalyze_key()
print ' conf %s' % threes.is_pure_main_conf()
print "OK"
def main():
pdb_inp = pdb.input(lines=model_1yjp, source_info='model_1yjp')
pdb_hierarchy = pdb_inp.construct_hierarchy()
geometry_restraints_manager = get_geometry_restraints_manager(
raw_records=model_1yjp)
pdb_hierarchy.reset_i_seq_if_necessary()
from mmtbx.conformation_dependent_library import generate_protein_fragments
for k in range(2, 6):
for j, threes in enumerate(
generate_protein_fragments(
pdb_hierarchy,
geometry_restraints_manager,
length=k,
#verbose=verbose,
)):
i = k - 2
print(i, j, k, threes)
rc = None
try:
rc = threes.get_omega_value()
except:
print(' omega is not valid') # intentional
if i > 0: assert rc == None
else:
print(' omega %5.1f' % rc)
assert rc == answers['omegas'][j]
rc = threes.get_omega_values()
print(' omegas %s' % rc)
assert rc == answers['omegas'][j:j + i + 1], '%s != %s' % (
rc, answers['omegas'][j:j + i + 1])
rc = None
try:
rc = threes.cis_group()
except:
pass # intentional
try:
print(" cis? %-5s %s" % (rc, threes.cis_group(limit=30)))
except:
print(' cis? is not valid') # intentional
if i >= 2:
assert (rc == None or rc == False), '%s!=%s' % (rc, None)
else:
assert rc == False
try:
print(" trans? %-5s %s" %
(threes.trans_group(), threes.trans_group(limit=30)))
except:
print(' tran? is not valid') # intentional
print(' cis/trans/twisted? %s' %
' '.join(threes.cis_trans_twisted_list()))
try:
print(" rama %s" % threes.get_ramalyze_key())
except:
print(' rama not specified') # intentional
print(' conf %s' % threes.is_pure_main_conf())
rc = None
try:
rc = threes.get_phi_psi_angles()
except:
print(' phi/psi not specified') # intentional
print(' phi/psi %s' % rc)
if i < 1: assert rc == None
else:
test = answers['phi_psi'][j * 2:(j + i) * 2]
assert rc == test, '%s!=%s' % (rc, test)
rc = None
try:
rc = threes.get_ca_dihedrals()
except:
print(' CA dihedrals not specified') # intentional
print(' CA dihedrals %s' % rc)
if i <= 1: assert rc == None
else:
test = answers['calphas'][j:j + i + 1 - 2]
assert rc == test
print("OK", i + 2)